H-InvDB x AHG DB
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H-InvDB_8.3 released on March 26, 2013.
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H-Invitational ID: HIT000034397 Accession number: BC009483 Created date: 26-Mar-2013 Last modified: 26-Mar-2013
Definition: Interferon regulatory factor 1.
 
 

Transcript original information
Accession number BC009483.2
CAGE tag ID NA
EST ID NA
Clone Number MGC:15355 IMAGE:3623414
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ; Antibody: searching human antibodies at "BIO-kaimono.com" Antibody (IRF1) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (IRF1);
Sequence data provider Provider:MGC/NCI
Annotation project H-Invitational FLcDNA
Length of cDNA 2061[bp] (No. of exon:10)[A:497 T:425 G:556 C:583]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type Pancreas, adenocarcinoma
Develpmental stage NA
Mini-G
Sequence quality information
CDS feature Complete CDS
Kozak sequence NA
PolyA Site: 2044(+)
Vector/adapter sequence NA
Frame shift NA
Remaining intron NA
Splice site acceptor (NAGNAG) CAGGAG; 
Transcript quality feature NA
Notes NA

Gene structure information  G-integra H-DBAS cDNA-genome alignment
H-Inv cluster ID HIX0005159
Genomic location  G-integra Help Chromosome 5
Location 5q31.1
Position 131818780- 131826434
Strand -
Possible duplicated location(s) NA
Gene structure 10 exon(s)
Database links RefSeq NM_002198
Ensembl ENST00000245414ENST00000405885ENST00000437654ENST00000439555ENST00000458069ENST00000459982ENST00000463784ENST00000472045ENST00000476613ENST00000493208
Entrez Gene Entrez Gene ID:3659
KEGG GENES KEGG GENES(3659)
GeneCard GeneCardIRF1*GeneCards is provided free to academic non-profit institutions.
Related H-InvDB links H-DBASH-DBAS G-integraG-integra cDNA-genome alignmentcDNA-genome alignment

Predicted CDS information
HIP ID HIP000084307
Predicted CDS 204..1181;  325[aa];  Orientation:+3; 
Codon Adaptation Index (CAI). 0.823
Database links RefSeq NP_002189
UniProt P10914Q6FHN8
CCDS CCDS4155

Motif information
ORF

length(325),orf(204:1181)
MPITRMRMRPWLEMQINSNQIPGLIWINKEEMIFQIPWKHAAKHGWDINK
DACLFRSWAIHTGRYKAGEKEPDPKTWKANFRCAMNSLPDIEEVKDQSRN
KGSSAVRVYRMLPPLTKNQRKERKSKSSRDAKSKAKRKSCGDSSPDTFSD
GLSSSTLPDDHSSYTVPGYMQDLEVEQALTPALSPCAVSSTLPDWHIPVE
VVPDSTSDLYNFQVSPMPSTSEATTDEDEEGKLPEDIMKLLEQSEWQPTN
VDGKGYLLNEPGVQPTSVYGDFSCKEEPEIDSPGGDIGLSLQRVFTDLKN
MDATWLDSLLTPVRLPSIQAIPCAP*
a.a.
length
InterPro Name
length(315), motif(1:315) 315 IPR017431 Interferon regulatory factor-1/2 [Family]
length(114), motif(1:114) 114 IPR001346 Interferon regulatory factor [Domain]
length(112), motif(2:113) 112 IPR011991 Winged helix-turn-helix transcription repressor DNA-binding [Domain]
length(109), motif(5:113) 109 IPR001346 Interferon regulatory factor [Domain]
length(20), motif(7:26) 20 IPR001346 Interferon regulatory factor [Domain]
length(34), motif(26:59) 34 IPR019817 Interferon regulatory factor, conserved site [Conserved_site]
length(14), motif(33:46) 14 IPR001346 Interferon regulatory factor [Domain]
length(18), motif(51:68) 18 IPR001346 Interferon regulatory factor [Domain]
length(23), motif(74:96) 23 IPR001346 Interferon regulatory factor [Domain]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000034397
H-Inv cluster ID Locus viewHIX0005159
Accession number BC009483.2
CAGE tag ID NA
EST ID NA
Transcript feature  Help Representative H-Inv IDRepresentative transcript;  Splicing isoformSplicing isoform
Coding potential  Help Protein coding; 
Definition Interferon regulatory factor 1.
Similarity category  Help Category: Identical to known human protein(Category I).
Identical to known human protein (NP_002189)  [Identity/coverage = 100.0%/100.0%] to Homo sapiens protein.
Experimental evidence Protein evidence
PubMed ID NA
Gene family/group Gene family H-Inv gene family/group ID NA
Gene family/group name NA
Evidence motif (InterPro) ID NA
Gene symbol/name HGNC symbol IRF1
HGNC aliases NA
HGNC name interferon regulatory factor 1
DDBJ IRF1
UniProt NA
EC number NA
GGDB
(GlycoGene Database)
Gene symbol NA
Familly NA
Designation NA
Expression NA
KEGG metabolic pathway NA
Protein-protein interaction (PPI) PPI viewer H-Inv protein ID HIP000084307
No. of interaction 12
Interaction partner(s) HIP000022609HIP000025414HIP000026075HIP000037612HIP000039881HIP000051820HIP000088757HIP000096721HIP000096938HIP000097433HIP000100966HIP000101884
BIND NA
DIP 115228E;  88067E;  88068E; 
MINT NA
HPRD 01238;  01241;  02777;  02829;  02867;  03336;  03554;  04078;  06780;  07223;  10556; 
IntAct EBI-3931236;  EBI-1067616;  EBI-3906874; 
Database links RefSeq NM_002198
Ensembl ENST00000245414ENST00000405885ENST00000437654ENST00000439555ENST00000458069ENST00000459982ENST00000463784ENST00000472045ENST00000476613ENST00000493208
Entrez Gene Entrez Gene ID:3659
KEGG GENES KEGG GENES(3659)
GeneCard GeneCardIRF1*GeneCards is provided free to academic non-profit institutions.
etc H-GOLDHuman-Gene diversity Of Life-style related Diseases
Curation status Human curated
Notes NA
Related H-InvDB links Gene familyGene family;  Similarity Search ToolSimilarity Search Tool TACTTACT
fRNAdb (The functional RNA database) : overlapping fRNAdb entries with H-InvDB transcripts based on the location of the genome. 
NA

Gene ontology information
Molecular function transcription factor activity (GO:0003700); 
Biological process regulation of transcription, DNA-dependent (GO:0006355); 
Cellular component nucleus (GO:0005634); 

Subcellular localization information  Last modified:26-Mar-2013
WoLF PSORT nuclear; 
Target P Not predicted
SOSUI soluble protein
TMHMM soluble protein
PTS1 Not targeted
Related H-InvDB links LIFEdb LIFEdb; 
JRE-1.4.0 or later is required. Download JRE at Sun's web site.

Protein structure information (GTOP) GTOP Last modified:26-Mar-2013
Start End PDB_ID E-value Identity Coverage SCOP_ID
7 111 1if1A 9e-47 100.0 105/105 a.4.5.23
Related H-InvDB links GTOP GTOP

Gene expression information  H-ANGEL DNAProbeLocator Last modified:26-Mar-2013
Tissue-specific expression  H-ANGEL NA
Probe
information DNAProbeLocator
AceGene AGhsA220418; 
Affymetrix
GeneChip
HG-Focus 202531_at; 
HG-U133 202531_at; 
HG-U133A 202531_at; 
HG-U133A_2 202531_at; 
HG-U133B NA
HG-U133_Plus_2 202531_at; 
HG-U95 669_s_at; 
HG-U95A 669_s_at; 
HG-U95B NA
HG-U95C NA
HG-U95D NA
HG-U95E NA
HG-U95Av2 NA
HuEx-1_0 2828595;  2875350;  2875351;  2875353;  2875356;  2875358;  2875360;  2875362;  2875363;  2875364;  2875365;  2875366;  2875372;  2875375; 
HuGeneFL L05072_s_at; 
Agilent Human 1A Oligo Microarray:PGID215 A_23_P41765; 
Whole Human Genome Oligo Microarray:PGID247 A_23_P41765; 
Related H-InvDB links H-ANGELH-ANGEL DNAProbeLocatorDNAProbeLocator

Disease/pathology information  DiseaseInfo Viewer LEGENDA Last modified:26-Mar-2013
Disease relation Disease name: Gastric cancer (137215);  Disease name: Macrocytic anemia, refractory, of 5q- syndrome (153550); 
Related information in OMIM OMIM ID:  147575;  Title: INTERFERON REGULATORY FACTOR 1
Co-localized orphan diseases OMIM ID:  601888608850611091612554612571
Disease related mutation MutationView:  147575
JRE-1.4.0 or later is required.Download JRE at Sun's web site.
Literature-Extracted GENe-Disease Associations (LEGENDA) LEGENDA Gene name Entrez Gene ID:(3659)
Disease Entrez Gene ID:(3659)
Substance Entrez Gene ID:(3659)
Related H-InvDB links DiseaseInfo ViewerDiseaseInfo ViewerLEGENDALEGENDA

Evolutionary information  Evola Help Last modified:26-Mar-2013
Relationship Species Accession number MGI Links
Orthology Mus sp. (Mouse) AK157347 G-integraG-integra
Orthology Bos sp. (Cow) BC102766 G-integraG-integra
Orthology Gallus sp. (Chicken) ENSGALT00000002244 G-integraG-integra
Orthology Macaca sp. (Macaque) ENSMMUT00000011322 G-integraG-integra
Orthology Pongo sp. (Orangutan) ENSPPYT00000018338 G-integraG-integra
Orthology Pan sp. (Chimpanzee) ENSPTRT00000031881 G-integraG-integra
Orthology Tetraodon sp. (Tetraodon) GSTENT00037577001 G-integraG-integra
Orthology Rattus sp. (Rat) M34253 G-integraG-integra
Orthology Takifugu sp. (Fugu) SINFRUT00000130702 G-integraG-integra
Orthology Monodelphis sp. (Opossum) XM_001371779 G-integraG-integra
Orthology Equus sp. (Horse) XM_001504445 G-integraG-integra
Orthology Canis sp. (Dog) XM_538621 G-integraG-integra
Phylogenetic tree [View by ATV]
Neighbor-joining (phb) 
Related H-InvDB links EvolaEvoladN/dS (under constraction); 

Polymorphism (SNP, indel), microsatellite (Short Tandem Repeat, STR) and repeat information  VaryGene Repeat mask viewer
 Single Nucleotide Polymorphism (SNP) and indel  VaryGene
Location Variation dbSNP ID Strand CDS/UTR Translation
22 .. 22 G/C rs11242115 + 5'UTR
113 .. 113 T/C rs10900809 + 5'UTR
125 .. 125 C/T rs960757 + 5'UTR
128 .. 128 C/T rs111285485 - 5'UTR
172 .. 172 G/A rs17848393 + 5'UTR
305 .. 305 C/T rs117282832 - CDS Synonymous[Phe34Phe]
548 .. 548 C/G rs17622685 - CDS Synonymous[Leu115Leu]
758 .. 758 A/G rs9282762 + CDS Synonymous[Pro185Pro]
782 .. 782 C/T rs17848410 + CDS Synonymous[Pro193Pro]
1055 .. 1055 G/C rs113976540 - CDS Synonymous[Gly284Gly]
1146 .. 1146 T/C rs55746618 - CDS Synonymous[Leu315Leu]
1218 .. 1218 C/G rs56288038 - 3'UTR
1323 .. 1323 C/T rs17848427 + 3'UTR
1562 .. 1562 C/T rs17848428 + 3'UTR
1609 .. 1609 G/A rs34850771 + 3'UTR
1625 .. 1625 C/T rs17848429 + 3'UTR
1627 .. 1627 C/G rs35642338 + 3'UTR
1690 .. 1690 T/C rs17848431 + 3'UTR
1693 .. 1693 G/A rs35178118 + 3'UTR
1698 .. 1698 G/A rs839 + 3'UTR
1834 .. 1834 C/A rs17848433 + 3'UTR
1876 .. 1876 C/T rs17848434 + 3'UTR
1994 .. 1994 A/- rs11347983 - 3'UTR
2009 .. 2009 A/G rs115945411 - 3'UTR
 Microsatellite (Short Tandem Repeat, STR)
No data available
 Microsatellite: Human-Gene diversity Of Life-style related Diseases (H-GOLD)
No data available
 Repeat  Repeat mask viewer
No data available
Database links H-GOLDHuman-Gene diversity Of Life-style related Diseases(H-GOLD)
Related H-InvDB links VaryGeneVaryGene Repeat mask viewerRepeat Mask Viewer