Ifna4 (interferon, alpha 4) - Rat Genome Database

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Gene: Ifna4 (interferon, alpha 4) Rattus norvegicus
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Symbol: Ifna4
Name: interferon, alpha 4
RGD ID: 1306334
Description: Predicted to enable cytokine activity and type I interferon receptor binding activity. Predicted to be involved in several processes, including lymphocyte activation involved in immune response; response to exogenous dsRNA; and type I interferon-mediated signaling pathway. Predicted to be active in extracellular space. Human ortholog(s) of this gene implicated in Crimean-Congo hemorrhagic fever; common cold; hepatitis B; liver disease (multiple); and sarcoidosis. Orthologous to several human genes including IFNA4 (interferon alpha 4); PARTICIPATES IN autoimmune thyroiditis pathway; autophagy pathway; cytokine mediated signaling pathway; INTERACTS WITH 2,2',5,5'-tetrachlorobiphenyl; Cuprizon; PCB138.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: If1ai2; interferon 1ai2; LOC298205
RGD Orthologs
Human
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85108,115,064 - 108,116,010 (-)NCBIGRCr8
mRatBN7.25103,069,174 - 103,070,120 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5103,069,483 - 103,070,052 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5105,424,191 - 105,424,760 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05107,214,640 - 107,215,209 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05107,275,278 - 107,275,847 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05106,922,563 - 106,923,132 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5106,922,563 - 106,923,132 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05110,900,533 - 110,901,102 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45107,886,554 - 107,887,123 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.15107,891,779 - 107,892,349 (-)NCBI
Celera5100,046,719 - 100,047,288 (+)NCBICelera
Cytogenetic Map5q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Acute Respiratory Infection in Human Dipeptidyl Peptidase 4-Transgenic Mice Infected with Middle East Respiratory Syndrome Coronavirus. Iwata-Yoshikawa N, etal., J Virol. 2019 Mar 5;93(6). pii: JVI.01818-18. doi: 10.1128/JVI.01818-18. Print 2019 Mar 15.
4. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:19130550  


Genomics

Comparative Map Data
Ifna4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85108,115,064 - 108,116,010 (-)NCBIGRCr8
mRatBN7.25103,069,174 - 103,070,120 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5103,069,483 - 103,070,052 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5105,424,191 - 105,424,760 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05107,214,640 - 107,215,209 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05107,275,278 - 107,275,847 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05106,922,563 - 106,923,132 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5106,922,563 - 106,923,132 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05110,900,533 - 110,901,102 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45107,886,554 - 107,887,123 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.15107,891,779 - 107,892,349 (-)NCBI
Celera5100,046,719 - 100,047,288 (+)NCBICelera
Cytogenetic Map5q32NCBI
IFNA4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38921,186,618 - 21,187,587 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl921,186,618 - 21,187,587 (-)EnsemblGRCh38hg38GRCh38
GRCh37921,186,617 - 21,187,586 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36921,176,693 - 21,177,670 (-)NCBINCBI36Build 36hg18NCBI36
Build 34921,176,692 - 21,177,670NCBI
Celera921,124,915 - 21,125,896 (-)NCBICelera
Cytogenetic Map9p21.3NCBI
HuRef921,149,768 - 21,150,749 (-)NCBIHuRef
CHM1_1921,186,422 - 21,187,403 (-)NCBICHM1_1
T2T-CHM13v2.0921,200,472 - 21,201,441 (-)NCBIT2T-CHM13v2.0

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:24
Count of miRNA genes:24
Interacting mature miRNAs:24
Transcripts:ENSRNOT00000046207
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357396Bw44Body weight QTL 444.19body mass (VT:0001259)body weight (CMO:0000012)568984307104251008Rat
1331796Thshl2Thyroid stimulating hormone level QTL 22.3blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)597059760147465714Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
61380Edpm5Estrogen-dependent pituitary mass QTL 54.50.92pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)568984307104251008Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1298070Scl18Serum cholesterol level QTL 183.7blood LDL cholesterol amount (VT:0000181)calculated plasma low density lipoprotein cholesterol level (CMO:0001245)579584860124584860Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
61452Ciaa5CIA Autoantibody QTL 53.5blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)594858972143070159Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)543726656129132602Rat
1357402Bw46Body weight QTL 464.47body mass (VT:0001259)body mass index (BMI) (CMO:0000105)568984307104251008Rat
2302381Bw84Body weight QTL 844.47body mass (VT:0001259)body mass index (BMI) (CMO:0000105)568984307104251008Rat
7411582Foco3Food consumption QTL 37.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)587468046132468046Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
1598859Cm66Cardiac mass QTL 662heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)579584860124584860Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
2317753Glom24Glomerulus QTL 243.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)597570330136479578Rat
1582212Livw2Liver weight QTL 23.50.0004liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)599016066119085810Rat
7411564Bw135Body weight QTL 1350.001body mass (VT:0001259)body weight gain (CMO:0000420)587468046132468046Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)550328551141643988Rat
7411601Foco12Food consumption QTL 1219.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)587468046132468046Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535189153141643988Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
7394708Emca11Estrogen-induced mammary cancer QTL 11mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)599753548113061097Rat
1576317Eutr2Estrogen induced uterine response QTL 20.01uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)534730116104251008Rat
1598846Bp293Blood pressure QTL 2933.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)579584860124584860Rat
1358909Kidm25Kidney mass QTL 251.87kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)590067849128034027Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555805606132207589Rat
631527Tls1T-lymphoma susceptibility QTL 100.001thymus integrity trait (VT:0010555)post-insult time to onset of T-cell lymphoma (CMO:0001907)590450144135450144Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531663789131345958Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)559793399143070159Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)569540295151018848Rat
1600362Mcs19Mammary carcinoma susceptibility QTL 192.5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)599485997103690167Rat
1298086Bp156Blood pressure QTL 156arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)584132602129132602Rat
2290005Mcs24Mammary carcinoma susceptibility QTL 24mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)564719390109719390Rat
2306971Anxrr21Anxiety related response QTL 219.47fear/anxiety-related behavior trait (VT:1000241)number of entries into a discrete space in an experimental apparatus (CMO:0000960)566174080124160948Rat
1358895Bp254Blood pressure QTL 2543.60.0003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)558829236128034027Rat
2316959Gluco59Glucose level QTL 594.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)534944474113558310Rat
2312671Scl64Serum cholesterol level QTL 640.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)568984307104251008Rat
6903316Bw113Body weight QTL 11320.0103body mass (VT:0001259)body weight (CMO:0000012)587765973132765973Rat
1358889Bp261Blood pressure QTL 2612.86arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)590067849128034027Rat
2316957Pur21Proteinuria QTL 216.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)559793528113558156Rat
1358187Emca1Estrogen-induced mammary cancer QTL 14.4mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)599216724148607142Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
4 4 4 31 27 27 5 23 5 2 53 39 18 2 10 22

Sequence


Ensembl Acc Id: ENSRNOT00000046207   ⟹   ENSRNOP00000048643
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5103,069,483 - 103,070,052 (-)Ensembl
Rnor_6.0 Ensembl5106,922,563 - 106,923,132 (-)Ensembl
RefSeq Acc Id: NM_001106667   ⟹   NP_001100137
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85108,115,064 - 108,116,010 (-)NCBI
mRatBN7.25103,069,174 - 103,070,120 (-)NCBI
Rnor_6.05106,922,563 - 106,923,132 (-)NCBI
Rnor_5.05110,900,533 - 110,901,102 (-)NCBI
RGSC_v3.45107,886,554 - 107,887,123 (-)RGD
Celera5100,046,719 - 100,047,288 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001100137 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAB0000180 (Get FASTA)   NCBI Sequence Viewer  
  EDL75997 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000048643.3
RefSeq Acc Id: NP_001100137   ⟸   NM_001106667
- Peptide Label: precursor
- UniProtKB: D3ZFH0 (UniProtKB/TrEMBL),   A6KRA3 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000048643   ⟸   ENSRNOT00000046207

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZFH0-F1-model_v2 AlphaFold D3ZFH0 1-189 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306334 AgrOrtholog
BioCyc Gene G2FUF-40823 BioCyc
Ensembl Genes ENSRNOG00000033823 Ensembl
  ENSRNOG00000063201 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000046207.4 UniProtKB/TrEMBL
Gene3D-CATH 1.20.1250.10 UniProtKB/TrEMBL
InterPro 4_helix_cytokine-like_core UniProtKB/TrEMBL
  Interferon_alpha/beta/delta UniProtKB/TrEMBL
KEGG Report rno:298205 UniProtKB/TrEMBL
NCBI Gene 298205 ENTREZGENE
PANTHER ALPHA-INTERFERON-RELATED UniProtKB/TrEMBL
  Interferon_abd UniProtKB/TrEMBL
Pfam Interferon UniProtKB/TrEMBL
PhenoGen Ifna4 PhenoGen
PRINTS INTERFERONAB UniProtKB/TrEMBL
PROSITE INTERFERON_A_B_D UniProtKB/TrEMBL
RatGTEx ENSRNOG00000033823 RatGTEx
  ENSRNOG00000063201 RatGTEx
SMART IFabd UniProtKB/TrEMBL
Superfamily-SCOP 4_helix_cytokine UniProtKB/TrEMBL
UniProt A6KRA3 ENTREZGENE, UniProtKB/TrEMBL
  D3ZFH0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Ifna4  interferon, alpha 4   Ifna4_predicted  interferon, alpha 4 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Ifna4_predicted  interferon, alpha 4 (predicted)      Symbol and Name status set to approved 70820 APPROVED