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PR00267

Identifier
INTFRNREGFCT  [View Relations]  [View Alignment]  
Accession
PR00267
No. of Motifs
4
Creation Date
19-JAN-1995  (UPDATE 07-JUN-1999)
Title
Interferon regulatory factor signature
Database References

PROSITE; PS00601 IRF
PFAM; PF00605 IRF
INTERPRO; IPR001346
Literature References
1. MIYAMOTO, M., FUJITA, T., KIMURA, Y., MARUYAMA, M., HARADA, H.,
SUDO, Y., MIYATA, T. AND TANIGUCHI, T.
Regulated expression of a gene encoding a nuclear factor, IRF-1, that
specifically binds to IFN-beta gene regulatory elements.
CELL 54 903-913 (1988).
 
2. WEISZ, A., MARX, P., SHARF, R., APPELLA, E., DRIGGERS, P.H., OZATO, K.
AND LEVI, B.Z.
Human interferon consensus sequence binding protein is a negative
regulator of enhancer elements common to interferon-inducible genes.
J.BIOL.CHEM. 267 25589-25596 (1992).
 
HARADA, H., FUJITA, T., MIYAMOTO, M., KIMURA, Y., MARUYAMA, M., FURIA, A.,
MIYATA, T. AND TANIGUCHI, T.
Structurally similar but functionally distinct factors, IRF-1 and IRF-2,
bind to the same regulatory elements of IFN and IFN-inducible genes.
CELL 58 729-739 (1989).

Documentation
The expression of type I interferon genes (interferons alpha and beta) is 
induced by many agents, including viral attack [1]. Induction is mediated
by the binding of interferon regulatory factor 1 (IRF-1) to a region known
as the interferon consensus sequence (ICS), located upstream of the
interferon genes [2]. Other factors may also bind to the ICS, including
IRF-2, which does not function as an activator, but rather suppresses the
function of IRF-1 under certain circumstances [3]. IRF proteins contain a
conserved N-terminal region of about 120 amino acids, which folds into a
structure that binds specifically to the ICS; the remaining parts of the
sequences vary depending on the precise function of the protein [2]. 
 
INTFRNREGFCT is a 4-element fingerprint that provides a signature for the 
ICS-binding region of interferon regulatory factors. The fingerprint was
derived from an initial alignment of 5 sequences: the motifs were drawn
from conserved regions spanning virtually the full length of the binding
domain, motif 4 including the region encoded by PROSITE pattern IRF
(PS00601). Two iterations on OWL25.1 were required to reach convergence,
at which point a true set comprising 9 sequences was identified.
 
An update on SPTR37_9f identified a true set of 29 sequences.
Summary Information
29 codes involving  4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
429292929
30000
20000
1234
True Positives
ICSB_CHICK    ICSB_HUMAN    ICSB_MOUSE    IRF1_CHICK    
IRF1_HUMAN IRF1_MOUSE IRF1_RAT IRF2_CHICK
IRF2_HUMAN IRF2_MOUSE IRF3_CHICK IRF3_HUMAN
IRF3_MOUSE IRF4_HUMAN IRF4_MOUSE IRF5_HUMAN
IRF5_MOUSE IRF6_HUMAN IRF7_HUMAN IRF7_MOUSE
IRTF_HUMAN IRTF_MOUSE O00331 O00332
O00333 O57578 O75924 P97431
Q99660
Sequence Titles
ICSB_CHICK  INTERFERON CONSENSUS SEQUENCE BINDING PROTEIN (ICSBP) - GALLUS GALLUS (CHICKEN). 
ICSB_HUMAN INTERFERON CONSENSUS SEQUENCE BINDING PROTEIN (ICSBP) - HOMO SAPIENS (HUMAN).
ICSB_MOUSE INTERFERON CONSENSUS SEQUENCE BINDING PROTEIN (ICSBP) - MUS MUSCULUS (MOUSE).
IRF1_CHICK INTERFERON REGULATORY FACTOR 1 (IRF-1) - GALLUS GALLUS (CHICKEN).
IRF1_HUMAN INTERFERON REGULATORY FACTOR 1 (IRF-1) - HOMO SAPIENS (HUMAN).
IRF1_MOUSE INTERFERON REGULATORY FACTOR 1 (IRF-1) - MUS MUSCULUS (MOUSE).
IRF1_RAT INTERFERON REGULATORY FACTOR 1 (IRF-1) - RATTUS NORVEGICUS (RAT).
IRF2_CHICK INTERFERON REGULATORY FACTOR 2 (IRF-2) - GALLUS GALLUS (CHICKEN).
IRF2_HUMAN INTERFERON REGULATORY FACTOR 2 (IRF-2) - HOMO SAPIENS (HUMAN).
IRF2_MOUSE INTERFERON REGULATORY FACTOR 2 (IRF-2) - MUS MUSCULUS (MOUSE).
IRF3_CHICK INTERFERON REGULATORY FACTOR 3 (IRF-3) - GALLUS GALLUS (CHICKEN).
IRF3_HUMAN INTERFERON REGULATORY FACTOR 3 (IRF-3) - HOMO SAPIENS (HUMAN).
IRF3_MOUSE INTERFERON REGULATORY FACTOR 3 (IRF-3) - MUS MUSCULUS (MOUSE).
IRF4_HUMAN INTERFERON REGULATORY FACTOR 4 (IRF-4) (LYMPHOCYTE SPECIFIC INTERFERON REGULATORY FACTOR) (LSIRF) (NF-EM5) - HOMO SAPIENS (HUMAN).
IRF4_MOUSE INTERFERON REGULATORY FACTOR 4 (IRF-4) (LYMPHOCYTE SPECIFIC INTERFERON REGULATORY FACTOR) (LSIRF) (NF-EM5) (PU.1 INTERACTION PARTNER) (TRANSCRIPTIONAL ACTIVATOR PIP) - MUS MUSCULUS (MOUSE).
IRF5_HUMAN INTERFERON REGULATORY FACTOR 5 (IRF-5) - HOMO SAPIENS (HUMAN).
IRF5_MOUSE INTERFERON REGULATORY FACTOR 5 (IRF-5) - MUS MUSCULUS (MOUSE).
IRF6_HUMAN INTERFERON REGULATORY FACTOR 6 (IRF-6) - HOMO SAPIENS (HUMAN).
IRF7_HUMAN INTERFERON REGULATORY FACTOR 7 (IRF-7) - HOMO SAPIENS (HUMAN).
IRF7_MOUSE INTERFERON REGULATORY FACTOR 7 (IRF-7) - MUS MUSCULUS (MOUSE).
IRTF_HUMAN TRANSCRIPTIONAL REGULATOR ISGF3 GAMMA SUBUNIT (IFN-ALPHA RESPONSIVE TRANSCRIPTION FACTOR SUBUNIT) (INTERFERON STIMULATED GENE FACTOR 3 GAMMA) (ISGF3 P48 SUBUNIT) (ISGF-3 GAMMA) - HOMO SAPIENS (HUMAN).
IRTF_MOUSE TRANSCRIPTIONAL REGULATOR ISGF3 GAMMA SUBUNIT (IFN-ALPHA RESPONSIVE TRANSCRIPTION FACTOR SUBUNIT) (INTERFERON STIMULATED GENE FACTOR 3 GAMMA) (ISGF3 P48 SUBUNIT) (ISGF-3 GAMMA) - MUS MUSCULUS (MOUSE).
O00331 INTERFERON REGULATORY FACTOR 4 ALPHA - HOMO SAPIENS (HUMAN).
O00332 INTERFERON REGULATORY FACTOR 4 BETA - HOMO SAPIENS (HUMAN).
O00333 INTERFERON REGULATORY FACTOR 4 GAMMA.1 - HOMO SAPIENS (HUMAN).
O57578 XIRF-6 - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
O75924 INTERFERON REGULATORY FACTOR 7H - HOMO SAPIENS (HUMAN).
P97431 INTERFERON REGULATORY FACTOR 6 - MUS MUSCULUS (MOUSE).
Q99660 MUM1 - HOMO SAPIENS (HUMAN).
Scan History
OWL25_1    2  100  NSINGLE    
SPTR37_9f 2 30 NSINGLE
Initial Motifs
Motif 1  width=20
Element Seqn Id St Int Rpt
RLRQWLIEQIDSSMYPGLIW ICSB_MOUSE 9 9 -
RMRPWLEMQINSNQIPGLSW IRF1_RAT 7 7 -
RMRPWLEEQINSNTIPGLKW IRF2_MOUSE 7 7 -
RMRPWLEMQINSNQIPGLIW IRF1_HUMAN 7 7 -
KLRNWVVEQVESGQFPGVCW IRTF_HUMAN 11 11 -

Motif 2 width=14
Element Seqn Id St Int Rpt
MFRIPWKHAGKQDY ICSB_MOUSE 35 6 -
IFQIPWKHAALHGW IRF1_RAT 33 6 -
IFQIPWMHAARHGW IRF2_MOUSE 33 6 -
ILEIPWKHAAKHGW IRF1_HUMAN 33 6 -
MFRIPWKHAGKQDF IRTF_HUMAN 37 6 -

Motif 3 width=18
Element Seqn Id St Int Rpt
DASIFKAWAVFKGKFKEG ICSB_MOUSE 53 4 -
DACLFRSWAIHTGRYKAG IRF1_RAT 51 4 -
DAPLFRNWAIHTGKHQPG IRF2_MOUSE 51 4 -
DACLFRSWAIHTGRYKAG IRF1_HUMAN 51 4 -
DAAFFKAWAIFKGKYKEG IRTF_HUMAN 55 4 -

Motif 4 width=23
Element Seqn Id St Int Rpt
PATWKTRLRCALNKSPDFEEVTD ICSB_MOUSE 75 4 -
PKTWKANFRCAMNSLPDIEEVKD IRF1_RAT 74 5 -
PKTWKANFRCAMNSLPDIEEVKD IRF2_MOUSE 74 5 -
PKTWKANFRCAMNSLPDIEEVKD IRF1_HUMAN 74 5 -
PAVWKTRLRCALNKSSEFKEVPE IRTF_HUMAN 77 4 -
Final Motifs
Motif 1  width=20
Element Seqn Id St Int Rpt
RLRQWLIEQIDSEQYPGLIW ICSB_CHICK 9 9 -
RLRQWLIEQIDSSMYPGLIW ICSB_HUMAN 9 9 -
RLRQWLIEQIDSSMYPGLIW ICSB_MOUSE 9 9 -
KLRQWLIDQIDSGKYPGLVW IRF4_HUMAN 23 23 -
KLRQWLIDQIDSGKYPGLVW Q99660 23 23 -
KLRQWLIDQIDSGKYPGLVW IRF4_MOUSE 23 23 -
RMRPWLEMQINSNQIPGLIW IRF1_MOUSE 7 7 -
RMRPWLEMQINSNQIPGLIW IRF1_CHICK 7 7 -
RLKPWLVAQVDSGLYPGLIW IRF6_HUMAN 9 9 -
RLKPWLVAQVDSGMYPGLIW O57578 9 9 -
RLKPWLVAQVDSGLYPGLIW P97431 9 9 -
RMRPWLEMQINSNQIPGLSW IRF1_RAT 7 7 -
RMRPWLEEQINSNTIPGLKW IRF2_CHICK 7 7 -
RLKPWLVAQVNSCQYPGLQW IRF5_HUMAN 16 16 -
RMRPWLEEQINSNTIPGLKW IRF2_MOUSE 7 7 -
RLKPWLVAQVNSCQYPGLQW IRF5_MOUSE 16 16 -
RMRPWLEMQINSNQIPGLIW IRF1_HUMAN 7 7 -
RMRPWLEEQINSNTIPGLKW IRF2_HUMAN 7 7 -
KLRNWVVEQVESGQFPGVCW IRTF_HUMAN 11 11 -
LFGEWLLGEISSGCYEGLQW IRF7_HUMAN 13 13 -
LFGEWLLGEISSGCYEGLQW O75924 26 26 -
LFGEWLLGEISSGCYEGLQW O00333 13 13 -
LFGEWLLGEISSGCYEGLQW O00332 13 13 -
LFGEWLLGEISSGCYEGLQW O00331 13 13 -
KLRSWIVEQVESGHFPGVCW IRTF_MOUSE 11 11 -
RFGPWLLNAVSSGLYRGLCW IRF3_CHICK 14 14 -
LFGDWLLGEVSSGQYEGLQW IRF7_MOUSE 11 11 -
RILPWLVSQLDLGQLEGVAW IRF3_HUMAN 7 7 -
RILPWLVSQLDLGQLEGVAW IRF3_MOUSE 7 7 -

Motif 2 width=14
Element Seqn Id St Int Rpt
MFRIPWKHAGKQDY ICSB_CHICK 35 6 -
MFRIPWKHAGKQDY ICSB_HUMAN 35 6 -
MFRIPWKHAGKQDY ICSB_MOUSE 35 6 -
IFRIPWKHAGKQDY IRF4_HUMAN 49 6 -
IFRIPWKHAGKQDY Q99660 49 6 -
VFRIPWKHAGKQDY IRF4_MOUSE 49 6 -
IFQIPWKHAAKHGW IRF1_MOUSE 33 6 -
IFQIPWKHAAKHGW IRF1_CHICK 33 6 -
RFQIPWKHATRHSP IRF6_HUMAN 35 6 -
RFQIPWKHATRHSP O57578 35 6 -
RFQIPWKHATRHSP P97431 35 6 -
IFQIPWKHAALHGW IRF1_RAT 33 6 -
IFQIPWMHAARHGW IRF2_CHICK 33 6 -
LFCIPWRHATRHGP IRF5_HUMAN 42 6 -
IFQIPWMHAARHGW IRF2_MOUSE 33 6 -
LFYIPWRHATRHGP IRF5_MOUSE 42 6 -
ILEIPWKHAAKHGW IRF1_HUMAN 33 6 -
IFQIPWMHAARHGW IRF2_HUMAN 33 6 -
MFRIPWKHAGKQDF IRTF_HUMAN 37 6 -
CFRVPWKHFARKDL IRF7_HUMAN 39 6 -
CFRVPWKHFARKDL O75924 52 6 -
CFRVPWKHFARKDL O00333 39 6 -
CFRVPWKHFARKDL O00332 39 6 -
CFRVPWKHFARKDL O00331 39 6 -
MFRIPWKHAGKQDF IRTF_MOUSE 37 6 -
IFRIPWKHNARKDV IRF3_CHICK 40 6 -
VFRVPWKHFGRRDL IRF7_MOUSE 37 6 -
RFRIPWKHGLRQDA IRF3_HUMAN 33 6 -
RFRIPWKHGLRQDA IRF3_MOUSE 33 6 -

Motif 3 width=18
Element Seqn Id St Int Rpt
DASIFKAWAVFKGKFKEG ICSB_CHICK 53 4 -
DASIFKAWAVFKGKFKEG ICSB_HUMAN 53 4 -
DASIFKAWAVFKGKFKEG ICSB_MOUSE 53 4 -
DAALFKAWALFKGKFREG IRF4_HUMAN 67 4 -
DAALFKAWALFKGKFREG Q99660 67 4 -
DAALFKAWALFKGKFREG IRF4_MOUSE 67 4 -
DACLFRSWAIHTGRYKAG IRF1_MOUSE 51 4 -
DACLFRSWAIHTGRYKVG IRF1_CHICK 51 4 -
ENTIFKAWAVETGKYQEG IRF6_HUMAN 53 4 -
ENTIFKAWAVETGKYQEG O57578 53 4 -
ENTIFKAWAVETGKYQEG P97431 53 4 -
DACLFRSWAIHTGRYKAG IRF1_RAT 51 4 -
DAPLFRNWAIHTGKYQSG IRF2_CHICK 51 4 -
DNTIFKAWAKETGKYTEG IRF5_HUMAN 60 4 -
DAPLFRNWAIHTGKHQPG IRF2_MOUSE 51 4 -
DNTIFKAWAKETGKYTEG IRF5_MOUSE 60 4 -
DACLFRSWAIHTGRYKAG IRF1_HUMAN 51 4 -
DAPLFRNRAIHTGKHQPG IRF2_HUMAN 51 4 -
DAAFFKAWAIFKGKYKEG IRTF_HUMAN 55 4 -
DARIFKAWAVARGRWPPS IRF7_HUMAN 56 3 -
DARIFKAWAVARGRWPPS O75924 69 3 -
DARIFKAWAVARGRWPPS O00333 56 3 -
DARIFKAWAVARGRWPPS O00332 56 3 -
DARIFKAWAVARGRWPPS O00331 56 3 -
DAAIFKAWALFKEKHKDG IRTF_MOUSE 55 4 -
DVEIFKAWAKASGRYEGN IRF3_CHICK 57 3 -
DAQIFKAWAVARGRWPPS IRF7_MOUSE 54 3 -
DFGIFQAWAEATGAYVPG IRF3_HUMAN 50 3 -
DFGIFQAWAEASGAYTPG IRF3_MOUSE 50 3 -

Motif 4 width=23
Element Seqn Id St Int Rpt
PATWKTRLRCALNKSPDFEEVTD ICSB_CHICK 75 4 -
PATWKTRLRCALNKSPDFEEVTD ICSB_HUMAN 75 4 -
PATWKTRLRCALNKSPDFEEVTD ICSB_MOUSE 75 4 -
PPTWKTRLRCALNKSNDFEELVE IRF4_HUMAN 90 5 -
PPTWKTRLRCALNKSNDFEELVE Q99660 90 5 -
PPTWKTRLRCALNKSNDFEELVE IRF4_MOUSE 90 5 -
PKTWKANFRCAMNSLPDIEEVKD IRF1_MOUSE 74 5 -
PKTWKANFRCAMNSLPDIEEVKD IRF1_CHICK 74 5 -
PAKWKAQLRCALNKSREFNLMYD IRF6_HUMAN 76 5 -
PAKWKAQLRCALNKSREFKLMYD O57578 76 5 -
PAKWKAQLRCALNKSREFNLMYD P97431 76 5 -
PKTWKANFRCAMNSLPDIEEVKD IRF1_RAT 74 5 -
PKTWKANFRCAMNSLPDIEEVKD IRF2_CHICK 74 5 -
PAKWKANLRCALNKSRDFRLIYD IRF5_HUMAN 83 5 -
PKTWKANFRCAMNSLPDIEEVKD IRF2_MOUSE 74 5 -
PAKWKANLRCALNKSRDFQLFYD IRF5_MOUSE 83 5 -
PKTWKANFRCAMNSLPDIEEVKD IRF1_HUMAN 74 5 -
PKTWKANFRCAMNSLPDIEEVKD IRF2_HUMAN 74 5 -
PAVWKTRLRCALNKSSEFKEVPE IRTF_HUMAN 77 4 -
RAGWKTNFRCALRSTRRFVMLRD IRF7_HUMAN 88 14 -
RAGWKTNFRCALRSTRRFVMLRD O75924 101 14 -
RAGWKTNFRCALRSTRRFVMLRD O00333 88 14 -
RAGWKTNFRCALRSTRRFVMLRD O00332 88 14 -
RAGWKTNFRCALRSTRRFVMLRD O00331 88 14 -
PAVWKTRLRCALNKSSEFEEVPE IRTF_MOUSE 77 4 -
PAKWKTNFRCALRSTHMFMLLED IRF3_CHICK 78 3 -
RRGWKTNFRCALHSTGRFILRQD IRF7_MOUSE 88 16 -
LPTWKRNFRSALNRKEGLRLAED IRF3_HUMAN 73 5 -
VSTWKRNFRSALNRKEVLRLAAD IRF3_MOUSE 73 5 -