Efnb1 (ephrin B1) - Rat Genome Database
Submit Data |  Help |  Video Tutorials |  News |  Publications |  FTP Download |  REST API |  Citing RGD |  Contact   
Gene: Efnb1 (ephrin B1) Rattus norvegicus
Analyze
Symbol: Efnb1
Name: ephrin B1
RGD ID: 2540
Description: Predicted to have ephrin receptor binding activity. Involved in presynapse assembly. Localizes to glutamatergic synapse and integral component of 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; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: EFL-3; ELK ligand; ELK-L; EPH-related receptor tyrosine kinase ligand 2; ephrin-B1; LERK-2; LERK2
Orthologs:
Homo sapiens (human) : EFNB1 (ephrin B1)  HGNC  Alliance
Mus musculus (house mouse) : Efnb1 (ephrin B1)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Efnb1 (ephrin B1)
Pan paniscus (bonobo/pygmy chimpanzee) : EFNB1 (ephrin B1)
Canis lupus familiaris (dog) : EFNB1 (ephrin B1)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Efnb1 (ephrin B1)
Sus scrofa (pig) : EFNB1 (ephrin B1)
Chlorocebus sabaeus (African green monkey) : EFNB1 (ephrin B1)
Heterocephalus glaber (naked mole-rat) : Efnb1 (ephrin B1)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 (+)NCBIRGSC3.4rn4RGSC3.4
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


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function
ephrin receptor binding  (IBA,IEA,ISO,TAS)
protein binding  (IPI,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
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  


Genomics

Comparative Map Data
Efnb1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 (+)NCBIRGSC3.4rn4RGSC3.4
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
GRCh38.p13 EnsemblX68,829,021 - 68,842,160 (+)EnsemblGRCh38hg38GRCh38
GRCh38X68,829,021 - 68,842,160 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X68,048,840 - 68,062,007 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X67,965,556 - 67,978,728 (+)NCBINCBI36hg18NCBI36
Build 34X67,831,851 - 67,845,023NCBI
CeleraX68,401,732 - 68,414,899 (+)NCBI
Cytogenetic MapXq13.1NCBI
HuRefX61,874,538 - 61,887,692 (+)NCBIHuRef
CHM1_1X67,941,979 - 67,955,149 (+)NCBICHM1_1
Efnb1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X98,179,667 - 98,192,628 (+)NCBI
GRCm38X99,136,061 - 99,149,022 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX99,136,130 - 99,148,991 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X96,331,469 - 96,344,330 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X95,338,849 - 95,351,710 (+)NCBImm8
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
PanPan1.1X68,139,078 - 68,152,127 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX68,139,078 - 68,152,131 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X58,075,744 - 58,088,838 (+)NCBIMhudiblu_PPA_v0panPan3
EFNB1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 EnsemblX53,292,565 - 53,304,600 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1X53,292,407 - 53,303,824 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Efnb1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 EnsemblX58,668,581 - 58,681,855 (+)Ensembl
ChlSab1.1X58,668,572 - 58,681,583 (+)NCBI
Efnb1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248911,394,948 - 1,407,898 (-)NCBI

Position Markers
AA964352  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
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


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X15688119127888215Rat
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)X44320616158345622Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX44557974120045269Rat
70221Bp56Blood pressure QTL 564.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X6139809770352120Rat

miRNA Target Status

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.


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 3 33 20 12 12 53 35 36 11
Low 10 37 29 19 29 8 11 21 5 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009635   ⟹   ENSRNOP00000009635
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
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 Sequences
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  
  P52796 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_058785   ⟸   NM_017089
- Peptide Label: precursor
- UniProtKB: Q6P7B6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000009635   ⟸   ENSRNOT00000009635
Protein Domains
Ephrin RBD

Transcriptome

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

Promoters
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

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2540 AgrOrtholog
Ensembl Genes ENSRNOG00000006877 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000009635 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009635 ENTREZGENE, 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 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
Superfamily-SCOP SSF49503 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene Rn.44398 ENTREZGENE
UniProt EFNB1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q6P7B6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
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

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in granule and Purkinje neurons 727396