IRF1 (interferon regulatory factor 1) - Chinchilla Research Resource Database
Submit Data |  Help |  Video Tutorials |  News |  Publications |  FTP Download |  REST API |  Citing RGD |  Contact   
Gene: IRF1 (interferon regulatory factor 1) Canis lupus familiaris
Analyze
Symbol: IRF1
Name: interferon regulatory factor 1
CRRD ID: 12143704
Description: ENCODES a protein that exhibits DNA binding (ortholog); sequence-specific DNA binding (ortholog); INVOLVED IN cellular response to exogenous dsRNA (ortholog); cellular response to interleukin-1 (ortholog); cellular response to peptide hormone stimulus (ortholog); PARTICIPATES IN interleukin-6 signaling pathway; Jak-Stat signaling pathway; nuclear factor kappa B signaling pathway; ASSOCIATED WITH allergic conjunctivitis (ortholog); bacterial pneumonia (ortholog); Brain Injuries (ortholog); FOUND IN chromatin (inferred); cytoplasm (inferred); nucleus (inferred)
Type: protein-coding
RefSeq Status: MODEL
Orthologs:
Homo sapiens (human) : IRF1 (interferon regulatory factor 1)  HGNC  Alliance
Mus musculus (house mouse) : Irf1 (interferon regulatory factor 1)  MGI  Alliance
Rattus norvegicus (Norway rat) : Irf1 (interferon regulatory factor 1)  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Irf1 (interferon regulatory factor 1)
Pan paniscus (bonobo/pygmy chimpanzee) : IRF1 (interferon regulatory factor 1)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Irf1 (interferon regulatory factor 1)
Sus scrofa (pig) : IRF1 (interferon regulatory factor 1)
Chlorocebus sabaeus (African green monkey) : IRF1 (interferon regulatory factor 1)
Heterocephalus glaber (naked mole-rat) : Irf1 (interferon regulatory factor 1)
more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1120,760,120 - 20,781,608 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11120,773,801 - 20,781,106 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
apoptotic process  (IEA)
CD8-positive, alpha-beta T cell differentiation  (IEA)
cell cycle arrest  (IEA)
cellular response to exogenous dsRNA  (ISO)
cellular response to interferon-beta  (IEA)
cellular response to interleukin-1  (ISO)
cellular response to mechanical stimulus  (IEA)
cellular response to peptide hormone stimulus  (ISO)
cellular response to retinoic acid  (ISO)
cellular response to tumor necrosis factor  (ISO)
defense response to virus  (IEA)
female pregnancy  (ISO)
I-kappaB kinase/NF-kappaB signaling  (ISO)
immune system process  (IBA)
interferon-gamma-mediated signaling pathway  (IEA)
negative regulation of cell population proliferation  (IEA)
negative regulation of regulatory T cell differentiation  (IEA)
negative regulation of transcription, DNA-templated  (IEA)
negative regulation of tyrosine phosphorylation of STAT protein  (ISO)
positive regulation of cell death  (ISO)
positive regulation of interferon-beta production  (IEA)
positive regulation of interleukin-12 production  (IEA)
positive regulation of transcription by RNA polymerase II  (IEA)
positive regulation of transcription, DNA-templated  (ISO)
positive regulation of type I interferon production  (ISO)
regulation of CD8-positive, alpha-beta T cell proliferation  (IEA)
regulation of gene expression  (ISO)
regulation of immune response  (IEA)
regulation of MyD88-dependent toll-like receptor signaling pathway  (IEA)
regulation of transcription, DNA-templated  (IEA)
response to growth hormone  (ISO)
response to heat  (ISO)

Cellular Component
chromatin  (IEA)
cytoplasm  (IEA)
nucleus  (IBA,IEA)

References

Genomics

Comparative Map Data
IRF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1120,760,120 - 20,781,608 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11120,773,801 - 20,781,106 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
IRF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl5132,481,609 - 132,490,777 (-)EnsemblGRCh38hg38GRCh38
GRCh385132,481,609 - 132,490,789 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh375131,817,301 - 131,826,465 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 365131,846,679 - 131,854,326 (-)NCBINCBI36hg18NCBI36
Build 345131,846,683 - 131,854,326NCBI
Celera5127,947,368 - 127,956,530 (-)NCBI
Cytogenetic Map5q31.1NCBI
HuRef5127,009,541 - 127,018,697 (-)NCBIHuRef
CHM1_15131,250,016 - 131,259,179 (-)NCBICHM1_1
Irf1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391153,660,841 - 53,669,200 (+)NCBI
GRCm381153,770,014 - 53,778,374 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1153,770,014 - 53,778,374 (+)EnsemblGRCm38mm10GRCm38
MGSCv371153,583,516 - 53,591,876 (+)NCBIGRCm37mm9NCBIm37
MGSCv361153,613,501 - 53,620,746 (+)NCBImm8
Celera1158,349,840 - 58,358,199 (+)NCBICelera
Cytogenetic Map11B1.3NCBI
cM Map1132.0NCBI
Irf1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01039,109,530 - 39,116,532 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1039,109,522 - 39,116,531 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01038,891,468 - 38,898,470 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41039,220,600 - 39,227,602 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11039,229,846 - 39,236,848 (+)NCBI
Celera1037,260,559 - 37,267,561 (+)NCBICelera
Cytogenetic Map10q22NCBI
RH 3.4 Map10405.3RGD
Irf1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554083,880,155 - 3,887,973 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554083,882,282 - 3,887,965 (-)NCBIChiLan1.0ChiLan1.0
IRF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.15134,066,250 - 134,075,035 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5134,067,441 - 134,075,035 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v05127,903,887 - 127,913,843 (-)NCBIMhudiblu_PPA_v0panPan3
Irf1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049366472,686,247 - 2,693,633 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
IRF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl2134,776,134 - 134,783,646 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.12134,776,122 - 134,783,646 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.22140,229,799 - 140,252,658 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap2q24-q29NCBI
IRF1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl2335,307,772 - 35,316,763 (-)Ensembl
ChlSab1.12335,309,058 - 35,317,765 (-)NCBI
Irf1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473339,596,565 - 39,603,428 (+)NCBI


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system reproductive system respiratory system adipose tissue
High
Medium 5 21 6 6 6 6 6 10 3
Low 5 1 6 6 1 3
Below cutoff 7

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_003639368 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AAEX03007772 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSCAFT00000001334   ⟹   ENSCAFP00000001223
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl1120,774,476 - 20,781,608 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000082208   ⟹   ENSCAFP00000060877
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl1120,760,120 - 20,781,608 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000083675   ⟹   ENSCAFP00000058096
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl1120,775,183 - 20,780,879 (-)Ensembl
RefSeq Acc Id: XM_003639368   ⟹   XP_003639416
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.11120,773,801 - 20,781,106 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_003639416 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_003639416   ⟸   XM_003639368
- UniProtKB: E2QT38 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000001223   ⟸   ENSCAFT00000001334
RefSeq Acc Id: ENSCAFP00000058096   ⟸   ENSCAFT00000083675
RefSeq Acc Id: ENSCAFP00000060877   ⟸   ENSCAFT00000082208
Promoters
RGD ID:13685169
Promoter ID:EPDNEW_C3238
Type:single initiation site
Name:IRF1_1
Description:interferon regulatory factor 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.11120,781,089 - 20,781,149EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000000851 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSCAFP00000001223 UniProtKB/TrEMBL
  ENSCAFP00000058096 UniProtKB/TrEMBL
  ENSCAFP00000060877 UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000001334 UniProtKB/TrEMBL
  ENSCAFT00000082208 UniProtKB/TrEMBL
  ENSCAFT00000083675 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/TrEMBL
InterPro Interferon_reg_fac_CS UniProtKB/TrEMBL
  Interferon_reg_fact_DNA-bd_dom UniProtKB/TrEMBL
  IRF1 UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/TrEMBL
NCBI Gene IRF1 ENTREZGENE
PANTHER PTHR11949 UniProtKB/TrEMBL
  PTHR11949:SF3 UniProtKB/TrEMBL
Pfam IRF UniProtKB/TrEMBL
PRINTS INTFRNREGFCT UniProtKB/TrEMBL
PROSITE IRF_1 UniProtKB/TrEMBL
  IRF_2 UniProtKB/TrEMBL
SMART IRF UniProtKB/TrEMBL
Superfamily-SCOP SSF46785 UniProtKB/TrEMBL
UniProt A0A5F4CZI3_CANLF UniProtKB/TrEMBL
  A0A5F4D537_CANLF UniProtKB/TrEMBL
  E2QT38 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:42091 ENTREZGENE