殷紅歌頌的殘缺

[生物資訊期末報告]Phylogenetics of The Interferon Regulatory Factor Family

selice — Mon, 24 Jan 2011 00:10:15 +0000

Phylogenetics of the family

[生物資訊期末報告]The analysis for nucleotide/protein sequence(IRF-1)

selice — Sun, 23 Jan 2011 21:29:57 +0000

        10         20         30         40         50         60
ATGCCCATCA CTCGGATGCG CATGAGACCC TGGCTAGAGA TGCAGATTAA TTCCAACCAA 

        70         80         90        100        110        120
ATCCCGGGGC TCATCTGGAT TAATAAAGAG GAGATGATCT TCCAGATCCC ATGGAAGCAT 

       130        140        150        160        170        180
GCTGCCAAGC ATGGCTGGGA CATCAACAAG GATGCCTGTT TGTTCCGGAG CTGGGCCATT 

       190        200        210        220        230        240
CACACAGGCC GATACAAAGC AGGGGAAAAG GAGCCAGATC CCAAGACGTG GAAGGCCAAC 

       250        260        270        280        290        300
TTTCGCTGTG CCATGAACTC CCTGCCAGAT ATCGAGGAGG TGAAAGACCA GAGCAGGAAC 

       310        320        330        340        350        360
AAGGGCAGCT CAGCTGTGCG AGTGTACCGG ATGCTTCCAC CTCTCACCAA GAACCAGAGA 

       370        380        390        400        410        420
AAAGAAAGAA AGTCGAAGTC CAGCCGAGAT GCTAAGAGCA AGGCCAAGAG GAAGTCATGT 

       430        440        450        460        470        480
GGGGATTCCA GCCCTGATAC CTTCTCTGAT GGACTCAGCA GCTCCACTCT GCCTGATGAC 

       490        500        510        520        530        540
CACAGCAGCT ACACAGTTCC AGGCTACATG CAGGACTTGG AGGTGGAGCA GGCCCTGACT 

       550        560        570        580        590        600
CCAGCACTGT CGCCATGTGC TGTCAGCAGC ACTCTCCCCG ACTGGCACAT CCCAGTGGAA 

       610        620        630        640        650        660
GTTGTGCCGG ACAGCACCAG TGATCTGTAC AACTTCCAGG TGTCACCCAT GCCCTCCACC 

       670        680        690        700        710        720
TCTGAAGCTA CAACAGATGA GGATGAGGAA GGGAAATTAC CTGAGGACAT CATGAAGCTC 

       730        740        750        760        770        780
TTGGAGCAGT CGGAGTGGCA GCCAACAAAC GTGGATGGGA AGGGGTACCT ACTCAATGAA 

       790        800        810        820        830        840
CCTGGAGTCC AGCCCACCTC TGTCTATGGA GACTTTAGCT GTAAGGAGGA GCCAGAAATT 

       850        860        870        880        890        900
GACAGCCCAG GGGGGGATAT TGGGCTGAGT CTACAGCGTG TCTTCACAGA TCTGAAGAAC 

       910        920        930        940        950        960
ATGGATGCCA CCTGGCTGGA CAGCCTGCTG ACCCCAGTCC GGTTGCCCTC CATCCAGGCC 

       970
ATTCCCTGTG CACCGTAG




Number of amino acids: 978

Molecular weight: 79750.5

Theoretical pI: 5.04
Amino acid composition: 
Ala (A) 261	 26.7%
Arg (R)   0	  0.0%
Asn (N)   0	  0.0%
Asp (D)   0	  0.0%
Cys (C) 265	 27.1%
Gln (Q)   0	  0.0%
Glu (E)   0	  0.0%
Gly (G) 269	 27.5%
His (H)   0	  0.0%
Ile (I)   0	  0.0%
Leu (L)   0	  0.0%
Lys (K)   0	  0.0%
Met (M)   0	  0.0%
Phe (F)   0	  0.0%
Pro (P)   0	  0.0%
Ser (S)   0	  0.0%
Thr (T) 183	 18.7%
Trp (W)   0	  0.0%
Tyr (Y)   0	  0.0%
Val (V)   0	  0.0%
Pyl (O)   0	  0.0%
Sec (U)   0	  0.0%

 (B)   0	  0.0%
 (Z)   0	  0.0%
 (X)   0	  0.0%


Total number of negatively charged residues (Asp + Glu): 0
Total number of positively charged residues (Arg + Lys): 0

Atomic composition:

Carbon      C	      2848
Hydrogen    H	      4720
Nitrogen    N	       978
Oxygen      O	      1162
Sulfur      S	       265

Formula: C₂₈₄₈H₄₇₂₀N₉₇₈O₁₁₆₂S₂₆₅
Total number of atoms: 9973

Extinction coefficients:

This protein does not contain any Trp residues. Experience shows that
this could result in more than 10% error in the computed extinction coefficient.

Extinction coefficients are in units of  M^-1 cm^-1, at 280 nm measured in water.

Ext. coefficient    16500
Abs 0.1% (=1 g/l)   0.207, assuming all pairs of Cys residues form cystines

Ext. coefficient        0
Abs 0.1% (=1 g/l)   0.000, assuming all Cys residues are reduced

Estimated half-life:

The N-terminal of the sequence considered is A (Ala).

The estimated half-life is: 4.4 hours (mammalian reticulocytes, in vitro).
                            >20 hours (yeast, in vivo).
                            >10 hours (Escherichia coli, in vivo).

Instability index:

The instability index (II) is computed to be 48.90
This classifies the protein as unstable.

Aliphatic index: 26.69

Grand average of hydropathicity (GRAVY): 0.917

[生物資訊期末報告]The Sequence Similarity among The Interferon Regulatory Factor Family

selice — Sun, 23 Jan 2011 21:00:28 +0000

[生物資訊期末報告]PROMO Search Result For The Interferon Regulatory Factor Family(IRF6-IRF8)

selice — Sun, 23 Jan 2011 14:52:46 +0000

Factors predicted by PROMO in IRF6 sequence:

NAME; MATRIX_WIDTH;
XBP-1 [T00902]; 6
Pax-5 [T00070]; 7
p53 [T00671]; 7
ENKTF-1 [T00255]; 8
TFII-I [T00824]; 6
ETF [T00270]; 11
RXR-alpha [T01345]; 7
MAZ [T00490]; 13
WT1 [T00899]; 9
E2F-1 [T01542]; 8
GR-alpha [T00337]; 5
PPAR-alpha:RXR-alpha [T05221]; 11
EBF [T05427]; 11
FOXP3 [T04280]; 6
STAT4 [T01577]; 6
c-Ets-1 [T00112]; 7
Elk-1 [T00250]; 9
RelA [T00594]; 11
IRF-1 [T00423]; 9
NF-AT1 [T00550]; 9
PR B [T00696]; 7
PR A [T01661]; 7
c-Ets-2 [T00113]; 9
MEF-2A [T01005]; 11
HNF-3alpha [T02512]; 8
GR-beta [T01920]; 5
YY1 [T00915]; 4
HOXD9 [T01424]; 10
HOXD10 [T01425]; 10
AP-2alphaA [T00035]; 6
ER-alpha [T00261]; 5
RAR-alpha1 [T00719]; 13
GCF [T00320]; 9
NFI/CTF [T00094]; 8
RBP-Jkappa [T01616]; 12
VDR [T00885]; 9
RAR-beta [T00721]; 10
PXR-1:RXR-alpha [T05671]; 8
GATA-1 [T00306]; 6
ATF3 [T01313]; 8
PEA3 [T00685]; 9
HNF-1C [T01951]; 9
HNF-1A [T00368]; 8
HNF-1B [T01950]; 9
C/EBPbeta [T00581]; 4
C/EBPalpha [T00105]; 7
c-Myb [T00137]; 8
GR [T05076]; 7
LEF-1 [T02905]; 8
NF-1 [T00539]; 8
c-Jun [T00133]; 7
COUP-TF1 [T00149]; 13
Ik-1 [T02702]; 13
CREB [T00163]; 9
ATF-2 [T00167]; 10
ATF [T00051]; 12
GATA-3 [T00311]; 12
TFIID [T00820]; 7
NF-Y [T00150]; 8
TCF-4 [T02918]; 10
AR [T00040]; 9
POU2F1 [T00641]; 11
GATA-2 [T00308]; 9
SRY [T00997]; 9
TCF-4E [T02878]; 7
T3R-beta1 [T00851]; 9
NF-AT2 [T01945]; 10
NF-AT1 [T01948]; 10
STAT1beta [T01573]; 10
IRF-2 [T01491]; 6
SRF [T00764]; 13
AP-1 [T00029]; 9
PU.1 [T02068]; 13
ELF-1 [T01113]; 13
NF-kappaB [T00590]; 12
USF2 [T00878]; 10

Distribution of the nucleotides over the given chain:

25.2%

27.6%

26.4%

20.9%

Factors predicted by PROMO in IRF7 sequence:

NAME; MATRIX_WIDTH;
XBP-1 [T00902]; 6
ENKTF-1 [T00255]; 8
C/EBPbeta [T00581]; 4
NF-1 [T00539]; 8
GR-alpha [T00337]; 5
Pax-5 [T00070]; 7
p53 [T00671]; 7
AhR:Arnt [T05394]; 10
AP-2alphaA [T00035]; 6
E2F-1 [T01542]; 8
USF2 [T00878]; 10
NF-AT2 [T01945]; 10
TFII-I [T00824]; 6
STAT4 [T01577]; 6
c-Ets-1 [T00112]; 7
STAT1beta [T01573]; 10
RAR-beta:RXR-alpha [T05420]; 12
Sp1 [T00759]; 10
ETF [T00270]; 11
IRF-1 [T00423]; 9
TFIID [T00820]; 7
FOXP3 [T04280]; 6
NF-AT1 [T00550]; 9
NFI/CTF [T00094]; 8
c-Myb [T00137]; 8
Elk-1 [T00250]; 9
GCF [T00320]; 9
RXR-alpha [T01345]; 7
PPAR-alpha:RXR-alpha [T05221]; 11
WT1 [T00899]; 9
AR [T00040]; 9
Ik-1 [T02702]; 13
EBF [T05427]; 11
YY1 [T00915]; 4
MAZ [T00490]; 13
PR B [T00696]; 7
PR A [T01661]; 7
c-Jun [T00133]; 7
NF-kappaB [T00590]; 12
NF-kappaB1 [T00593]; 11
RelA [T00594]; 11
RBP-Jkappa [T01616]; 12
T3R-beta1 [T00851]; 9
ER-alpha [T00261]; 5
HIF-1 [T01609]; 9
c-Ets-2 [T00113]; 9
c-Myc [T00140]; 6
USF1 [T00874]; 10
GR-beta [T01920]; 5
RAR-beta [T00721]; 10
ATF3 [T01313]; 8
E2F [T00221]; 10
GATA-1 [T00306]; 6
AhR [T01795]; 11
Egr-3 [T00243]; 13
ATF-1 [T00968]; 11
AP-1 [T00029]; 9
ELF-1 [T01113]; 13
NF-AT1 [T01948]; 10

17.7%

34.7%

33.1%

14.5%

Factors predicted by PROMO in IRF8 sequence:

NAME; MATRIX_WIDTH;
ER-alpha [T00261]; 5
GR-beta [T01920]; 5
ENKTF-1 [T00255]; 8
C/EBPbeta [T00581]; 4
C/EBPalpha [T00105]; 7
TFII-I [T00824]; 6
GATA-1 [T00306]; 6
GR-alpha [T00337]; 5
NF-1 [T00539]; 8
XBP-1 [T00902]; 6
STAT4 [T01577]; 6
c-Ets-1 [T00112]; 7
IRF-1 [T00423]; 9
TFIID [T00820]; 7
FOXP3 [T04280]; 6
NF-AT1 [T00550]; 9
PR B [T00696]; 7
PR A [T01661]; 7
AhR:Arnt [T05394]; 10
c-Ets-2 [T00113]; 9
YY1 [T00915]; 4
AP-2alphaA [T00035]; 6
SRY [T00997]; 9
TCF-4E [T02878]; 7
GR [T05076]; 7
VDR [T00885]; 9
PXR-1:RXR-alpha [T05671]; 8
LEF-1 [T02905]; 8
TCF-4 [T02918]; 10
HOXD9 [T01424]; 10
HOXD10 [T01425]; 10
Pax-5 [T00070]; 7
p53 [T00671]; 7
IRF-2 [T01491]; 6
ATF3 [T01313]; 8
NFI/CTF [T00094]; 8
c-Myb [T00137]; 8
NF-AT2 [T01945]; 10
STAT1beta [T01573]; 10
HNF-3alpha [T02512]; 8
NF-kappaB [T00590]; 12
NF-kappaB1 [T00593]; 11
RelA [T00594]; 11
Elk-1 [T00250]; 9
E2F-1 [T01542]; 8
AP-1 [T00029]; 9
c-Jun [T00133]; 7
c-Fos [T00123]; 10
USF2 [T00878]; 10
ETF [T00270]; 11
AR [T00040]; 9
PEA3 [T00685]; 9
EBF [T05427]; 11
HNF-1C [T01951]; 9
HNF-1B [T01950]; 9
NF-AT1 [T01948]; 10
T3R-beta1 [T00851]; 9
MEF-2A [T01005]; 11
E2F [T00221]; 10
Ik-1 [T02702]; 13
GATA-2 [T00308]; 9
RXR-alpha [T01345]; 7
AhR [T01795]; 11
GCF [T00320]; 9
SRF [T00764]; 13
POU2F1 [T00641]; 11
PU.1 [T02068]; 13
HNF-4alpha [T03828]; 13
ELF-1 [T01113]; 13

Distribution of the nucleotides over the given chain:

22.2%

26.3%

31.9%

19.5%

[生物資訊期末報告]PROMO Search Result For The Interferon Regulatory Factor Family(IRF1-IRF5)

selice — Fri, 21 Jan 2011 09:54:40 +0000

Factors predicted by PROMO in IRF1 sequence:

NAME; MATRIX_WIDTH;
XBP-1 [T00902]; 6
YY1 [T00915]; 4
RXR-alpha [T01345]; 7
ENKTF-1 [T00255]; 8
GR-beta [T01920]; 5
TFII-I [T00824]; 6
STAT4 [T01577]; 6
c-Ets-1 [T00112]; 7
FOXP3 [T04280]; 6
NFI/CTF [T00094]; 8
GR [T05076]; 7
TFIID [T00820]; 7
GR-alpha [T00337]; 5
Elk-1 [T00250]; 9
PR B [T00696]; 7
PR A [T01661]; 7
C/EBPbeta [T00581]; 4
AP-2alphaA [T00035]; 6
SRY [T00997]; 9
TCF-4E [T02878]; 7
IRF-1 [T00423]; 9
NF-AT1 [T00550]; 9
c-Myb [T00137]; 8
VDR [T00885]; 9
PXR-1:RXR-alpha [T05671]; 8
GATA-1 [T00306]; 6
c-Ets-2 [T00113]; 9
T3R-beta1 [T00851]; 9
AP-1 [T00029]; 9
c-Jun [T00133]; 7
Pax-5 [T00070]; 7
p53 [T00671]; 7
ER-alpha [T00261]; 5
ATF3 [T01313]; 8
PEA3 [T00685]; 9
MAZ [T00490]; 13
NF-1 [T00539]; 8
C/EBPalpha [T00105]; 7
EBF [T05427]; 11
NF-Y [T00150]; 8
USF2 [T00878]; 10
RAR-alpha1 [T00719]; 13
ETF [T00270]; 11
NF-kappaB [T00590]; 12
RelA [T00594]; 11
AR [T00040]; 9
GATA-2 [T00308]; 9
Ik-1 [T02702]; 13
NF-AT2 [T01945]; 10
STAT1beta [T01573]; 10
c-Fos [T00123]; 10
ELF-1 [T01113]; 13
PU.1 [T02068]; 13
LEF-1 [T02905]; 8
PPAR-alpha:RXR-alpha [T05221]; 11
POU2F1 [T00641]; 11

Distribution of the nucleotides over the given chain:

26.7%

27.1%

27.5%

18.7%

Factors predicted by PROMO in IRF-2 sequence:

NAME; MATRIX_WIDTH;
XBP-1 [T00902]; 6
IRF-1 [T00423]; 9
GR-alpha [T00337]; 5
NF-AT1 [T00550]; 9
Pax-5 [T00070]; 7
p53 [T00671]; 7
ENKTF-1 [T00255]; 8
FOXP3 [T04280]; 6
TFII-I [T00824]; 6
c-Myb [T00137]; 8
PR B [T00696]; 7
PR A [T01661]; 7
HNF-1A [T00368]; 8
c-Ets-2 [T00113]; 9
TFIID [T00820]; 7
GR-beta [T01920]; 5
YY1 [T00915]; 4
NFI/CTF [T00094]; 8
GR [T05076]; 7
AP-2alphaA [T00035]; 6
STAT4 [T01577]; 6
c-Ets-1 [T00112]; 7
C/EBPbeta [T00581]; 4
C/EBPalpha [T00105]; 7
AP-1 [T00029]; 9
c-Jun [T00133]; 7
HNF-3alpha [T02512]; 8
EBF [T05427]; 11
GATA-2 [T00308]; 9
GATA-1 [T00306]; 6
STAT5A [T04683]; 13
SRY [T00997]; 9
TCF-4E [T02878]; 7
c-Fos [T00123]; 10
IRF-2 [T01491]; 6
ATF3 [T01313]; 8
TBP [T00794]; 10
VDR [T00885]; 9
PXR-1:RXR-alpha [T05671]; 8
T3R-beta1 [T00851]; 9
E2F-1 [T01542]; 8
ER-alpha [T00261]; 5
RXR-alpha [T01345]; 7
Elk-1 [T00250]; 9
ETF [T00270]; 11
RAR-alpha1 [T00719]; 13
PEA3 [T00685]; 9
POU2F2 (Oct-2.1) [T00646]; 11
LEF-1 [T02905]; 8
TCF-4 [T02918]; 10
NF-1 [T00539]; 8
Sp1 [T00759]; 10
E2F [T00221]; 10
NF-Y [T00150]; 8
AR [T00040]; 9
PU.1 [T02068]; 13
PPAR-alpha:RXR-alpha [T05221]; 11
HNF-1C [T01951]; 9
HNF-1B [T01950]; 9
NF-AT2 [T01945]; 10
STAT1beta [T01573]; 10
HOXD9 [T01424]; 10
HOXD10 [T01425]; 10
NF-AT1 [T01948]; 10
Ik-1 [T02702]; 13

Distribution of the nucleotides over the given chain:

30.5%

25.4%

25.2%

18.9%

Factors predicted by PROMO in IRF3(transcript variant 1) sequence:

NAME; MATRIX_WIDTH;
RXR-alpha [T01345]; 7
RAR-beta [T00721]; 10
SRY [T00997]; 9
TCF-4E [T02878]; 7
NFI/CTF [T00094]; 8
GR [T05076]; 7
Pax-5 [T00070]; 7
p53 [T00671]; 7
ENKTF-1 [T00255]; 8
FOXP3 [T04280]; 6
c-Myb [T00137]; 8
GR-alpha [T00337]; 5
VDR [T00885]; 9
PXR-1:RXR-alpha [T05671]; 8
PR B [T00696]; 7
PR A [T01661]; 7
E2F-1 [T01542]; 8
AhR:Arnt [T05394]; 10
STAT4 [T01577]; 6
c-Ets-1 [T00112]; 7
Elk-1 [T00250]; 9
PEA3 [T00685]; 9
C/EBPbeta [T00581]; 4
NF-1 [T00539]; 8
XBP-1 [T00902]; 6
GR-beta [T01920]; 5
AP-2alphaA [T00035]; 6
c-Ets-2 [T00113]; 9
NF-AT2 [T01945]; 10
TFII-I [T00824]; 6
STAT1beta [T01573]; 10
HNF-3alpha [T02512]; 8
NF-kappaB [T00590]; 12
HNF-1C [T01951]; 9
ETF [T00270]; 11
Ik-1 [T02702]; 13
RAR-beta:RXR-alpha [T05420]; 12
PPAR-alpha:RXR-alpha [T05221]; 11
TFIID [T00820]; 7
YY1 [T00915]; 4
AP-1 [T00029]; 9
c-Jun [T00133]; 7
AR [T00040]; 9
E2F [T00221]; 10
NF-kappaB1 [T00593]; 11
ER-alpha [T00261]; 5
C/EBPalpha [T00105]; 7
T3R-beta1 [T00851]; 9
c-Fos [T00123]; 10
c-Myc [T00140]; 6
USF1 [T00874]; 10
EBF [T05427]; 11
STAT5A [T04683]; 13
NF-AT1 [T01948]; 10
Egr-3 [T00243]; 13
MAZ [T00490]; 13
IRF-1 [T00423]; 9
NF-AT1 [T00550]; 9
HIF-1 [T01609]; 9
COUP-TF1 [T00149]; 13
GATA-1 [T00306]; 6
NF-Y [T00150]; 8
LEF-1 [T02905]; 8
RelA [T00594]; 11

Distribution of the nucleotides over the given chain:

19.9%

29.7%

32.4%

18.0%

Factors predicted by PROMO in IRF4 sequence:

NAME; MATRIX_WIDTH;
XBP-1 [T00902]; 6
FOXP3 [T04280]; 6
PXR-1:RXR-alpha [T05671]; 8
GR-alpha [T00337]; 5
AP-2alphaA [T00035]; 6
E2F-1 [T01542]; 8
ENKTF-1 [T00255]; 8
RXR-alpha [T01345]; 7
STAT4 [T01577]; 6
c-Ets-1 [T00112]; 7
Elk-1 [T00250]; 9
PEA3 [T00685]; 9
AhR:Arnt [T05394]; 10
GCF [T00320]; 9
C/EBPbeta [T00581]; 4
NF-1 [T00539]; 8
c-Ets-2 [T00113]; 9
IRF-1 [T00423]; 9
NF-AT1 [T00550]; 9
TFII-I [T00824]; 6
MAZ [T00490]; 13
USF2 [T00878]; 10
VDR [T00885]; 9
LEF-1 [T02905]; 8
TCF-4 [T02918]; 10
PR B [T00696]; 7
PR A [T01661]; 7
GR-beta [T01920]; 5
c-Myb [T00137]; 8
SRY [T00997]; 9
TCF-4E [T02878]; 7
GR [T05076]; 7
C/EBPalpha [T00105]; 7
NFI/CTF [T00094]; 8
SRF [T00764]; 13
T3R-beta1 [T00851]; 9
AR [T00040]; 9
YY1 [T00915]; 4
Pax-5 [T00070]; 7
p53 [T00671]; 7
Ik-1 [T02702]; 13
RBP-Jkappa [T01616]; 12
ATF3 [T01313]; 8
PPAR-alpha:RXR-alpha [T05221]; 11
TFIID [T00820]; 7
HNF-3alpha [T02512]; 8
E2F [T00221]; 10
ER-alpha [T00261]; 5
ETF [T00270]; 11
c-Jun [T00133]; 7
NF-AT2 [T01945]; 10
NF-AT1 [T01948]; 10
STAT1beta [T01573]; 10
GATA-1 [T00306]; 6
MEF-2A [T01005]; 11
HOXD9 [T01424]; 10
HOXD10 [T01425]; 10
AP-1 [T00029]; 9
c-Fos [T00123]; 10
EBF [T05427]; 11
NF-kappaB [T00590]; 12
RelA [T00594]; 11
CREB [T00163]; 9
ATF-2 [T00167]; 10
ATF [T00051]; 12
NF-Y [T00150]; 8
CTF [T00174]; 12
HNF-4alpha [T03828]; 13
PU.1 [T02068]; 13
RAR-beta:RXR-alpha [T05420]; 12
Sp1 [T00759]; 10

Distribution of the nucleotides over the given chain:

25.0%

30.2%

27.5%

17.3%

Factors predicted by PROMO in IRF-5(transcript variant 2) sequence:

NAME; MATRIX_WIDTH;
XBP-1 [T00902]; 6
FOXP3 [T04280]; 6
PXR-1:RXR-alpha [T05671]; 8
TFII-I [T00824]; 6
YY1 [T00915]; 4
PEA3 [T00685]; 9
ENKTF-1 [T00255]; 8
RXR-alpha [T01345]; 7
MAZ [T00490]; 13
E2F-1 [T01542]; 8
Pax-5 [T00070]; 7
p53 [T00671]; 7
GR-alpha [T00337]; 5
PPAR-alpha:RXR-alpha [T05221]; 11
VDR [T00885]; 9
PR B [T00696]; 7
PR A [T01661]; 7
EBF [T05427]; 11
GR-beta [T01920]; 5
c-Jun [T00133]; 7
IRF-1 [T00423]; 9
NF-AT1 [T00550]; 9
HNF-3alpha [T02512]; 8
AP-2alphaA [T00035]; 6
NFI/CTF [T00094]; 8
GCF [T00320]; 9
RAR-beta:RXR-alpha [T05420]; 12
HNF-1A [T00368]; 8
STAT4 [T01577]; 6
c-Ets-1 [T00112]; 7
Elk-1 [T00250]; 9
ETF [T00270]; 11
Egr-3 [T00243]; 13
Ik-1 [T02702]; 13
C/EBPbeta [T00581]; 4
NF-1 [T00539]; 8
c-Ets-2 [T00113]; 9
Sp1 [T00759]; 10
NF-kappaB1 [T00593]; 11
RAR-beta [T00721]; 10
ER-alpha [T00261]; 5
T3R-beta1 [T00851]; 9
RelA [T00594]; 11
AR [T00040]; 9
COUP-TF1 [T00149]; 13
TFIID [T00820]; 7
GR [T05076]; 7
LEF-1 [T02905]; 8
GATA-1 [T00306]; 6
SRY [T00997]; 9
TCF-4E [T02878]; 7
C/EBPalpha [T00105]; 7
TCF-4 [T02918]; 10
GATA-3 [T00311]; 12
USF2 [T00878]; 10
AP-1 [T00029]; 9
c-Fos [T00123]; 10
ATF3 [T01313]; 8
PU.1 [T02068]; 13
WT1 [T00899]; 9
c-Myb [T00137]; 8
NF-Y [T00150]; 8
AhR:Arnt [T05394]; 10
NF-AT2 [T01945]; 10
STAT1beta [T01573]; 10
RAR-alpha1 [T00719]; 13

Distribution of the nucleotides over the given chain:

20.7%

34.2%

27.3%

17.8%

[生物資訊期末報告]ORF Finder Results For The Interferon Regulatory Factor Family (IRF6-IRF9)

selice — Thu, 20 Jan 2011 10:08:00 +0000

ORF Finder results for IRF-6

Results for 1404 residue sequence 「IRF-6」 starting 「ATGGCCCTCC」

>ORF number 1 in reading frame 1 on the direct strand extends from base 1 to base 1404.
ATGGCCCTCCACCCCCGCAGAGTCCGGCTAAAGCCCTGGCTGGTGGCCCAGGTGGATAGT
GGCCTCTACCCTGGGCTCATCTGGCTACACAGGGACTCTAAACGCTTCCAGATTCCCTGG
AAACATGCCACCCGGCATAGCCCTCAACAAGAAGAGGAAAATACCATTTTTAAGGCCTGG
GCTGTAGAGACAGGGAAGTACCAGGAAGGGGTGGATGACCCTGACCCAGCTAAATGGAAG
GCCCAGCTGCGCTGTGCTCTCAATAAGAGCAGAGAATTCAACCTGATGTATGATGGCACC
AAGGAGGTGCCCATGAACCCAGTGAAGATATATCAAGTGTGTGACATCCCTCAGCCCCAG
GGCTCGATCATTAACCCAGGATCCACAGGGTCTGCTCCCTGGGATGAGAAGGATAATGAT
GTGGATGAAGAAGATGAGGAAGATGAGCTGGATCAGTCGCAGCACCATGTTCCCATCCAG
GACACCTTCCCCTTCCTGAACATCAATGGTTCTCCCATGGCGCCAGCCAGTGTGGGCAAT
TGCAGTGTGGGCAACTGCAGCCCGGAGGCAGTGTGGCCCAAAACTGAACCCCTGGAGATG
GAAGTACCCCAGGCACCTATACAGCCCTTCTATAGCTCTCCAGAACTGTGGATCAGCTCT
CTCCCAATGACTGACCTGGACATCAAGTTTCAGTACCGTGGGAAGGAGTACGGGCAGACC
ATGACCGTGAGCAACCCTCAGGGCTGCCGACTCTTCTATGGGGACCTGGGTCCCATGCCT
GACCAGGAGGAGCTCTTTGGTCCCGTCAGCCTGGAGCAGGTCAAATTCCCAGGTCCTGAG
CATATTACCAATGAGAAGCAGAAGCTGTTCACTAGCAAGCTGCTGGACGTCATGGACAGA
GGACTGATCCTGGAGGTCAGCGGTCATGCCATTTATGCCATCAGGCTGTGCCAGTGCAAG
GTGTACTGGTCTGGGCCATGTGCCCCATCACTTGTTGCTCCCAACCTGATTGAGAGACAA
AAGAAGGTCAAGCTATTTTGTCTGGAAACATTCCTTAGCGATCTCATTGCCCACCAGAAA
GGACAGATAGAGAAGCAGCCACCGTTTGAGATCTACTTATGCTTTGGGGAAGAATGGCCA
GATGGGAAACCATTGGAAAGGAAACTCATCTTGGTTCAGGTCATTCCAGTAGTGGCTCGG
ATGATCTACGAGATGTTTTCTGGTGATTTCACACGATCCTTTGATAGTGGCAGTGTCCGC
CTGCAGATCTCAACCCCAGACATCAAGGATAACATCGTTGCTCAGCTGAAGCAGCTGTAC
CGCATCCTTCAAACCCAGGAGAGCTGGCAGCCCATGCAGCCCACCCCCAGCATGCAACTG
CCCCCTGCCCTGCCTCCCCAGTAA

>Translation of ORF number 1 in reading frame 1 on the direct strand.
MALHPRRVRLKPWLVAQVDSGLYPGLIWLHRDSKRFQIPWKHATRHSPQQEEENTIFKAW
AVETGKYQEGVDDPDPAKWKAQLRCALNKSREFNLMYDGTKEVPMNPVKIYQVCDIPQPQ
GSIINPGSTGSAPWDEKDNDVDEEDEEDELDQSQHHVPIQDTFPFLNINGSPMAPASVGN
CSVGNCSPEAVWPKTEPLEMEVPQAPIQPFYSSPELWISSLPMTDLDIKFQYRGKEYGQT
MTVSNPQGCRLFYGDLGPMPDQEELFGPVSLEQVKFPGPEHITNEKQKLFTSKLLDVMDR
GLILEVSGHAIYAIRLCQCKVYWSGPCAPSLVAPNLIERQKKVKLFCLETFLSDLIAHQK
GQIEKQPPFEIYLCFGEEWPDGKPLERKLILVQVIPVVARMIYEMFSGDFTRSFDSGSVR
LQISTPDIKDNIVAQLKQLYRILQTQESWQPMQPTPSMQLPPALPPQ*


ORF Finder results for IRF-7(isoform a)
Results for 1512 residue sequence 「IRF-7」 starting 「ATGGCCTTGG」
>ORF number 1 in reading frame 1 on the direct strand extends from base 1 to base 1512.
ATGGCCTTGGCTCCTGAGAGGGCAGCCCCACGCGTGCTGTTCGGAGAGTGGCTCCTTGGA
GAGATCAGCAGCGGCTGCTATGAGGGGCTGCAGTGGCTGGACGAGGCCCGCACCTGTTTC
CGCGTGCCCTGGAAGCACTTCGCGCGCAAGGACCTGAGCGAGGCCGACGCGCGCATCTTC
AAGGCCTGGGCTGTGGCCCGCGGCAGGTGGCCGCCTAGCAGCAGGGGAGGTGGCCCGCCC
CCCGAGGCTGAGACTGCGGAGCGCGCCGGCTGGAAAACCAACTTCCGCTGCGCACTGCGC
AGCACGCGTCGCTTCGTGATGCTGCGGGATAACTCGGGGGACCCGGCCGACCCGCACAAG
GTGTACGCGCTCAGCCGGGAGCTGTGCTGGCGAGAAGGCCCAGGCACGGACCAGACTGAG
GCAGAGGCCCCCGCAGCTGTCCCACCACCACAGGGTGGGCCCCCAGGGCCATTCCTGGCA
CACACACATGCTGGACTCCAAGCCCCAGGCCCCCTCCCTGCCCCAGCTGGTGACAAGGGG
GACCTCCTGCTCCAGGCAGTGCAACAGAGCTGCCTGGCAGACCATCTGCTGACAGCGTCA
TGGGGGGCAGATCCAGTCCCAACCAAGGCTCCTGGAGAGGGACAAGAAGGGCTTCCCCTG
ACTGGGGCCTGTGCTGGAGGCCCAGGGCTCCCTGCTGGGGAGCTGTACGGGTGGGCAGTA
GAGACGACCCCCAGCCCCGGGCCCCAGCCCGCGGCACTAACGACAGGCGAGGCCGCGGCC
CCAGAGTCCCCGCACCAGGCAGAGCCGTACCTGTCACCCTCCCCAAGCGCCTGCACCGCG
GTGCAAGAGCCCAGCCCAGGGGCGCTGGACGTGACCATCATGTACAAGGGCCGCACGGTG
CTGCAGAAGGTGGTGGGACACCCGAGCTGCACGTTCCTATACGGCCCCCCAGACCCAGCT
GTCCGGGCCACAGACCCCCAGCAGGTAGCATTCCCCAGCCCTGCCGAGCTCCCGGACCAG
AAGCAGCTGCGCTACACGGAGGAACTGCTGCGGCACGTGGCCCCTGGGTTGCACCTGGAG
CTTCGGGGGCCACAGCTGTGGGCCCGGCGCATGGGCAAGTGCAAGGTGTACTGGGAGGTG
GGCGGACCCCCAGGCTCCGCCAGCCCCTCCACCCCAGCCTGCCTGCTGCCTCGGAACTGT
GACACCCCCATCTTCGACTTCAGAGTCTTCTTCCAAGAGCTGGTGGAATTCCGGGCACGG
CAGCGCCGTGGCTCCCCACGCTATACCATCTACCTGGGCTTCGGGCAGGACCTGTCAGCT
GGGAGGCCCAAGGAGAAGAGCCTGGTCCTGGTGAAGCTGGAACCCTGGCTGTGCCGAGTG
CACCTAGAGGGCACGCAGCGTGAGGGTGTGTCTTCCCTGGATAGCAGCAGCCTCAGCCTC
TGCCTGTCCAGCGCCAACAGCCTCTATGACGACATCGAGTGCTTCCTTATGGAGCTGGAG
CAGCCCGCCTAG

>Translation of ORF number 1 in reading frame 1 on the direct strand.
MALAPERAAPRVLFGEWLLGEISSGCYEGLQWLDEARTCFRVPWKHFARKDLSEADARIF
KAWAVARGRWPPSSRGGGPPPEAETAERAGWKTNFRCALRSTRRFVMLRDNSGDPADPHK
VYALSRELCWREGPGTDQTEAEAPAAVPPPQGGPPGPFLAHTHAGLQAPGPLPAPAGDKG
DLLLQAVQQSCLADHLLTASWGADPVPTKAPGEGQEGLPLTGACAGGPGLPAGELYGWAV
ETTPSPGPQPAALTTGEAAAPESPHQAEPYLSPSPSACTAVQEPSPGALDVTIMYKGRTV
LQKVVGHPSCTFLYGPPDPAVRATDPQQVAFPSPAELPDQKQLRYTEELLRHVAPGLHLE
LRGPQLWARRMGKCKVYWEVGGPPGSASPSTPACLLPRNCDTPIFDFRVFFQELVEFRAR
QRRGSPRYTIYLGFGQDLSAGRPKEKSLVLVKLEPWLCRVHLEGTQREGVSSLDSSSLSL
CLSSANSLYDDIECFLMELEQPA*
ORF Finder results for IRF-8
Results for 1281 residue sequence 「IRF-8」 starting 「ATGTGTGACC」
>ORF number 1 in reading frame 1 on the direct strand extends from base 1 to base 1281.
ATGTGTGACCGGAATGGTGGTCGGCGGCTTCGACAGTGGCTGATCGAGCAGATTGACAGT
AGCATGTATCCAGGACTGATTTGGGAGAATGAGGAGAAGAGCATGTTCCGGATCCCTTGG
AAACACGCTGGCAAGCAAGATTATAATCAGGAAGTGGATGCCTCCATTTTTAAGGCCTGG
GCAGTTTTTAAAGGGAAGTTTAAAGAAGGGGACAAAGCTGAACCAGCCACTTGGAAGACG
AGGTTACGCTGTGCTTTGAATAAGAGCCCAGATTTTGAGGAAGTGACGGACCGGTCCCAA
CTGGACATTTCCGAGCCATACAAAGTTTACCGAATTGTTCCTGAGGAAGAGCAAAAATGC
AAACTAGGCGTGGCAACTGCTGGCTGCGTGAATGAAGTTACAGAGATGGAGTGCGGTCGC
TCTGAAATCGACGAGCTGATCAAGGAGCCTTCTGTGGACGATTACATGGGGATGATCAAA
AGGAGCCCTTCCCCGCCGGAGGCCTGTCGGAGTCAGCTCCTTCCAGACTGGTGGGCGCAG
CAGCCCAGCACAGGCGTGCCGCTGGTGACGGGGTACACCACCTACGACGCGCACCATTCA
GCATTCTCCCAGATGGTGATCAGCTTCTACTATGGGGGCAAGCTGGTGGGCCAGGCCACC
ACCACCTGCCCCGAGGGCTGCCGCCTGTCCCTGAGCCAGCCTGGGCTGCCCGGCACCAAG
CTGTATGGGCCCGAGGGCCTGGAGCTGGTGCGCTTCCCGCCGGCCGACGCCATCCCCAGC
GAGCGACAGAGGCAGGTGACGCGGAAGCTGTTCGGGCACCTGGAGCGCGGGGTGCTGCTG
CACAGCAGCCGGCAGGGCGTGTTCGTCAAGCGGCTGTGCCAGGGCCGCGTGTTCTGCAGC
GGCAACGCCGTGGTGTGCAAAGGCAGGCCCAACAAGCTGGAGCGTGATGAGGTGGTCCAG
GTCTTCGACACCAGCCAGTTCTTCCGAGAGCTGCAGCAGTTCTATAACAGCCAGGGCCGG
CTTCCTGACGGCAGGGTGGTGCTGTGCTTTGGGGAAGAGTTTCCGGATATGGCCCCCTTG
CGCTCCAAACTCATTCTCGTGCAGATTGAGCAGCTGTATGTCCGGCAACTGGCAGAAGAG
GCTGGGAAGAGCTGTGGAGCCGGCTCTGTGATGCAGGCCCCCGAGGAGCCGCCGCCAGAC
CAGGTCTTCCGGATGTTTCCAGATATTTGTGCCTCACACCAGAGATCATTTTTCAGAGAA
AACCAACAGATCACCGTCTAA

>Translation of ORF number 1 in reading frame 1 on the direct strand.
MCDRNGGRRLRQWLIEQIDSSMYPGLIWENEEKSMFRIPWKHAGKQDYNQEVDASIFKAW
AVFKGKFKEGDKAEPATWKTRLRCALNKSPDFEEVTDRSQLDISEPYKVYRIVPEEEQKC
KLGVATAGCVNEVTEMECGRSEIDELIKEPSVDDYMGMIKRSPSPPEACRSQLLPDWWAQ
QPSTGVPLVTGYTTYDAHHSAFSQMVISFYYGGKLVGQATTTCPEGCRLSLSQPGLPGTK
LYGPEGLELVRFPPADAIPSERQRQVTRKLFGHLERGVLLHSSRQGVFVKRLCQGRVFCS
GNAVVCKGRPNKLERDEVVQVFDTSQFFRELQQFYNSQGRLPDGRVVLCFGEEFPDMAPL
RSKLILVQIEQLYVRQLAEEAGKSCGAGSVMQAPEEPPPDQVFRMFPDICASHQRSFFRE
NQQITV*
No ORF Finder results for IRF-9

[生物資訊期末報告]ORF Finder Results For The Interferon Regulatory Factor Family (IRF1-IRF5)

selice — Thu, 20 Jan 2011 06:55:34 +0000

ORF Finder results for IRF-1

Results for 978 residue sequence 「IRF1」 starting 「ATGCCCATCA」

>ORF number 1 in reading frame 1 on the direct strand extends from base 1 to base 978.
ATGCCCATCACTCGGATGCGCATGAGACCCTGGCTAGAGATGCAGATTAATTCCAACCAA
ATCCCGGGGCTCATCTGGATTAATAAAGAGGAGATGATCTTCCAGATCCCATGGAAGCAT
GCTGCCAAGCATGGCTGGGACATCAACAAGGATGCCTGTTTGTTCCGGAGCTGGGCCATT
CACACAGGCCGATACAAAGCAGGGGAAAAGGAGCCAGATCCCAAGACGTGGAAGGCCAAC
TTTCGCTGTGCCATGAACTCCCTGCCAGATATCGAGGAGGTGAAAGACCAGAGCAGGAAC
AAGGGCAGCTCAGCTGTGCGAGTGTACCGGATGCTTCCACCTCTCACCAAGAACCAGAGA
AAAGAAAGAAAGTCGAAGTCCAGCCGAGATGCTAAGAGCAAGGCCAAGAGGAAGTCATGT
GGGGATTCCAGCCCTGATACCTTCTCTGATGGACTCAGCAGCTCCACTCTGCCTGATGAC
CACAGCAGCTACACAGTTCCAGGCTACATGCAGGACTTGGAGGTGGAGCAGGCCCTGACT
CCAGCACTGTCGCCATGTGCTGTCAGCAGCACTCTCCCCGACTGGCACATCCCAGTGGAA
GTTGTGCCGGACAGCACCAGTGATCTGTACAACTTCCAGGTGTCACCCATGCCCTCCACC
TCTGAAGCTACAACAGATGAGGATGAGGAAGGGAAATTACCTGAGGACATCATGAAGCTC
TTGGAGCAGTCGGAGTGGCAGCCAACAAACGTGGATGGGAAGGGGTACCTACTCAATGAA
CCTGGAGTCCAGCCCACCTCTGTCTATGGAGACTTTAGCTGTAAGGAGGAGCCAGAAATT
GACAGCCCAGGGGGGGATATTGGGCTGAGTCTACAGCGTGTCTTCACAGATCTGAAGAAC
ATGGATGCCACCTGGCTGGACAGCCTGCTGACCCCAGTCCGGTTGCCCTCCATCCAGGCC
ATTCCCTGTGCACCGTAG

>Translation of ORF number 1 in reading frame 1 on the direct strand.
MPITRMRMRPWLEMQINSNQIPGLIWINKEEMIFQIPWKHAAKHGWDINKDACLFRSWAI
HTGRYKAGEKEPDPKTWKANFRCAMNSLPDIEEVKDQSRNKGSSAVRVYRMLPPLTKNQR
KERKSKSSRDAKSKAKRKSCGDSSPDTFSDGLSSSTLPDDHSSYTVPGYMQDLEVEQALT
PALSPCAVSSTLPDWHIPVEVVPDSTSDLYNFQVSPMPSTSEATTDEDEEGKLPEDIMKL
LEQSEWQPTNVDGKGYLLNEPGVQPTSVYGDFSCKEEPEIDSPGGDIGLSLQRVFTDLKN
MDATWLDSLLTPVRLPSIQAIPCAP*


ORF Finder results for IRF-2

 
Results for 1050 residue sequence 「IRF-2」 starting 「ATGCCGGTGG」

 
>ORF number 1 in reading frame 1 on the direct strand extends from base 1 to base 1050.
ATGCCGGTGGAAAGGATGCGCATGCGCCCGTGGCTGGAGGAGCAGATAAACTCCAACACG
ATCCCGGGGCTCAAGTGGCTTAACAAGGAAAAGAAGATTTTTCAGATCCCCTGGATGCAT
GCGGCTAGACATGGGTGGGATGTGGAAAAAGATGCACCACTCTTTAGAAACTGGGCAATC
CATACAGGAAAGCATCAACCAGGAGTAGATAAACCTGATCCCAAAACATGGAAGGCGAAT
TTCAGATGCGCCATGAATTCCTTGCCTGATATTGAAGAAGTCAAGGATAAAAGCATAAAG
AAAGGAAATAATGCCTTCAGGGTCTACCGAATGCTGCCCCTATCAGAACGGCCTTCTAAG
AAAGGAAAGAAACCAAAGACAGAAAAAGAAGACAAAGTTAAGCACATCAAGCAAGAACCA
GTTGAGTCATCTCTGGGGCTTAGTAATGGAGTAAGTGATCTTTCTCCTGAGTATGCGGTC
CTGACTTCAACTATAAAAAATGAAGTGGATAGTACGGTGAACATCATAGTTGTAGGACAG
TCCCATCTGGACAGCAACATTGAGAATCAAGAGATTGTCACCAATCCGCCAGACATTTGC
CAAGTTGTAGAGGTGACCACTGAGAGCGACGAGCAGCCGGTCAGCATGAGCGAGCTCTAC
CCTCTGCAGATCTCCCCCGTGTCTTCCTATGCAGAAAGCGAAACGACTGATAGTGTGCCC
AGCGATGAAGAGAGTGCCGAGGGGCGGCCACACTGGCGGAAGAGGAATATTGAAGGCAAA
CAGTACCTCAGCAACATGGGGACTCGAGGCTCCTACCTGCTGCCCGGCATGGCGTCCTTC
GTCACTTCCAACAAACCGGACCTCCAGGTCACCATCAAAGAGGAGAGCAATCCGGTGCCT
TACAACAGCTCCTGGCCCCCTTTTCAAGACCTCCCCCTTTCTTCCTCCATGACCCCAGCA
TCCAGCAGCAGTCGGCCAGACCGGGAGACCCGGGCCAGCGTCATCAAGAAAACATCGGAT
ATCACCCAGGCCCGCGTCAAGAGCTGTTAA

>Translation of ORF number 1 in reading frame 1 on the direct strand.
MPVERMRMRPWLEEQINSNTIPGLKWLNKEKKIFQIPWMHAARHGWDVEKDAPLFRNWAI
HTGKHQPGVDKPDPKTWKANFRCAMNSLPDIEEVKDKSIKKGNNAFRVYRMLPLSERPSK
KGKKPKTEKEDKVKHIKQEPVESSLGLSNGVSDLSPEYAVLTSTIKNEVDSTVNIIVVGQ
SHLDSNIENQEIVTNPPDICQVVEVTTESDEQPVSMSELYPLQISPVSSYAESETTDSVP
SDEESAEGRPHWRKRNIEGKQYLSNMGTRGSYLLPGMASFVTSNKPDLQVTIKEESNPVP
YNSSWPPFQDLPLSSSMTPASSSSRPDRETRASVIKKTSDITQARVKSC*

ORF Finder results for IRF-3(transcript variant 1)
Results for 1284 residue sequence 「IRF-3」 starting 「ATGGGAACCC」
>ORF number 1 in reading frame 1 on the direct strand extends from base 1 to base 1284.
ATGGGAACCCCAAAGCCACGGATCCTGCCCTGGCTGGTGTCGCAGCTGGACCTGGGGCAA
CTGGAGGGCGTGGCCTGGGTGAACAAGAGCCGCACGCGCTTCCGCATCCCTTGGAAGCAC
GGCCTACGGCAGGATGCACAGCAGGAGGATTTCGGAATCTTCCAGGCCTGGGCCGAGGCC
ACTGGTGCATATGTTCCCGGGAGGGATAAGCCAGACCTGCCAACCTGGAAGAGGAATTTC
CGCTCTGCCCTCAACCGCAAAGAAGGGTTGCGTTTAGCAGAGGACCGGAGCAAGGACCCT
CACGACCCACATAAAATCTACGAGTTTGTGAACTCAGGAGTTGGGGACTTTTCCCAGCCA
GACACCTCTCCGGACACCAATGGTGGAGGCAGTACTTCTGATACCCAGGAAGACATTCTG
GATGAGTTACTGGGTAACATGGTGTTGGCCCCACTCCCAGATCCGGGACCCCCAAGCCTG
GCTGTAGCCCCTGAGCCCTGCCCTCAGCCCCTGCGGAGCCCCAGCTTGGACAATCCCACT
CCCTTCCCAAACCTGGGGCCCTCTGAGAACCCACTGAAGCGGCTGTTGGTGCCGGGGGAA
GAGTGGGAGTTCGAGGTGACAGCCTTCTACCGGGGCCGCCAAGTCTTCCAGCAGACCATC
TCCTGCCCGGAGGGCCTGCGGCTGGTGGGGTCCGAAGTGGGAGACAGGACGCTGCCTGGA
TGGCCAGTCACACTGCCAGACCCTGGCATGTCCCTGACAGACAGGGGAGTGATGAGCTAC
GTGAGGCATGTGCTGAGCTGCCTGGGTGGGGGACTGGCTCTCTGGCGGGCCGGGCAGTGG
CTCTGGGCCCAGCGGCTGGGGCACTGCCACACATACTGGGCAGTGAGCGAGGAGCTGCTC
CCCAACAGCGGGCATGGGCCTGATGGCGAGGTCCCCAAGGACAAGGAAGGAGGCGTGTTT
GACCTGGGGCCCTTCATTGTAGATCTGATTACCTTCACGGAAGGAAGCGGACGCTCACCA
CGCTATGCCCTCTGGTTCTGTGTGGGGGAGTCATGGCCCCAGGACCAGCCGTGGACCAAG
AGGCTCGTGATGGTCAAGGTTGTGCCCACGTGCCTCAGGGCCTTGGTAGAAATGGCCCGG
GTAGGGGGTGCCTCCTCCCTGGAGAATACTGTGGACCTGCACATTTCCAACAGCCACCCA
CTCTCCCTCACCTCCGACCAGTACAAGGCCTACCTGCAGGACTTGGTGGAGGGCATGGAT
TTCCAGGGCCCTGGGGAGAGCTGA

>Translation of ORF number 1 in reading frame 1 on the direct strand.
MGTPKPRILPWLVSQLDLGQLEGVAWVNKSRTRFRIPWKHGLRQDAQQEDFGIFQAWAEA
TGAYVPGRDKPDLPTWKRNFRSALNRKEGLRLAEDRSKDPHDPHKIYEFVNSGVGDFSQP
DTSPDTNGGGSTSDTQEDILDELLGNMVLAPLPDPGPPSLAVAPEPCPQPLRSPSLDNPT
PFPNLGPSENPLKRLLVPGEEWEFEVTAFYRGRQVFQQTISCPEGLRLVGSEVGDRTLPG
WPVTLPDPGMSLTDRGVMSYVRHVLSCLGGGLALWRAGQWLWAQRLGHCHTYWAVSEELL
PNSGHGPDGEVPKDKEGGVFDLGPFIVDLITFTEGSGRSPRYALWFCVGESWPQDQPWTK
RLVMVKVVPTCLRALVEMARVGGASSLENTVDLHISNSHPLSLTSDQYKAYLQDLVEGMD
FQGPGES*

 
ORF Finder results for IRF-4(transcript variant 1)

 
Results for 1356 residue sequence「IRF-4」 starting 「ATGAACCTGG」

 
>ORF number 1 in reading frame 1 on the direct strand extends from base 1 to base 1356.
ATGAACCTGGAGGGCGGCGGCCGAGGCGGAGAGTTCGGCATGAGCGCGGTGAGCTGCGGC
AACGGGAAGCTCCGCCAGTGGCTGATCGACCAGATCGACAGCGGCAAGTACCCCGGGCTG
GTGTGGGAGAACGAGGAGAAGAGCATCTTCCGCATCCCCTGGAAGCACGCGGGCAAGCAG
GACTACAACCGCGAGGAGGACGCCGCGCTCTTCAAGGCTTGGGCACTGTTTAAAGGAAAG
TTCCGAGAAGGCATCGACAAGCCGGACCCTCCCACCTGGAAGACGCGCCTGCGGTGCGCT
TTGAACAAGAGCAATGACTTTGAGGAACTGGTTGAGCGGAGCCAGCTGGACATCTCAGAC
CCGTACAAAGTGTACAGGATTGTTCCTGAGGGAGCCAAAAAAGGAGCCAAGCAGCTCACC
CTGGAGGACCCGCAGATGTCCATGAGCCACCCCTACACCATGACAACGCCTTACCCTTCG
CTCCCAGCCCAGCAGGTTCACAACTACATGATGCCACCCCTCGACCGAAGCTGGAGGGAC
TACGTCCCGGATCAGCCACACCCGGAAATCCCGTACCAATGTCCCATGACGTTTGGACCC
CGCGGCCACCACTGGCAAGGCCCAGCTTGTGAAAATGGTTGCCAGGTGACAGGAACCTTT
TATGCTTGTGCCCCACCTGAGTCCCAGGCTCCCGGAGTCCCCACAGAGCCAAGCATAAGG
TCTGCCGAAGCCTTGGCGTTCTCAGACTGCCGGCTGCACATCTGCCTGTACTACCGGGAA
ATCCTCGTGAAGGAGCTGACCACGTCCAGCCCCGAGGGCTGCCGGATCTCCCATGGACAT
ACGTATGACGCCAGCAACCTGGACCAGGTCCTGTTCCCCTACCCAGAGGACAATGGCCAG
AGGAAAAACATTGAGAAGCTGCTGAGCCACCTGGAGAGGGGCGTGGTCCTCTGGATGGCC
CCCGACGGGCTCTATGCGAAAAGACTGTGCCAGAGCAGGATCTACTGGGACGGGCCCCTG
GCGCTGTGCAACGACCGGCCCAACAAACTGGAGAGAGACCAGACCTGCAAGCTCTTTGAC
ACACAGCAGTTCTTGTCAGAGCTGCAAGCGTTTGCTCACCACGGCCGCTCCCTGCCAAGA
TTCCAGGTGACTCTATGCTTTGGAGAGGAGTTTCCAGACCCTCAGAGGCAAAGAAAGCTC
ATCACAGCTCACGTAGAACCTCTGCTAGCCAGACAACTATATTATTTTGCTCAACAAAAC
AGTGGACATTTCCTGAGGGGCTACGATTTACCAGAACACATCAGCAATCCAGAAGATTAC
CACAGATCTATCCGCCATTCCTCTATTCAAGAATGA

>Translation of ORF number 1 in reading frame 1 on the direct strand.
MNLEGGGRGGEFGMSAVSCGNGKLRQWLIDQIDSGKYPGLVWENEEKSIFRIPWKHAGKQ
DYNREEDAALFKAWALFKGKFREGIDKPDPPTWKTRLRCALNKSNDFEELVERSQLDISD
PYKVYRIVPEGAKKGAKQLTLEDPQMSMSHPYTMTTPYPSLPAQQVHNYMMPPLDRSWRD
YVPDQPHPEIPYQCPMTFGPRGHHWQGPACENGCQVTGTFYACAPPESQAPGVPTEPSIR
SAEALAFSDCRLHICLYYREILVKELTTSSPEGCRISHGHTYDASNLDQVLFPYPEDNGQ
RKNIEKLLSHLERGVVLWMAPDGLYAKRLCQSRIYWDGPLALCNDRPNKLERDQTCKLFD
TQQFLSELQAFAHHGRSLPRFQVTLCFGEEFPDPQRQRKLITAHVEPLLARQLYYFAQQN
SGHFLRGYDLPEHISNPEDYHRSIRHSSIQE*
ORF Finder results for IRF-5(transcript variant 2)
Results for 1497 residue sequence 「IRF-5」 starting「ATGAACCAGT」
>ORF number 1 in reading frame 1 on the direct strand extends from base 1 to base 1497.
ATGAACCAGTCCATCCCAGTGGCTCCCACCCCACCCCGCCGCGTGCGGCTGAAGCCCTGG
CTGGTGGCCCAGGTGAACAGCTGCCAGTACCCAGGGCTTCAATGGGTCAACGGGGAAAAG
AAATTATTCTGCATCCCCTGGAGGCATGCCACAAGGCATGGTCCCAGCCAGGACGGAGAT
AACACCATCTTCAAGGCCTGGGCCAAGGAGACAGGGAAATACACCGAAGGCGTGGATGAA
GCCGATCCGGCCAAGTGGAAGGCCAACCTGCGCTGTGCCCTTAACAAGAGCCGGGACTTC
CGCCTCATCTACGACGGGCCCCGGGACATGCCACCTCAGCCCTACAAGATCTACGAGGTC
TGCTCCAATGGCCCTGCTCCCACAGACTCCCAGCCCCCTGAGGATTACTCTTTTGGTGCA
GGAGAGGAGGAGGAAGAAGAGGAAGAGCTGCAGAGGATGTTGCCAAGCCTGAGCCTCACA
GAGGATGTCAAGTGGCCGCCCACTCTGCAGCCGCCCACTCTGCGGCCGCCTACTCTGCAG
CCGCCCACTCTGCAGCCGCCCGTGGTGCTGGGTCCCCCTGCTCCAGACCCCAGCCCCCTG
GCTCCTCCCCCTGGCAACCCTGCTGGCTTCAGGGAGCTTCTCTCTGAGGTCCTGGAGCCT
GGGCCCCTGCCTGCCAGCCTGCCCCCTGCAGGCGAACAGCTCCTGCCAGACCTGCTGATC
AGCCCCCACATGCTGCCTCTGACCGACCTGGAGATCAAGTTTCAGTACCGGGGGCGGCCA
CCCCGGGCCCTCACCATCAGCAACCCCCATGGCTGCCGGCTCTTCTACAGCCAGCTGGAG
GCCACCCAGGAGCAGGTGGAACTCTTCGGCCCCATAAGCCTGGAGCAAGTGCGCTTCCCC
AGCCCTGAGGACATCCCCAGTGACAAGCAGCGCTTCTACACGAACCAGCTGCTGGATGTC
CTGGACCGCGGGCTCATCCTCCAGCTACAGGGCCAGGACCTTTATGCCATCCGCCTGTGT
CAGTGCAAGGTGTTCTGGAGCGGGCCTTGTGCCTCAGCCCATGACTCATGCCCCAACCCC
ATCCAGCGGGAGGTCAAGACCAAGCTTTTCAGCCTGGAGCATTTTCTCAATGAGCTCATC
CTGTTCCAAAAGGGCCAGACCAACACCCCACCACCCTTCGAGATCTTCTTCTGCTTTGGG
GAAGAATGGCCTGACCGCAAACCCCGAGAGAAGAAGCTCATTACTGTACAGGTGGTGCCT
GTAGCAGCTCGACTGCTGCTGGAGATGTTCTCAGGGGAGCTATCTTGGTCAGCTGATAGT
ATCCGGCTACAGATCTCAAACCCAGACCTCAAAGACCGCATGGTGGAGCAATTCAAGGAG
CTCCATCACATCTGGCAGTCCCAGCAGCGGTTGCAGCCTGTGGCCCAGGCCCCTCCTGGA
GCAGGCCTTGGTGTTGGCCAGGGGCCCTGGCCTATGCACCCAGCTGGCATGCAATAA

>Translation of ORF number 1 in reading frame 1 on the direct strand.
MNQSIPVAPTPPRRVRLKPWLVAQVNSCQYPGLQWVNGEKKLFCIPWRHATRHGPSQDGD
NTIFKAWAKETGKYTEGVDEADPAKWKANLRCALNKSRDFRLIYDGPRDMPPQPYKIYEV
CSNGPAPTDSQPPEDYSFGAGEEEEEEEELQRMLPSLSLTEDVKWPPTLQPPTLRPPTLQ
PPTLQPPVVLGPPAPDPSPLAPPPGNPAGFRELLSEVLEPGPLPASLPPAGEQLLPDLLI
SPHMLPLTDLEIKFQYRGRPPRALTISNPHGCRLFYSQLEATQEQVELFGPISLEQVRFP
SPEDIPSDKQRFYTNQLLDVLDRGLILQLQGQDLYAIRLCQCKVFWSGPCASAHDSCPNP
IQREVKTKLFSLEHFLNELILFQKGQTNTPPPFEIFFCFGEEWPDRKPREKKLITVQVVP
VAARLLLEMFSGELSWSADSIRLQISNPDLKDRMVEQFKELHHIWQSQQRLQPVAQAPPG
AGLGVGQGPWPMHPAGMQ*

[生物資訊期末報告] Introduction of The Interferon Regulatory Factor Family

selice — Tue, 18 Jan 2011 07:15:55 +0000

Interferon Regulatory Factor(IRF) Family，屬於一種干擾素轉錄調控因子(Interferon regulatory factors)，此因子利用JAK-STAT訊息傳遞路徑(signaling pathway)調控干擾素的生理功能。基因分型分為IRF-1、IRF-2、IRF-3、IRF-4、IRF-5、IRF-6、IRF-7、IRF-8、IRF-9；而此蛋白家族成員在N端的DNA結合位置為一高保留度(conserved)的tryptophan重複序列，是一種helix-turn-helix構型，分型的主要依據則為經alternative splice過程後所產生的蛋白C端序列相異性而分類。

JAK-STAT signaling pathway

IRF Family功能茲列如下：

IRF-1：為Interferon beta(IFN-β)的活化因子，並可透過p300正向調控p53的活性。其與人類細胞中的免疫反應(immune response)、凋亡(Apoptosis)，以及腫瘤抑制功能(tumor suppression)有關。可與CHIP、GAGE、HSP70 / HSP90、IRF8、KPNA2、MYD88、PCAF、STAT1、TAT、VEGFR2進行interaction。

PDB rendering based on 1if1

IRF-2：可抑制IRF-1對IFN-α以及IFN-β的轉錄活性。其亦為histone H4的正向調控因子。IRF-2可與BRD7、EP300、PCAF進行interaction。

PDB rendering based on 1irf.

IRF-3：為IFN-α及IFN-β的活化因子，受到Toll-like receptor-TLR3及TLR4活化。平時以不活化態(inactive form)位於細胞質內；但當其與CREBBP以serine/threonine phosphorylation forms形成複合物時，便會進入細胞核活化IFN-α及IFN-β的表現。其與IRF-7可進行interaction。

PDB rendering based on 1j2f

Signaling pathway of toll-like receptors.

IRF4/MUM1：在黑色素細胞(melanocytic cells)中，IRF4的表現受到Microphthalmia-associated transcription factor (MITF)的調控，其可與STAT6、NFATC2、BCL6、SPI1進行interaction。

PDB rendering based on 2dll

IRF-5：其由IRF5基因表現而來，該基因除了表現IRF-5蛋白之外，尚會表現許多有關干擾素轉錄調控的因子，例如：由病毒引起的干擾素活化機制所需的轉錄因子(virus-mediated activation of interferon)；而該基因也與人類細胞的生長(cell growth)、分化(cell differentiation)、細胞凋亡(apoptosis)，以及免疫機制活化(immune system activity)有關。

PDB rendering based on 3dsh

IRF-6：與人類結締組織的形成有關，研究發現：若IRF6基因表現缺失，則會造成Van der Woude syndrome或是Popliteal pterygium syndrome。

IRF-7：其為許多受病毒感染而活化的細胞蛋白轉錄活化因子，並可活化第一型干擾素基因，例如：IFN-α genes。IRF-7並可在許多組織內活化，特別是淋巴組織。其與IRF-3可產生interaction。

IRF-8：在病毒感染宿主細胞時，IRF-8正向調控pDCs和CD8α+ Dendritic cell的分化及成熟，進而執行細胞抗病毒機制。IRF-8可與IRF1及COPS2進行interaction。

A model for the regulation of antiviral immune response by IRF-8

IRF-9：其與第一型干擾素抗病毒機制相關：IRF-9由CBP活化後可正向調控STAT1與STAT2，並與其形成ISGF3 complex，進而活化IFN-α及IFN-β。

[電波]caramelldansen in mabinogi

selice — Mon, 17 Nov 2008 05:34:13 +0000

caramelldansen in mabinogi

作者blog：http://e-bi-e-bi.cocolog-nifty.com/blog/
えび日記(蝦子日記)-えびｳｯｰｳｯｰｳﾏｳﾏ（ﾟ∀ﾟ）(蝦子ｳｯｰｳｯｰｳﾏｳﾏ（ﾟ∀ﾟ）)
蝦子應該指的是他自己的人物髮型至於後面還加ｳｯｰｳｯｰｳﾏｳﾏ（ﾟ∀ﾟ）
看來這個作者對於caramelldansen很有愛(炸
看他發在youtube的影片背景音樂幾乎都是用caramelldansen 囧

ｳｯｰｳｯｰｳﾏｳﾏ(ﾟ∀ﾟ)ｳｯｰｳｯｰｳﾏｳﾏ(ﾟ∀ﾟ)ｳｯｰｳｯｰｳﾏｳﾏ(ﾟ∀ﾟ)ｳｯｰｳｯｰｳﾏｳﾏ(ﾟ∀ﾟ)

相信大家前一段時間早就被這首電波歌給洗腦了吧

看了網路上許多關於caramelldansen的同人創作

沒想到連瑪奇都中caramelldansen的毒了(死)

而本篇重點是這個日本玩家創作的作品完成度還頗高的

在這就先分享給大家啦XD

P.S. 不過一想到製藥地獄就…(抖)

[動畫]CLANNAD 第二話觀後感

selice — Thu, 21 Feb 2008 08:30:55 +0000

CLANNAD 工作人員列表如下

監督：石原立也
系列構成、腳本：志茂文彥
人物原案：樋上いたる
人物設計、總作畫監督：池田和美
動畫製作：京都動畫

第二話最初の一歩/ 放送時間：2007/10/12 in TBS

(以下嚴重捏他請酌量服用)

Reference: Wikipedia

前段時間為了趕實驗室Data 以至於很久沒有更新Blog了

實驗室的生活也十分忙碌雖然想寫點什麼不過常常會因為實驗卡住自己的時間所以什麼事都做不了

抱怨完後回到本篇的話題

第二話我已經看完很久了但是遲遲沒時間寫下觀後感倒是讓我重複觀看了第二話很多次(笑)

第二話印象最讓我深刻的是一開始的孤獨少女以及誕生在』什麼都不會誕生什麼都不會死去』世界的人工生命體

這讓我不禁聯想是否所謂的』誕生.死去.得到.失去』之類的詞彙都在人與人產生互動之後產生

當人是孤獨的時候週遭事物的變化便顯得不是那麼重要因為可以說是自己獨佔了空間及時間

因為少了與他人』比較』因此得到和失去便顯得沒有意義表情也沒有了意義因此少女沒有太明顯的情緒起伏

在這個看似如同天堂般靜止的世界隱含了地獄的恐懼也就是人們最害怕的』孤獨』

所以當我看到這個安靜世界的畫面時總覺得有些許的違和感

所以少女製造了一個人工生命體陪她少女向人工生命體伸出手迎接的同時

讓人感到溫馨那是與其他個體正面互動所產生的感覺-溫馨

所以與他人要有正面的互動才會有正面的回應

這種安插小品故事在片頭的方式讓我想到Chobits漫畫單行本排版的方式

接著是第二話故事的開始春原不怕死的個性又去招惹大姊頭智代

想當然是被痛毆一頓最後還掉進垃圾通道內

第二話前半段多在搞笑杏和朋也的互動十分有趣一些角色也在此段慢慢浮出檯面

圖書館少女一之瀨琴美當她問朋也『要吃(便當)嗎?』時

能登的聲音會讓我想到下一句該不會是=>琴美: 要死一遍看看嗎?(イッペン死ンデミル？)

很可惜在下技術不足沒辦法惡搞(死)

而古河也在朋也的建議下打算讓演劇部起死回生結果宣傳海報上畫了一堆糰子(だんご)

這是古河最初的一步

超人氣角色-風子也在這之後不久登場了

後半段劇情急轉直下朋也情緒從正面趨於負面當他回家幫助古河製作糰子模型時直幸(朋也的父親)表示想要幫忙

卻被朋也的負面情緒回饋父子關係再度降到冰點

而跑出屋外的朋也和古河見面後情緒又趨於平緩兩人開心的交談

並約定隔日放學後在操場見面打球

那天是陰雨天擔心古河會因單純個性而去籃球場赴約的朋也最後還是去籃球場確認古河是否赴約了

朋也見到了在雨中呆站的古河古河笑著請朋也投球但某些原因讓朋也舉起雙手投球的瞬間球掉了

『右手…舉不起來』

『咦？』

『國中三年級的時候　我跟老爸打了一架　右肩受了傷沒辦法…舉到肩膀以上…』

『我…已經無法打籃球了』

雖然是悲傷的情緒但是願意向古河敞開心胸的朋也也算是踏出了最初的一步了吧

殷紅歌頌的殘缺

[生物資訊期末報告]Phylogenetics of The Interferon Regulatory Factor Family

[生物資訊期末報告]The analysis for nucleotide/protein sequence(IRF-1)

[生物資訊期末報告]The Sequence Similarity among The Interferon Regulatory Factor Family

[生物資訊期末報告]PROMO Search Result For The Interferon Regulatory Factor Family(IRF6-IRF8)

[生物資訊期末報告]PROMO Search Result For The Interferon Regulatory Factor Family(IRF1-IRF5)

[生物資訊期末報告]ORF Finder Results For The Interferon Regulatory Factor Family (IRF6-IRF9)

[生物資訊期末報告]ORF Finder Results For The Interferon Regulatory Factor Family (IRF1-IRF5)

[生物資訊期末報告] Introduction of The Interferon Regulatory Factor Family

[電波]caramelldansen in mabinogi

[動畫]CLANNAD 第二話 觀後感

[動畫]CLANNAD 第二話觀後感