Efnb1 (ephrin B1) - Rat Genome Database

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Gene: Efnb1 (ephrin B1) Rattus norvegicus
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Symbol: Efnb1
Name: ephrin B1
RGD ID: 2540
Description: Predicted to enable ephrin receptor binding activity. Involved in presynapse assembly. Located in synapse. Is active in glutamatergic synapse and presynaptic membrane. Human ortholog(s) of this gene implicated in craniofrontonasal syndrome and dysostosis. Orthologous to human EFNB1 (ephrin B1); PARTICIPATES IN altered ephrin - ephrin receptor bidirectional signaling pathway; ephrin - ephrin receptor bidirectional signaling axis; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3,3',4,4',5-pentachlorobiphenyl; 4,4'-sulfonyldiphenol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: EFL-3; ELK ligand; ELK-L; EPH-related receptor tyrosine kinase ligand 2; ephrin-B1; LERK-2; LERK2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X68,297,529 - 68,310,335 (+)NCBIGRCr8
mRatBN7.2X64,257,351 - 64,270,158 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX64,257,351 - 64,270,157 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX65,740,847 - 65,753,653 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X69,241,199 - 69,254,005 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X66,802,140 - 66,814,947 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X68,891,227 - 68,904,034 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX68,891,227 - 68,904,038 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X69,764,314 - 69,777,121 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X87,163,176 - 87,175,982 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1X87,236,467 - 87,249,273 (+)NCBI
CeleraX64,624,957 - 64,637,749 (+)NCBICelera
Cytogenetic MapXq22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model



  
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Original Reference(s)
Efnb1Ratdysostosis  ISOEFNB1 (Homo sapiens)1599802DNA:missense mutations and deletionRGD 
Efnb1Ratstomach cancer disease_progressionISOEFNB1 (Homo sapiens)153323289mRNA:increased expression:stomach (human)RGD 
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Efnb1Ratautistic disorder  ISOEFNB1 (Homo sapiens)8554872ClinVar Annotator: match by term: AutismClinVarPMID:21681106 and PMID:30208311
Efnb1Ratautosomal hemophilia A  ISOEFNB1 (Homo sapiens)8554872ClinVar Annotator: match by term: AUTOSOMAL HEMOPHILIA AClinVarPMID:31690835
Efnb1Ratcraniofrontonasal syndrome  ISOEFNB1 (Homo sapiens)8554872ClinVar more ...ClinVarPMID:1468459 more ...
Efnb1Ratfactor VIII deficiency  ISOEFNB1 (Homo sapiens)8554872ClinVar Annotator: match by term: Factor 8 deficiency and congenitalClinVarPMID:31690835
Efnb1Ratgenetic disease  ISOEFNB1 (Homo sapiens)8554872ClinVar Annotator: match by term: Inborn genetic diseasesClinVarPMID:11780069 more ...
Efnb1Ratsyndromic X-linked intellectual disability Lubs type  ISOEFNB1 (Homo sapiens)8554872ClinVar Annotator: match by term: Syndromic X-linked intellectual disability Lubs typeClinVarPMID:25741868
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Efnb1Ratcraniofrontonasal syndrome  ISOEFNB1 (Homo sapiens)11554173CTD Direct Evidence: marker/mechanismCTDPMID:15124102 more ...
Efnb1Ratcraniosynostosis  ISOEFNB1 (Homo sapiens)11554173CTD Direct Evidence: marker/mechanismCTDPMID:15166289
Efnb1Ratfrontonasal dysplasia  ISOEFNB1 (Homo sapiens)11554173CTD Direct Evidence: marker/mechanismCTDPMID:15166289
Efnb1RatHypertelorism  ISOEFNB1 (Homo sapiens)11554173CTD Direct Evidence: marker/mechanismCTDPMID:15166289
Efnb1RatInflammation  ISOEFNB1 (Homo sapiens)11554173CTD Direct Evidence: marker/mechanismCTDPMID:24098442
Efnb1Ratobesity  ISOEFNB1 (Homo sapiens)11554173CTD Direct Evidence: marker/mechanismCTDPMID:24098442
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Efnb1Ratcraniofrontonasal syndrome  ISSEfnb1 (Mus musculus)13592920OMIM:304110MouseDO 
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Efnb1Ratcraniofrontonasal syndrome  ISOEFNB1 (Homo sapiens)7240710 OMIM 

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Efnb1Rat1,2-dimethylhydrazine multiple interactionsISOEfnb1 (Mus musculus)6480464[1 and 2-Dimethylhydrazine co-treated with Folic Acid] results in decreased expression of EFNB1 mRNACTDPMID:22206623
Efnb1Rat17alpha-ethynylestradiol affects expressionISOEfnb1 (Mus musculus)6480464Ethinyl Estradiol affects the expression of EFNB1 mRNACTDPMID:17555576
Efnb1Rat17beta-estradiol affects expressionISOEfnb1 (Mus musculus)6480464Estradiol affects the expression of EFNB1 mRNACTDPMID:15598610
Efnb1Rat2,3,7,8-tetrachlorodibenzodioxine multiple interactionsEXP 6480464[Tetrachlorodibenzodioxin binds to and results in increased activity of AHR protein] which results in decreased expression of EFNB1 mRNACTDPMID:21602191
Efnb1Rat2,3,7,8-tetrachlorodibenzodioxine decreases expressionEXP 6480464Tetrachlorodibenzodioxin results in decreased expression of EFNB1 mRNACTDPMID:33387578
Efnb1Rat2,3,7,8-tetrachlorodibenzodioxine increases expressionEXP 6480464Tetrachlorodibenzodioxin results in increased expression of EFNB1 mRNACTDPMID:34747641
Efnb1Rat2,3,7,8-tetrachlorodibenzodioxine affects expressionISOEfnb1 (Mus musculus)6480464Tetrachlorodibenzodioxin affects the expression of EFNB1 mRNACTDPMID:21570461
Efnb1Rat2,4-dibromophenyl 2,4,5-tribromophenyl ether affects expressionISOEfnb1 (Mus musculus)64804642 more ...CTDPMID:38648751
Efnb1Rat3,3',4,4',5-pentachlorobiphenyl decreases expressionEXP 64804643 more ...CTDPMID:23196670
Efnb1Rat3-isobutyl-1-methyl-7H-xanthine multiple interactionsISOEFNB1 (Homo sapiens)6480464[INS protein co-treated with Dexamethasone co-treated with 1-Methyl-3-isobutylxanthine co-treated with Indomethacin co-treated with bisphenol A] results in increased expression of EFNB1 mRNA and [INS protein co-treated with Dexamethasone co-treated with 1-Methyl-3-isobutylxanthine co-treated with Indomethacin co-treated with bisphenol F] results in increased expression of EFNB1 mRNACTDPMID:28628672
Efnb1Rat3-methylcholanthrene increases expressionISOEfnb1 (Mus musculus)6480464Methylcholanthrene results in increased expression of EFNB1 mRNACTDPMID:20713471
Efnb1Rat4,4'-sulfonyldiphenol multiple interactionsEXP 6480464[bisphenol A co-treated with bisphenol F co-treated with bisphenol S] results in decreased expression of EFNB1 mRNACTDPMID:36041667
Efnb1Rat6-propyl-2-thiouracil increases expressionEXP 6480464Propylthiouracil results in increased expression of EFNB1 mRNACTDPMID:24780913
Efnb1Ratacrylamide decreases expressionISOEFNB1 (Homo sapiens)6480464Acrylamide results in decreased expression of EFNB1 mRNACTDPMID:32763439
Efnb1Ratactinomycin D multiple interactionsISOEFNB1 (Homo sapiens)6480464[Dactinomycin co-treated with nutlin 3] results in increased expression of EFNB1 mRNACTDPMID:38460933
Efnb1Rataflatoxin B1 increases expressionISOEFNB1 (Homo sapiens)6480464Aflatoxin B1 results in increased expression of EFNB1 mRNACTDPMID:21641981 and PMID:22100608
Efnb1Rataflatoxin B1 decreases methylationISOEFNB1 (Homo sapiens)6480464Aflatoxin B1 results in decreased methylation of EFNB1 geneCTDPMID:27153756
Efnb1Ratall-trans-retinoic acid increases expressionISOEfnb1 (Mus musculus)6480464Tretinoin results in increased expression of EFNB1 mRNACTDPMID:16604517
Efnb1Ratall-trans-retinoic acid decreases expressionISOEFNB1 (Homo sapiens)6480464Tretinoin results in decreased expression of EFNB1 mRNACTDPMID:23724009
Efnb1Ratammonium chloride affects expressionEXP 6480464Ammonium Chloride affects the expression of EFNB1 mRNACTDPMID:16483693

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Biological Process
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Efnb1Rataxon guidance  TAS 727396 RGD 
Efnb1Rataxon guidance acts_upstream_of_or_withinISOEfnb1 (Mus musculus)1624291 PMID:11731465RGDPMID:11731465
Efnb1Rataxon guidance involved_inIBAFB:FBgn0040324 more ...1600115GO_REF:0000033GO_CentralGO_REF:0000033
Efnb1Rataxon guidance involved_inIEAUniProtKB:P52795 and ensembl:ENSMUSP000000507161600115GO_REF:0000107EnsemblGO_REF:0000107
Efnb1Ratembryonic pattern specification involved_inIEAUniProtKB:P52795 and ensembl:ENSMUSP000000507161600115GO_REF:0000107EnsemblGO_REF:0000107
Efnb1Ratembryonic pattern specification acts_upstream_of_or_withinISOEfnb1 (Mus musculus)1624291MGI:3039289 PMID:15037550RGDPMID:15037550
Efnb1Ratephrin receptor signaling pathway  TAS 727396 RGD 
Efnb1Ratephrin receptor signaling pathway involved_inIBAMGI:102707 more ...1600115GO_REF:0000033GO_CentralGO_REF:0000033
Efnb1Ratephrin receptor signaling pathway involved_inIEAInterPro:IPR0342551600115GO_REF:0000002InterProGO_REF:0000002
Efnb1Ratnervous system development  IMP 727396 RGD 
Efnb1Ratneural crest cell migration involved_inIEAUniProtKB:P52795 and ensembl:ENSMUSP000000507161600115GO_REF:0000107EnsemblGO_REF:0000107
Efnb1Ratneural crest cell migration acts_upstream_of_or_withinISOEfnb1 (Mus musculus)1624291MGI:3039290 PMID:15037550RGDPMID:15037550
Efnb1Ratpositive regulation of T cell proliferation involved_inIEAUniProtKB:P52795 and ensembl:ENSMUSP000000507161600115GO_REF:0000107EnsemblGO_REF:0000107
Efnb1Ratpositive regulation of T cell proliferation acts_upstream_of_or_withinISOEfnb1 (Mus musculus)1624291 PMID:15502157RGDPMID:15502157
Efnb1Ratpresynapse assembly involved_inIMP 13702172PMID:19915143SynGO 
Efnb1Ratpresynapse assembly involved_inIDA 13702172PMID:19915143SynGO 
Efnb1Ratregulation of autophagosome assembly acts_upstream_of_positive_effectISOEFNB1 (Homo sapiens)1624291 PMID:33280498RGDPMID:33280498
Efnb1Ratregulation of autophagosome assembly involved_inIEAUniProtKB:P98172 and ensembl:ENSP000002049611600115GO_REF:0000107EnsemblGO_REF:0000107
Efnb1RatT cell costimulation involved_inIEAUniProtKB:P52795 and ensembl:ENSMUSP000000507161600115GO_REF:0000107EnsemblGO_REF:0000107
Efnb1RatT cell costimulation acts_upstream_of_or_withinISOEfnb1 (Mus musculus)1624291 PMID:15599401RGDPMID:15599401
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Cellular Component
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Efnb1Ratcell surface is_active_inISOEFNB1 (Homo sapiens)1624291 PMID:12970314RGDPMID:12970314
Efnb1Ratcell surface located_inIEAUniProtKB:P98172 and ensembl:ENSP000002049611600115GO_REF:0000107EnsemblGO_REF:0000107
Efnb1Ratcytoplasm located_inIEAUniProtKB:P52795 and ensembl:ENSMUSP000000507161600115GO_REF:0000107EnsemblGO_REF:0000107
Efnb1Ratcytoplasm located_inISOEfnb1 (Mus musculus)1624291 PMID:19515908RGDPMID:19515908
Efnb1Ratglutamatergic synapse is_active_inIDA 13702172PMID:19915143SynGO 
Efnb1Ratglutamatergic synapse is_active_inIBAPANTHER:PTN002601663 and Efnb1 (Rattus norvegicus)1600115GO_REF:0000033GO_CentralGO_REF:0000033
Efnb1Ratglutamatergic synapse is_active_inIMP 13702172PMID:19915143SynGO 
Efnb1Ratmembrane raft located_inISOEfnb1 (Mus musculus)1624291 PMID:10197531RGDPMID:10197531
Efnb1Ratmembrane raft located_inIEAUniProtKB:P52795 and ensembl:ENSMUSP000000507161600115GO_REF:0000107EnsemblGO_REF:0000107
Efnb1Ratnucleus located_inIEAUniProtKB:P52795 and ensembl:ENSMUSP000000507161600115GO_REF:0000107EnsemblGO_REF:0000107
Efnb1Ratnucleus located_inISOEfnb1 (Mus musculus)1624291 PMID:19515908RGDPMID:19515908
Efnb1Ratplasma membrane located_inIEAUniProtKB:P98172 and ensembl:ENSP000002049611600115GO_REF:0000107EnsemblGO_REF:0000107
Efnb1Ratplasma membrane is_active_inIBAFB:FBgn0040324 more ...1600115GO_REF:0000033GO_CentralGO_REF:0000033
Efnb1Ratplasma membrane located_inISOEFNB1 (Homo sapiens)1624291 RGDGO_REF:0000052
Efnb1Ratpresynaptic membrane is_active_inIDA 13702172PMID:19915143SynGO 
Efnb1Ratpresynaptic membrane is_active_inIBAPANTHER:PTN002601663 and Efnb1 (Rattus norvegicus)1600115GO_REF:0000033GO_CentralGO_REF:0000033
Efnb1Ratsynapse located_inIDA 8554504PMID:9883737UniProt 
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Molecular Function
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RGD Manual Annotations


  
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Efnb1Rataltered ephrin - ephrin receptor bidirectional signaling pathway  ISS 1304509Present in neuroblastoma and leukemia and lung cancerRGD 
Efnb1Ratephrin - ephrin receptor bidirectional signaling axis  TAS 727396 RGD 

Imported Annotations - PID (archival)

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Efnb1Ratephrin - ephrin receptor bidirectional signaling axis  ISOEFNB1 (Homo sapiens)6484113 PIDPID:200052
Efnb1Ratephrin - ephrin receptor bidirectional signaling axis  ISOEFNB1 (Homo sapiens)6484113 PIDPID:200204

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#
Reference Title
Reference Citation
1. LERK-2, a binding protein for the receptor-tyrosine kinase ELK, is evolutionarily conserved and expressed in a developmentally regulated pattern. Fletcher FA, etal., Oncogene 1994 Nov;9(11):3241-7.
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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. Expression profile of EFNB1, EFNB2, two ligands of EPHB2 in human gastric cancer. Kataoka H, etal., J Cancer Res Clin Oncol. 2002 Jul;128(7):343-8. doi: 10.1007/s00432-002-0355-0. Epub 2002 Jun 26.
5. Ephrin-B1 and ephrin-B2 mediate EphB-dependent presynaptic development via syntenin-1. McClelland AC, etal., Proc Natl Acad Sci U S A. 2009 Dec 1;106(48):20487-92. doi: 10.1073/pnas.0811862106. Epub 2009 Nov 13.
6. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
7. Ephrin-B1 promotes dendrite outgrowth on cerebellar granule neurons. Moreno-Flores MT, etal., Mol Cell Neurosci 2002 Jul;20(3):429-46.
8. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
9. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
10. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
11. GOA pipeline RGD automated data pipeline
12. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
13. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
14. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
15. The role of ephrins and Eph receptors in cancer. Surawska H, etal., Cytokine Growth Factor Rev 2004 Dec;15(6):419-33.
16. PDZ proteins bind, cluster, and synaptically colocalize with Eph receptors and their ephrin ligands. Torres R, etal., Neuron. 1998 Dec;21(6):1453-63.
17. Mutations of the ephrin-B1 gene cause craniofrontonasal syndrome. Wieland I, etal., Am J Hum Genet. 2004 Jun;74(6):1209-15. Epub 2004 Apr 29.
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PMID:10197531   PMID:10558890   PMID:11731465   PMID:14988728   PMID:15037550   PMID:15502157   PMID:15599401   PMID:16052680   PMID:17667985   PMID:18321739   PMID:18448254   PMID:19056867  
PMID:19515908   PMID:20633976   PMID:23376485   PMID:23881165   PMID:25922200   PMID:29602834   PMID:33356837  



Efnb1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X68,297,529 - 68,310,335 (+)NCBIGRCr8
mRatBN7.2X64,257,351 - 64,270,158 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX64,257,351 - 64,270,157 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX65,740,847 - 65,753,653 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X69,241,199 - 69,254,005 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X66,802,140 - 66,814,947 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X68,891,227 - 68,904,034 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX68,891,227 - 68,904,038 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X69,764,314 - 69,777,121 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X87,163,176 - 87,175,982 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1X87,236,467 - 87,249,273 (+)NCBI
CeleraX64,624,957 - 64,637,749 (+)NCBICelera
Cytogenetic MapXq22NCBI
EFNB1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X68,829,021 - 68,842,160 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX68,829,021 - 68,842,160 (+)EnsemblGRCh38hg38GRCh38
GRCh37X68,048,864 - 68,062,003 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X67,965,556 - 67,978,728 (+)NCBINCBI36Build 36hg18NCBI36
Build 34X67,831,851 - 67,845,023NCBI
CeleraX68,401,732 - 68,414,899 (+)NCBICelera
Cytogenetic MapXq13.1NCBI
HuRefX61,874,538 - 61,887,692 (+)NCBIHuRef
CHM1_1X67,941,979 - 67,955,149 (+)NCBICHM1_1
T2T-CHM13v2.0X67,262,362 - 67,275,507 (+)NCBIT2T-CHM13v2.0
Efnb1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X98,179,667 - 98,192,628 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX98,179,736 - 98,192,597 (+)EnsemblGRCm39 Ensembl
GRCm38X99,136,061 - 99,149,022 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX99,136,130 - 99,148,991 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X96,331,469 - 96,344,330 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X95,338,849 - 95,351,710 (+)NCBIMGSCv36mm8
CeleraX86,077,235 - 86,090,145 (+)NCBICelera
Cytogenetic MapXC3NCBI
cM MapX43.22NCBI
Efnb1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554758,360,465 - 8,373,578 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554758,360,504 - 8,372,431 (+)NCBIChiLan1.0ChiLan1.0
EFNB1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X68,484,373 - 68,497,581 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X68,488,001 - 68,501,112 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X58,075,744 - 58,088,838 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X68,139,078 - 68,152,127 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX68,139,078 - 68,152,131 (+)Ensemblpanpan1.1panPan2
EFNB1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X53,292,407 - 53,303,824 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX53,292,565 - 53,304,600 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX44,117,929 - 44,130,926 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X54,257,764 - 54,270,762 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX54,257,610 - 54,436,363 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X52,225,889 - 52,238,885 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X53,554,687 - 53,567,686 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X53,478,390 - 53,491,387 (+)NCBIUU_Cfam_GSD_1.0
Efnb1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X48,786,595 - 48,799,574 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936777434,692 - 447,780 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936777434,729 - 447,778 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
EFNB1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX54,948,342 - 54,973,629 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X54,947,339 - 54,961,403 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X62,073,418 - 62,080,778 (+)NCBISscrofa10.2Sscrofa10.2susScr3
EFNB1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X58,668,572 - 58,681,583 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX58,668,581 - 58,681,855 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666065523,181 - 536,271 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Efnb1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248911,394,852 - 1,407,959 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248911,394,948 - 1,407,898 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

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Variants in Efnb1
34 total Variants

Predicted Target Of
Summary Value
Count of predictions:457
Count of miRNA genes:238
Interacting mature miRNAs:305
Transcripts:ENSRNOT00000009635
Prediction methods:Miranda, Pita, Pita,Targetscan, Rnahybrid, Targetscan
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.


The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Name
LOD
P Value
Trait
Sub Trait
Chr
Start
Stop
Species
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
70221Bp56Blood pressure QTL 564.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X5704214165612192Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat

AA964352  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X64,269,831 - 64,270,039 (+)MAPPERmRatBN7.2
Rnor_6.0X68,903,708 - 68,903,915NCBIRnor6.0
Rnor_5.0X69,776,795 - 69,777,002UniSTSRnor5.0
RGSC_v3.4X87,175,656 - 87,175,863UniSTSRGSC3.4
CeleraX64,637,423 - 64,637,630UniSTS
Cytogenetic MapXq22.1UniSTS
EFNB1_609  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X64,268,788 - 64,269,460 (+)MAPPERmRatBN7.2
Rnor_6.0X68,902,665 - 68,903,336NCBIRnor6.0
Rnor_5.0X69,775,752 - 69,776,423UniSTSRnor5.0
RGSC_v3.4X87,174,613 - 87,175,284UniSTSRGSC3.4
CeleraX64,636,394 - 64,637,065UniSTS
Cytogenetic MapXq22.1UniSTS




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
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31



Ensembl Acc Id: ENSRNOT00000009635   ⟹   ENSRNOP00000009635
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX64,257,351 - 64,270,157 (+)Ensembl
Rnor_6.0 EnsemblX68,891,227 - 68,904,038 (+)Ensembl
RefSeq Acc Id: NM_017089   ⟹   NP_058785
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X68,297,529 - 68,310,335 (+)NCBI
mRatBN7.2X64,257,351 - 64,270,158 (+)NCBI
Rnor_6.0X68,891,227 - 68,904,034 (+)NCBI
Rnor_5.0X69,764,314 - 69,777,121 (+)NCBI
RGSC_v3.4X87,163,176 - 87,175,982 (+)RGD
CeleraX64,624,957 - 64,637,749 (+)RGD
Sequence:
Protein RefSeqs NP_058785 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA53092 (Get FASTA)   NCBI Sequence Viewer  
  AAH61744 (Get FASTA)   NCBI Sequence Viewer  
  EDL95949 (Get FASTA)   NCBI Sequence Viewer  
  EDL95950 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000009635.3
GenBank Protein P52796 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_058785   ⟸   NM_017089
- Peptide Label: precursor
- UniProtKB: P52796 (UniProtKB/Swiss-Prot),   Q6P7B6 (UniProtKB/TrEMBL),   F7FBR1 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000009635   ⟸   ENSRNOT00000009635
Ephrin RBD

Name Modeler Protein Id AA Range Protein Structure
AF-P52796-F1-model_v2 AlphaFold P52796 1-345 view protein structure


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

RGD ID:13701859
Promoter ID:EPDNEW_R12383
Type:initiation region
Name:Efnb1_1
Description:ephrin B1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X68,891,221 - 68,891,281EPDNEW


1 to 26 of 26 rows
Database
Acc Id
Source(s)
BioCyc Gene G2FUF-2152 BioCyc
Ensembl Genes ENSRNOG00000006877 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009635.7 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.420 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:5599058 IMAGE-MGC_LOAD
InterPro Cupredoxin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ephrin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ephrin-B_Ecto UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ephrin_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ephrin_RBD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25186 UniProtKB/TrEMBL
MGC_CLONE MGC:72504 IMAGE-MGC_LOAD
NCBI Gene 25186 ENTREZGENE
PANTHER EPHRIN-B1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR11304 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Ephrin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Efnb1 PhenoGen
PRINTS EPHRIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE EPHRIN_RBD_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EPHRIN_RBD_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000006877 RatGTEx
Superfamily-SCOP SSF49503 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt EFNB1_RAT UniProtKB/Swiss-Prot
  F7FBR1 ENTREZGENE, UniProtKB/TrEMBL
  P52796 ENTREZGENE
  Q6P7B6 ENTREZGENE, UniProtKB/TrEMBL
1 to 26 of 26 rows


Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Efnb1  Ephrin B1      Symbol and Name status set to approved 70586 APPROVED

Note Type Note Reference
gene_expression expressed in granule and Purkinje neurons 727396