EFNB1 ephrin-B1 [Homo sapiens (human)] - Gene

Summary

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Official Symbol: EFNB1provided by HGNC
Official Full Name: ephrin-B1provided by HGNC
Primary source: HGNC:3226
Locus tag: RP3-496G1.1
See related: Ensembl:ENSG00000090776; HPRD:02072; MIM:300035; Vega:OTTHUMG00000021751
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: CFND; CFNS; EFL3; EPLG2; Elk-L; LERK2
Summary: The protein encoded by this gene is a type I membrane protein and a ligand of Eph-related receptor tyrosine kinases. It may play a role in cell adhesion and function in the development or maintenance of the nervous system. [provided by RefSeq, Jul 2008]

Genomic context

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Location :: Xq12

Sequence :: Chromosome: X; NC_000023.10 (68048840..68062007)

See EFNB1 in Epigenomics, MapViewer

Chromosome X - NC_000023.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence

Go to nucleotideGraphics FASTA GenBank

Go to reference sequence details

Bibliography

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GeneRIFs: Gene References Into Functions What's a GeneRIF?

These results indicate a novel function of Nm23-H1 to control contact inhibition of locomotion, and its negative regulation by ephrin-B1.
Title: Nm23-H1 regulates contact inhibition of locomotion, which is affected by ephrin-B1.
Data show that EphrinB1, a PTPN13 substrate, interacts with ErbB2, and Src kinase mediates EphrinB1 phosphorylation and subsequent MAP Kinase signaling.
Title: ErbB2, EphrinB1, Src kinase and PTPN13 signaling complex regulates MAP kinase signaling in human cancers.
X-linked cases resembling Teebi hypertelorism may have a similar mechanism to CFNS, and that cellular mosaicism for different levels of ephrin-B1 (as well as simple presence/absence) leads to craniofacial abnormalities.
Title: Duplication of the EFNB1 gene in familial hypertelorism: imbalance in ephrin-B1 expression and abnormal phenotypes in humans and mice.
Observational study of gene-disease association. (HuGE Navigator)
Title: Prevalence and complications of single-gene and chromosomal disorders in craniosynostosis.
Unreported mutation in EFNB1 predicts occurrence of congenital diaphragmatic hernia, phenotypic differences between males and female.
Title: A novel EFNB1 mutation (c.712delG) in a family with craniofrontonasal syndrome and diaphragmatic hernia.
The impact of craniofrontonasal syndrome-causing EFNB1 mutations on ephrin-B1 function is reported.
Title: The impact of CFNS-causing EFNB1 mutations on ephrin-B1 function.
study reports that the expression of ephrin-B1 is controlled by a feedback loop involving posttranscriptional regulatory mechanisms
Title: Ephrin-B1 reverse signaling controls a posttranscriptional feedback mechanism via miR-124.
combination of SDF-1, PTN, IGF2, and EFNB1 mimics the DA phenotype-inducing property of SDIA and was sufficient to promote differentiation of hESC to functional midbrain DA neurons
Title: A novel combination of factors, termed SPIE, which promotes dopaminergic neuron differentiation from human embryonic stem cells.
Several new EFNB1 mutations have been identified in craniofrontonasal syndrome.
Title: Additional EFNB1 mutations in craniofrontonasal syndrome.
EFNB1 mutant transcripts with nonsense codons are degraded by the nonsense-mediated mRNA decay pathway and lead to craniofrontonasal syndrome.
Title: Dissecting the molecular mechanisms in craniofrontonasal syndrome: differential mRNA expression of mutant EFNB1 and the cellular mosaic.

Submit: New GeneRIF Correction See all (29)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Interactions

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Products	Interactant	Other Gene	Source	Pubs	Description
NP_004420.1	NP_004432.1	EPHB1	BIND	PubMed	The membrane bound ligand ELK-L interacts with the receptor ELK. This interaction was modeled on a demonstrated interaction between ELK-L from human and ELK from rat.
NP_004420.1	NP_004433.2	EPHB2	BIND	PubMed	The membrane bound ligand ELK-L interacts with the receptor NUK. This interaction was modeled on a demonstrated interaction between ELK-L from human and NUK from mouse.
P98172	P98172	EFNB1	HPRD	PubMed
P98172	P54762	EPHB1	HPRD	PubMed
P98172	P29323	EPHB2	HPRD	PubMed
P98172	Q9Y3R0	GRIP1	HPRD	PubMed
P98172	O43639	NCK2	HPRD	PubMed
P98172	Q9NRD5	PICK1	HPRD	PubMed
P98172	Q12923	PTPN13	HPRD	PubMed
P98172	P49796	RGS3	HPRD	PubMed
P98172	O00560	SDCBP	HPRD	PubMed
P98172	Q9BX66	SORBS1	HPRD	PubMed
P98172	P12931	SRC	HPRD	PubMed
P98172	Q13009	TIAM1	HPRD	PubMed
BioGRID:108267	BioGRID:115750	CAP1	BioGRID	PubMed	Affinity Capture-Western; Co-localization
BioGRID:108267	BioGRID:116305	CAPN10	BioGRID	PubMed	Two-hybrid
BioGRID:108267	BioGRID:114030	CUL3	BioGRID	PubMed	Two-hybrid
BioGRID:108267	BioGRID:108356	EPHA3	BioGRID	PubMed	Reconstituted Complex
BioGRID:108267	BioGRID:110694	MYC	BioGRID	PubMed	Two-hybrid
BioGRID:108267	BioGRID:114020	NCK2	BioGRID	PubMed	Affinity Capture-Western; Co-localization; Reconstituted Complex
BioGRID:108267	BioGRID:111747	PTPN13	BioGRID	PubMed	Reconstituted Complex
BioGRID:108267	BioGRID:112287	SDCBP	BioGRID	PubMed	Affinity Capture-Western; Reconstituted Complex
BioGRID:108267	BioGRID:121411	SMURF1	BioGRID	PubMed	Affinity Capture-Western
BioGRID:108267	BioGRID:122265	SMURF2	BioGRID	PubMed	Affinity Capture-Western
BioGRID:108267	BioGRID:112592	SRC	BioGRID	PubMed	Biochemical Activity
BioGRID:108267	BioGRID:113164	UBC	BioGRID	PubMed	Affinity Capture-MS; Affinity Capture-Western
BioGRID:108267	BioGRID:116168	YWHAQ	BioGRID	PubMed	Two-hybrid

Pathways from BioSystems

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Axon guidance, organism-specific biosystem (from KEGG)
Axon guidance, organism-specific biosystemAxon guidance represents a key stage in the formation of neuronal network. Axons are guided by a variety of guidance factors, such as netrins, ephrins, Slits, and semaphorins. These guidance cues are...
Axon guidance, conserved biosystem (from KEGG)
Axon guidance, conserved biosystemAxon guidance represents a key stage in the formation of neuronal network. Axons are guided by a variety of guidance factors, such as netrins, ephrins, Slits, and semaphorins. These guidance cues are...
EPHB forward signaling, organism-specific biosystem (from Pathway Interaction Database)
EPHB forward signaling, organism-specific biosystem
EPHB forward signaling
Ephrin B reverse signaling, organism-specific biosystem (from Pathway Interaction Database)
Ephrin B reverse signaling, organism-specific biosystem
Ephrin B reverse signaling
EphrinB-EPHB pathway, organism-specific biosystem (from Pathway Interaction Database)
EphrinB-EPHB pathway, organism-specific biosystem
EphrinB-EPHB pathway

General gene information

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Markers

G64129 (e-PCR)
- UniSTS:146717

RH17985 (e-PCR)
- UniSTS:47192

AA964352 (e-PCR)
- UniSTS:248424

DXS159 (e-PCR)
- UniSTS:23152

EPLG2 (e-PCR)
- UniSTS:98985

EFNB1_609 (e-PCR)
- UniSTS:277189

EFNB1 (e-PCR)
- UniSTS:506601

Genotypes

See EFNB1 SNP Geneview Report
See EFNB1 SNP Genotype Report
See EFNB1 SNP Variation Viewer Report

Homology

Homologs of the EFNB1 gene: The EFNB1 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, and C.elegans.
Map Viewer (Mouse, Rat)
OrthoDB: The Hierarchical Catalog of Eukaryotic Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
ephrin receptor binding	IEA Inferred from Electronic Annotation more info
protein binding	IPI Inferred from Physical Interaction more info

Process	Evidence Code	Pubs
axon guidance	IEA Inferred from Electronic Annotation more info
cell adhesion	TAS Traceable Author Statement more info	PubMed
cell-cell signaling	TAS Traceable Author Statement more info	PubMed
embryonic pattern specification	IEA Inferred from Electronic Annotation more info
neural crest cell migration	IEA Inferred from Electronic Annotation more info
positive regulation of T cell proliferation	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
cytoplasm	IEA Inferred from Electronic Annotation more info
integral to plasma membrane	TAS Traceable Author Statement more info	PubMed
membrane raft	IEA Inferred from Electronic Annotation more info
nucleus	IEA Inferred from Electronic Annotation more info
synapse	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: ephrin-B1

Names: ephrin-B1; EFL-3; LERK-2; ELK ligand; ligand of eph-related kinase 2; eph-related receptor tyrosine kinase ligand 2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_008887.1 RefSeqGene

Range

5001..18168

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_004429.4 → NP_004420.1 ephrin-B1 precursor

Status: REVIEWED

Source sequence(s)

BC016649, BM972960, CB132233

Consensus CDS

CCDS14391.1

UniProtKB/Swiss-Prot

P98172

Related

ENSP00000204961, OTTHUMP00000023456, ENST00000204961, OTTHUMT00000057029

Conserved Domains (1) summary

cd10426
Location:31 – 165
Blast Score: 683

Ephrin-B_RBD; Receptor Binding Domain of Ephrin B

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 104

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh37.p10 Primary Assembly

Genomic

NC_000023.10 Reference GRCh37.p10 Primary Assembly

Range

68048840..68062007

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

AC_000155.1 Alternate HuRef

Range

61874538..61887692

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.0

Genomic

NC_018934.1 Alternate CHM1_1.0

Range

68056251..68069421

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Nucleotide		Protein
Heading	Accession and Version	Protein
genomic	ABBA01067395.1 (3828..16982)	None
genomic	AL136092.8 (40389..53556)	None
genomic	AMYH01022520.1 (235940..249110)	None
genomic	CH471132.2	EAX05370.1
		EAX05371.1
mRNA	BC016649.1	AAH16649.1
mRNA	BC052979.1	AAH52979.1
mRNA	BM972960.1	None
mRNA	BU172498.1	None
mRNA	CB132233.1	None
mRNA	L37361.1	AAA52369.1
mRNA	U09303.1	AAB41127.1
mRNA	U09304.1	AAA53093.1
other-genetic	DQ891817.2	ABM82743.1
other-genetic	DQ895005.2	ABM85931.1