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

Phylogenetics of the family

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

        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

[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)

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:

A

25.2%

C

27.6%

G

26.4%

T

20.9%

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

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:

A

26.7%

C

27.1%

G

27.5%

T

18.7%

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

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*

 

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

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*

 

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

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：

[電波]caramelldansen in mabinogi

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

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