Ebi3 (Epstein-Barr virus induced 3) - Rat Genome Database

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Gene: Ebi3 (Epstein-Barr virus induced 3) Rattus norvegicus
Analyze
Symbol: Ebi3
Name: Epstein-Barr virus induced 3
RGD ID: 1589467
Description: Predicted to enable cytokine binding activity; cytokine receptor activity; and interleukin-27 receptor binding activity. Predicted to be involved in T cell proliferation and cytokine-mediated signaling pathway. Predicted to be located in extracellular region. Predicted to be part of receptor complex. Predicted to be active in external side of plasma membrane. Biomarker of pre-eclampsia. Orthologous to human EBI3 (Epstein-Barr virus induced 3); PARTICIPATES IN interleukin-27 signaling pathway; INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Epstein-Barr virus induced gene 3; Epstein-Barr virus induced gene 3 (similar to Interleukin-27 beta chain precursor); interleukin-27 subunit beta; LOC680609; similar to Interleukin-27 beta chain precursor (IL-27B) (Epstein-Barr virus-induced gene 3 protein homolog)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr89861,441 - 874,731 (+)NCBIGRCr8
mRatBN7.29774,252 - 787,544 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl9783,617 - 787,544 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx91,230,702 - 1,234,687 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.096,577,870 - 6,581,839 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.095,535,739 - 5,539,724 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0911,110,874 - 11,114,843 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl911,110,874 - 11,114,843 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0910,096,038 - 10,100,007 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera97,718,999 - 7,722,962 (-)NCBICelera
Cytogenetic Map9q11NCBI
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

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. EBI3 deficiency leads to diminished T helper type 1 and increased T helper type 2 mediated airway inflammation. Dokmeci E, etal., Immunology. 2011 Jan 24. doi: 10.1111/j.1365-2567.2010.03401.x.
2. 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.
3. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
4. GOA pipeline RGD automated data pipeline
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Metformin exhibits its therapeutic effect in the treatment of pre-eclampsia via modulating the Met/H19/miR-148a-5p/P28 and Met/H19/miR-216-3p/EBI3 signaling pathways. Shu C, etal.
Additional References at PubMed
PMID:9342359   PMID:12121660   PMID:26994309  


Genomics

Comparative Map Data
Ebi3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr89861,441 - 874,731 (+)NCBIGRCr8
mRatBN7.29774,252 - 787,544 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl9783,617 - 787,544 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx91,230,702 - 1,234,687 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.096,577,870 - 6,581,839 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.095,535,739 - 5,539,724 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0911,110,874 - 11,114,843 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl911,110,874 - 11,114,843 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0910,096,038 - 10,100,007 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera97,718,999 - 7,722,962 (-)NCBICelera
Cytogenetic Map9q11NCBI
EBI3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38194,229,523 - 4,237,528 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl194,229,523 - 4,237,528 (+)EnsemblGRCh38hg38GRCh38
GRCh37194,229,520 - 4,237,525 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36194,180,540 - 4,188,525 (+)NCBINCBI36Build 36hg18NCBI36
Build 34194,180,539 - 4,188,522NCBI
Celera194,168,924 - 4,176,909 (+)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef193,992,754 - 4,000,739 (+)NCBIHuRef
CHM1_1194,229,199 - 4,237,144 (+)NCBICHM1_1
T2T-CHM13v2.0194,210,322 - 4,220,831 (+)NCBIT2T-CHM13v2.0
Ebi3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391756,259,623 - 56,264,022 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1756,259,640 - 56,264,022 (+)EnsemblGRCm39 Ensembl
GRCm381755,952,623 - 55,957,022 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1755,952,640 - 55,957,022 (+)EnsemblGRCm38mm10GRCm38
MGSCv371756,092,046 - 56,096,445 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361755,545,916 - 55,550,315 (+)NCBIMGSCv36mm8
Celera1759,371,150 - 59,375,549 (+)NCBICelera
Cytogenetic Map17DNCBI
cM Map1729.08NCBI
Ebi3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554954,609,841 - 4,615,686 (-)NCBIChiLan1.0ChiLan1.0
EBI3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2208,626,213 - 8,643,824 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1197,856,358 - 7,873,817 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0193,252,194 - 3,266,893 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1194,199,989 - 4,205,982 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl194,199,983 - 4,205,825 (+)Ensemblpanpan1.1panPan2
EBI3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12055,382,975 - 55,391,252 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2055,383,247 - 55,390,336 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2055,110,917 - 55,118,563 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02056,042,170 - 56,049,818 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2056,042,439 - 56,049,530 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12055,102,035 - 55,109,677 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02055,583,246 - 55,590,892 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02055,782,118 - 55,789,767 (-)NCBIUU_Cfam_GSD_1.0
Ebi3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118215,408,287 - 215,414,159 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365882,421,934 - 2,425,207 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365882,420,859 - 2,425,473 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
EBI3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl274,530,730 - 74,539,583 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1274,530,728 - 74,540,433 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2275,025,377 - 75,035,026 (-)NCBISscrofa10.2Sscrofa10.2susScr3
EBI3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.163,975,805 - 3,985,389 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl63,976,228 - 3,984,962 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660814,230,285 - 4,239,817 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ebi3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248285,402,961 - 5,407,891 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248285,402,589 - 5,409,914 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ebi3
24 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:38
Count of miRNA genes:36
Interacting mature miRNAs:38
Transcripts:ENSRNOT00000072031
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
10054141Gmadr4Adrenal mass QTL 42.450.0074adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)9114209783Rat
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9125661317Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9137999212Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9137999212Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9137999212Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9140594091Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat


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 renal system reproductive system respiratory system appendage
High
Medium 7 2
Low 3 43 54 38 12 38 8 11 74 35 39 11 8
Below cutoff 3 3 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000072031   ⟹   ENSRNOP00000067573
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl9783,617 - 787,544 (+)Ensembl
Rnor_6.0 Ensembl911,110,874 - 11,114,843 (-)Ensembl
RefSeq Acc Id: NM_001109421   ⟹   NP_001102891
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr89870,762 - 874,731 (+)NCBI
mRatBN7.29783,575 - 787,544 (+)NCBI
Rnor_6.0911,110,874 - 11,114,843 (-)NCBI
Rnor_5.0910,096,038 - 10,100,007 (-)NCBI
Celera97,718,999 - 7,722,962 (-)RGD
Sequence:
RefSeq Acc Id: XM_039084203   ⟹   XP_038940131
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr89861,441 - 874,731 (+)NCBI
mRatBN7.29774,252 - 787,544 (+)NCBI
RefSeq Acc Id: XM_063267725   ⟹   XP_063123795
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr89861,441 - 874,731 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001102891 (Get FASTA)   NCBI Sequence Viewer  
  XP_038940131 (Get FASTA)   NCBI Sequence Viewer  
  XP_063123795 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL83682 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000067573
  ENSRNOP00000067573.1
Reference Protein Sequences
RefSeq Acc Id: NP_001102891   ⟸   NM_001109421
- Peptide Label: precursor
- UniProtKB: M0RD76 (UniProtKB/TrEMBL),   A6KR24 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000067573   ⟸   ENSRNOT00000072031
RefSeq Acc Id: XP_038940131   ⟸   XM_039084203
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063123795   ⟸   XM_063267725
- Peptide Label: isoform X1
Protein Domains
Fibronectin type-III

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0RD76-F1-model_v2 AlphaFold M0RD76 1-228 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:1589467 AgrOrtholog
BioCyc Gene G2FUF-28574 BioCyc
Ensembl Genes ENSRNOG00000050509 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000072031 ENTREZGENE
  ENSRNOT00000072031.2 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
InterPro Fibronectin_type3 UniProtKB/TrEMBL
  FN3_sf UniProtKB/TrEMBL
  Hematopoietin_rcpt_L_F3_CS UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Interferon_alpha/beta_rcpt_bsu UniProtKB/TrEMBL
KEGG Report rno:680609 UniProtKB/TrEMBL
NCBI Gene 680609 ENTREZGENE
PANTHER INTERLEUKIN-27 SUBUNIT BETA UniProtKB/TrEMBL
  INTERLEUKIN-27 SUBUNIT BETA UniProtKB/TrEMBL
Pfam Interfer-bind UniProtKB/TrEMBL
PhenoGen Ebi3 PhenoGen
PROSITE FN3 UniProtKB/TrEMBL
  HEMATOPO_REC_L_F3 UniProtKB/TrEMBL
  PROKAR_LIPOPROTEIN UniProtKB/TrEMBL
RatGTEx ENSRNOG00000050509 RatGTEx
SMART FN3 UniProtKB/TrEMBL
Superfamily-SCOP FN_III-like UniProtKB/TrEMBL
UniProt A6KR24 ENTREZGENE, UniProtKB/TrEMBL
  M0RD76 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-23 Ebi3  Epstein-Barr virus induced 3  Ebi3  Epstein-Barr virus induced gene 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-07-08 Ebi3  Epstein-Barr virus induced gene 3  LOC682552  similar to Interleukin-27 beta chain precursor (IL-27B) (Epstein-Barr virus-induced gene 3 protein homolog)  Data merged from RGD:1597923 1643240 APPROVED
2008-05-15 Ebi3  Epstein-Barr virus induced gene 3  Ebi3  Epstein-Barr virus induced gene 3 (similar to Interleukin-27 beta chain precursor)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-05 Ebi3  Epstein-Barr virus induced gene 3 (similar to Interleukin-27 beta chain precursor)  LOC680609  similar to Interleukin-27 beta chain precursor (IL-27B) (Epstein-Barr virus-induced gene 3 protein homolog)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC682552  similar to Interleukin-27 beta chain precursor (IL-27B) (Epstein-Barr virus-induced gene 3 protein homolog)      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC680609  similar to Interleukin-27 beta chain precursor (IL-27B) (Epstein-Barr virus-induced gene 3 protein homolog)      Symbol and Name status set to provisional 70820 PROVISIONAL