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    EPHB6 EPH receptor B6 [ Homo sapiens (human) ]

    Gene ID: 2051, updated on 9-Dec-2024

    Summary

    Official Symbol
    EPHB6provided by HGNC
    Official Full Name
    EPH receptor B6provided by HGNC
    Primary source
    HGNC:HGNC:3396
    See related
    Ensembl:ENSG00000106123 MIM:602757; AllianceGenome:HGNC:3396
    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
    HEP
    Summary
    This gene encodes a member of a family of transmembrane proteins that function as receptors for ephrin-B family proteins. Unlike other members of this family, the encoded protein does not contain a functional kinase domain. Activity of this protein can influence cell adhesion and migration. Expression of this gene is downregulated during tumor progression, suggesting that the protein may suppress tumor invasion and metastasis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
    Expression
    Biased expression in skin (RPKM 52.0), brain (RPKM 17.5) and 11 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See EPHB6 in Genome Data Viewer
    Location:
    7q34
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (142855076..142871093)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (144210901..144226909)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (142552838..142568847)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene T cell receptor beta locus Neighboring gene uncharacterized LOC105375541 Neighboring gene CRISPRi-validated cis-regulatory element chr7.5168 Neighboring gene T cell receptor beta variable 30 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:142564181-142564714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:142564989-142565924 Neighboring gene Sharpr-MPRA regulatory region 15349 Neighboring gene MPRA-validated peak6804 silencer Neighboring gene transient receptor potential cation channel subfamily V member 6 Neighboring gene transient receptor potential cation channel subfamily V member 5

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Pr55(Gag) gag The amplified luminescent proximity homogeneous assay (AlphaScreen) identifies the interaction of HIV-1 Gag with EPHB6 PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC129910, MGC129911

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables ephrin receptor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables signaling receptor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables transmembrane-ephrin receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Process Evidence Code Pubs
    involved_in axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in ephrin receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    is_active_in dendrite IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in extracellular region TAS
    Traceable Author Statement
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    ephrin type-B receptor 6
    Names
    human kinase-defective Eph-family receptor protein
    tyrosine-protein kinase-defective receptor EPH-6
    NP_001267723.2
    NP_001267724.2
    NP_004436.4
    XP_011514181.1
    XP_011514182.1
    XP_011514183.1
    XP_011514184.1
    XP_024302443.1
    XP_047275939.1
    XP_047275940.1
    XP_054184674.1
    XP_054184675.1
    XP_054184676.1
    XP_054184677.1
    XP_054184678.1
    XP_054184679.1
    XP_054213437.1
    XP_054213438.1
    XP_054213439.1
    XP_054213440.1
    XP_054213441.1
    XP_054213442.1
    XP_054213443.1
    XP_054213444.1
    XP_054213445.1
    XP_054213446.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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.

    mRNA and Protein(s)

    1. NM_001280794.3NP_001267723.2  ephrin type-B receptor 6 isoform b

      See identical proteins and their annotated locations for NP_001267723.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks an exon in the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (b) has a shorter N-terminus, compared to isoform a. Both variants 2 and 3 encode the same isoform (b).
      Source sequence(s)
      AC245427
      Consensus CDS
      CCDS75672.1
      UniProtKB/TrEMBL
      A0A0G2JNC5
      Conserved Domains (7) summary
      smart00454
      Location:654714
      SAM; Sterile alpha motif
      cd00063
      Location:196287
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam07699
      Location:1253
      GCC2_GCC3; GCC2 and GCC3
      pfam07714
      Location:378623
      Pkinase_Tyr; Protein tyrosine kinase
      pfam14575
      Location:320373
      EphA2_TM; Ephrin type-A receptor 2 transmembrane domain
      cl15755
      Location:653721
      SAM_superfamily; SAM (Sterile alpha motif )
      cl21453
      Location:373627
      PKc_like; Protein Kinases, catalytic domain
    2. NM_001280795.2NP_001267724.2  ephrin type-B receptor 6 isoform b

      See identical proteins and their annotated locations for NP_001267724.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in the 5' UTR, lacks an exon in the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (b) has a shorter N-terminus, compared to isoform a. Both variants 2 and 3 encode the same isoform (b).
      Source sequence(s)
      AL832533, BC047892, BC056159, BC110606, BX410199
      Consensus CDS
      CCDS75672.1
      UniProtKB/TrEMBL
      A0A0G2JNC5
      Conserved Domains (7) summary
      smart00454
      Location:654714
      SAM; Sterile alpha motif
      cd00063
      Location:196287
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam07699
      Location:1253
      GCC2_GCC3; GCC2 and GCC3
      pfam07714
      Location:378623
      Pkinase_Tyr; Protein tyrosine kinase
      pfam14575
      Location:320373
      EphA2_TM; Ephrin type-A receptor 2 transmembrane domain
      cl15755
      Location:653721
      SAM_superfamily; SAM (Sterile alpha motif )
      cl21453
      Location:373627
      PKc_like; Protein Kinases, catalytic domain
    3. NM_004445.6NP_004436.4  ephrin type-B receptor 6 isoform a precursor

      See identical proteins and their annotated locations for NP_004436.4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (a).
      Source sequence(s)
      AC245427, AL532843, BC110607, BX419816, CN283345, CN283348
      Consensus CDS
      CCDS5873.2
      UniProtKB/TrEMBL
      F8WCM8
      Related
      ENSP00000498670.1, ENST00000652003.1
      Conserved Domains (7) summary
      cd09555
      Location:9461014
      SAM_EPH-B6; SAM domain of EPH-B6 subfamily of tyrosine kinase receptors
      cd10475
      Location:33232
      EphR_LBD_B6; Ligand Binding Domain of Ephrin type-B Receptor 6
      cd00063
      Location:371472
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam00041
      Location:490572
      fn3; Fibronectin type III domain
      pfam07699
      Location:305346
      Ephrin_rec_like; Putative ephrin-receptor like
      pfam14575
      Location:613665
      EphA2_TM; Ephrin type-A receptor 2 transmembrane domain
      cl21453
      Location:666920
      PKc_like; Protein Kinases, catalytic domain

    RNA

    1. NR_104001.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) includes an additional 5' exon and contains multiple differences in the internal exon structure, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
      Source sequence(s)
      AL832533, BC047892, BC051028
      Related
      ENST00000611578.4

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      142855076..142871093
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011515879.2XP_011514181.1  ephrin type-B receptor 6 isoform X1

      See identical proteins and their annotated locations for XP_011514181.1

      UniProtKB/TrEMBL
      F8WCM8
      Conserved Domains (7) summary
      cd09555
      Location:9461014
      SAM_EPH-B6; SAM domain of EPH-B6 subfamily of tyrosine kinase receptors
      cd10475
      Location:33232
      EphR_LBD_B6; Ligand Binding Domain of Ephrin type-B Receptor 6
      cd00063
      Location:371472
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam00041
      Location:490572
      fn3; Fibronectin type III domain
      pfam07699
      Location:305346
      Ephrin_rec_like; Putative ephrin-receptor like
      pfam14575
      Location:613665
      EphA2_TM; Ephrin type-A receptor 2 transmembrane domain
      cl21453
      Location:666920
      PKc_like; Protein Kinases, catalytic domain
    2. XM_047419983.1XP_047275939.1  ephrin type-B receptor 6 isoform X2

    3. XM_047419984.1XP_047275940.1  ephrin type-B receptor 6 isoform X3

    4. XM_011515880.2XP_011514182.1  ephrin type-B receptor 6 isoform X1

      See identical proteins and their annotated locations for XP_011514182.1

      UniProtKB/TrEMBL
      F8WCM8
      Conserved Domains (7) summary
      cd09555
      Location:9461014
      SAM_EPH-B6; SAM domain of EPH-B6 subfamily of tyrosine kinase receptors
      cd10475
      Location:33232
      EphR_LBD_B6; Ligand Binding Domain of Ephrin type-B Receptor 6
      cd00063
      Location:371472
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam00041
      Location:490572
      fn3; Fibronectin type III domain
      pfam07699
      Location:305346
      Ephrin_rec_like; Putative ephrin-receptor like
      pfam14575
      Location:613665
      EphA2_TM; Ephrin type-A receptor 2 transmembrane domain
      cl21453
      Location:666920
      PKc_like; Protein Kinases, catalytic domain
    5. XM_011515881.4XP_011514183.1  ephrin type-B receptor 6 isoform X2

      Conserved Domains (8) summary
      cd09555
      Location:9451013
      SAM_EPH-B6; SAM domain of EPH-B6 subfamily of tyrosine kinase receptors
      smart00454
      Location:9461006
      SAM; Sterile alpha motif
      cd10475
      Location:33232
      EphR_LBD_B6; Ligand Binding Domain of Ephrin type-B Receptor 6
      cd00063
      Location:489580
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam07699
      Location:305346
      GCC2_GCC3; GCC2 and GCC3
      pfam07714
      Location:671915
      Pkinase_Tyr; Protein tyrosine kinase
      pfam14575
      Location:613666
      EphA2_TM; Ephrin type-A receptor 2 transmembrane domain
      cl21453
      Location:666919
      PKc_like; Protein Kinases, catalytic domain
    6. XM_011515882.3XP_011514184.1  ephrin type-B receptor 6 isoform X3

      Conserved Domains (8) summary
      cd09555
      Location:915983
      SAM_EPH-B6; SAM domain of EPH-B6 subfamily of tyrosine kinase receptors
      smart00454
      Location:916976
      SAM; Sterile alpha motif
      cd10475
      Location:33232
      EphR_LBD_B6; Ligand Binding Domain of Ephrin type-B Receptor 6
      cd00063
      Location:371472
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam07699
      Location:305346
      GCC2_GCC3; GCC2 and GCC3
      pfam07714
      Location:640885
      Pkinase_Tyr; Protein tyrosine kinase
      pfam14575
      Location:582635
      EphA2_TM; Ephrin type-A receptor 2 transmembrane domain
      cl21453
      Location:635889
      PKc_like; Protein Kinases, catalytic domain
    7. XM_024446675.2XP_024302443.1  ephrin type-B receptor 6 isoform X4

      Conserved Domains (7) summary
      cd09555
      Location:914982
      SAM_EPH-B6; SAM domain of EPH-B6 subfamily of tyrosine kinase receptors
      cd10475
      Location:33232
      EphR_LBD_B6; Ligand Binding Domain of Ephrin type-B Receptor 6
      cd00063
      Location:489549
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam00041
      Location:372472
      fn3; Fibronectin type III domain
      pfam07699
      Location:305346
      Ephrin_rec_like; Putative ephrin-receptor like
      pfam14575
      Location:582634
      EphA2_TM; Ephrin type-A receptor 2 transmembrane domain
      cl21453
      Location:635888
      PKc_like; Protein Kinases, catalytic domain

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_187562.1 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      878132..894136
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054328699.1XP_054184674.1  ephrin type-B receptor 6 isoform X1

      UniProtKB/TrEMBL
      A0A0G2JNH7
    2. XM_054328700.1XP_054184675.1  ephrin type-B receptor 6 isoform X1

      UniProtKB/TrEMBL
      A0A0G2JNH7
    3. XM_054328702.1XP_054184677.1  ephrin type-B receptor 6 isoform X2

    4. XM_054328703.1XP_054184678.1  ephrin type-B receptor 6 isoform X3

    5. XM_054328701.1XP_054184676.1  ephrin type-B receptor 6 isoform X1

      UniProtKB/TrEMBL
      A0A0G2JNH7
    6. XM_054328704.1XP_054184679.1  ephrin type-B receptor 6 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      144210901..144226909
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054357462.1XP_054213437.1  ephrin type-B receptor 6 isoform X1

      UniProtKB/Swiss-Prot
      A4D2I7, A8CDT5, D3DXD3, O15197, Q2TB23, Q2TB24
    2. XM_054357466.1XP_054213441.1  ephrin type-B receptor 6 isoform X2

    3. XM_054357469.1XP_054213444.1  ephrin type-B receptor 6 isoform X3

    4. XM_054357463.1XP_054213438.1  ephrin type-B receptor 6 isoform X1

      UniProtKB/Swiss-Prot
      A4D2I7, A8CDT5, D3DXD3, O15197, Q2TB23, Q2TB24
    5. XM_054357465.1XP_054213440.1  ephrin type-B receptor 6 isoform X2

    6. XM_054357468.1XP_054213443.1  ephrin type-B receptor 6 isoform X3

    7. XM_054357471.1XP_054213446.1  ephrin type-B receptor 6 isoform X4

    8. XM_054357464.1XP_054213439.1  ephrin type-B receptor 6 isoform X1

      UniProtKB/Swiss-Prot
      A4D2I7, A8CDT5, D3DXD3, O15197, Q2TB23, Q2TB24
    9. XM_054357467.1XP_054213442.1  ephrin type-B receptor 6 isoform X2

    10. XM_054357470.1XP_054213445.1  ephrin type-B receptor 6 isoform X3