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    COL4A6 collagen type IV alpha 6 chain [ Homo sapiens (human) ]

    Gene ID: 1288, updated on 14-Nov-2024

    Summary

    Official Symbol
    COL4A6provided by HGNC
    Official Full Name
    collagen type IV alpha 6 chainprovided by HGNC
    Primary source
    HGNC:HGNC:2208
    See related
    Ensembl:ENSG00000197565 MIM:303631; AllianceGenome:HGNC:2208
    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
    DFNX6; DELXq22.3; CXDELq22.3
    Summary
    This gene encodes one of the six subunits of type IV collagen, the major structural component of basement membranes. Like the other members of the type IV collagen gene family, this gene is organized in a head-to-head conformation with another type IV collagen gene, alpha 5 type IV collagen, so that the gene pair shares a common promoter. Deletions in the alpha 5 gene that extend into the alpha 6 gene result in diffuse leiomyomatosis accompanying the X-linked Alport syndrome caused by the deletion in the alpha 5 gene. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2013]
    Expression
    Broad expression in endometrium (RPKM 9.0), gall bladder (RPKM 7.4) and 16 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See COL4A6 in Genome Data Viewer
    Location:
    Xq22.3
    Exon count:
    50
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (108155614..108439458, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (106593205..106877000, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (107398844..107682688, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene V-set and immunoglobulin domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29838 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29839 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:107370111-107370674 Neighboring gene proteasome 26S subunit, non-ATPase 10 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:107399852-107400352 Neighboring gene autophagy related 4A cysteine peptidase Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:107421110-107421795 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:107420425-107421109 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:107419738-107420424 Neighboring gene uncharacterized LOC124905205 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chrX:107513459-107514658 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:107596629-107597181 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:107609798-107610337 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:107634248-107634889 Neighboring gene collagen type IV alpha 5 chain Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:107843610-107844540 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:107884720-107885919 Neighboring gene IRS4 antisense RNA 1 Neighboring gene insulin receptor substrate 4

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues 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
    Tat tat Treatment with cannabinoids inhibits HIV-1 Tat-enhanced attachment of U937 cells to collagen IV, laminin, or ECM1 proteins, which is linked to the cannabinoid receptor type 2 and the modulation of beta1-integrin and actin distribution PubMed
    tat HIV-1 Tat enhances adhesion of human U937 monocyte-like cells to proteins of the extracellular matrix, such as collagen IV, laminin, and ECM1 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

    • MGC88184

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to amino acid stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in collagen-activated tyrosine kinase receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    part_of collagen type IV trimer IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of collagen type IV trimer NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in collagen-containing extracellular matrix HDA PubMed 
    is_active_in collagen-containing extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
     
    located_in extracellular region TAS
    Traceable Author Statement
    more info
     
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    collagen alpha-6(IV) chain
    Names
    collagen IV, alpha-6 polypeptide
    collagen of basement membrane, alpha-6
    collagen, type IV, alpha 6
    dJ889N15.4 (Collagen Alpha 6(IV))

    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.

    Genomic

    1. NG_012059.2 RefSeqGene

      Range
      6053..288861
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_233

    mRNA and Protein(s)

    1. NM_001287758.2NP_001274687.1  collagen alpha-6(IV) chain isoform 3 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) represents the longest transcript and encodes the longest protein (isoform 3).
      Source sequence(s)
      AL031177, AL136080, AW082083, BG680578, CA396616, CA489342, CB050016, CN313332, CN313341, CN313343, CN313347, CN313351, CX872164, DA748513
      Consensus CDS
      CCDS76010.1
      UniProtKB/TrEMBL
      A8MXH5, B7ZMM7
      Related
      ENSP00000378340.3, ENST00000394872.6
      Conserved Domains (2) summary
      pfam01391
      Location:680739
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01413
      Location:15921704
      C4; C-terminal tandem repeated domain in type 4 procollagen
    2. NM_001287759.2NP_001274688.1  collagen alpha-6(IV) chain isoform 4 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks several alternate in-frame exons compared to variant 3. The resulting protein (isoform 4) is shorter compared to isoform 3.
      Source sequence(s)
      AL136080, BC000874, BC144669, CB050016, CN313332, CN313347, DB260304, EU182215
      Consensus CDS
      CCDS76009.1
      UniProtKB/TrEMBL
      A0A087WZY5, B7ZMM7
      Related
      ENSP00000482970.1, ENST00000621266.4
      Conserved Domains (2) summary
      pfam01391
      Location:663722
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01413
      Location:15511663
      C4; C-terminal tandem repeated domain in type 4 procollagen
    3. NM_001287760.2NP_001274689.1  collagen alpha-6(IV) chain isoform 5 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks several alternate in-frame exons compared to variant 3. The resulting protein (isoform 5) is shorter compared to isoform 3.
      Source sequence(s)
      AL034369, AL136080, BC000874, BC140855, CB050016, DB260304, U04845
      Consensus CDS
      CCDS76008.1
      UniProtKB/TrEMBL
      B2RTX6, F5H3Q5
      Related
      ENSP00000445236.1, ENST00000538570.5
      Conserved Domains (2) summary
      pfam01391
      Location:663722
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01413
      Location:15181630
      C4; C-terminal tandem repeated domain in type 4 procollagen
    4. NM_001847.4NP_001838.2  collagen alpha-6(IV) chain isoform A precursor

      See identical proteins and their annotated locations for NP_001838.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (A) utilizes a different alternative exon in the 5' UTR and coding region, exon 1A, which results in use of an alternate upstream translation start, compared to variant 3. The resulting protein (isoform A) has a distinct and shorter N-terminus, compared to isoform 3.
      Source sequence(s)
      AL031177, AL136080, CB050016, U04845
      Consensus CDS
      CCDS14541.1
      UniProtKB/Swiss-Prot
      Q12823, Q14031, Q14053, Q5JYH6, Q5JYH8, Q9NQM5, Q9NTX3, Q9UJ76, Q9UMG6, Q9Y4L4
      UniProtKB/TrEMBL
      B7ZMM7
      Related
      ENSP00000361290.4, ENST00000372216.8
      Conserved Domains (2) summary
      pfam01391
      Location:664723
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01413
      Location:15761688
      C4; C-terminal tandem repeated domain in type 4 procollagen
    5. NM_033641.4NP_378667.1  collagen alpha-6(IV) chain isoform B precursor

      See identical proteins and their annotated locations for NP_378667.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (B) utilizes the same 5' exon as variant 3 (exon 1B) but lacks several alternate in-frame exons. The resulting protein (isoform B) is shorter compared to isoform 3.
      Source sequence(s)
      AL136080, BF726518, BQ331638, CB050016, CN313347, D21337, U04845
      Consensus CDS
      CCDS14542.1
      UniProtKB/TrEMBL
      B7ZMM7
      Related
      ENSP00000334733.7, ENST00000334504.12
      Conserved Domains (2) summary
      pfam01391
      Location:663722
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01413
      Location:15751687
      C4; C-terminal tandem repeated domain in type 4 procollagen

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      108155614..108439458 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047441813.1XP_047297769.1  collagen alpha-6(IV) chain isoform X4

    2. XM_011530852.3XP_011529154.1  collagen alpha-6(IV) chain isoform X2

      UniProtKB/TrEMBL
      B7ZMM7
      Conserved Domains (2) summary
      pfam01391
      Location:681740
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01413
      Location:15691681
      C4; C-terminal tandem repeated domain in type 4 procollagen
    3. XM_006724617.4XP_006724680.1  collagen alpha-6(IV) chain isoform X1

      UniProtKB/TrEMBL
      B7ZMM7
      Conserved Domains (2) summary
      pfam01391
      Location:681740
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01413
      Location:15931705
      C4; C-terminal tandem repeated domain in type 4 procollagen
    4. XM_011530853.4XP_011529155.1  collagen alpha-6(IV) chain isoform X3

      Conserved Domains (2) summary
      pfam01391
      Location:653712
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01413
      Location:15651677
      C4; C-terminal tandem repeated domain in type 4 procollagen
    5. XM_047441818.1XP_047297774.1  collagen alpha-6(IV) chain isoform X9

    6. XM_047441816.1XP_047297772.1  collagen alpha-6(IV) chain isoform X7

    7. XM_011530854.3XP_011529156.1  collagen alpha-6(IV) chain isoform X5

      Conserved Domains (1) summary
      pfam01391
      Location:681740
      Collagen; Collagen triple helix repeat (20 copies)
    8. XM_047441819.1XP_047297775.1  collagen alpha-6(IV) chain isoform X10

    9. XM_047441817.1XP_047297773.1  collagen alpha-6(IV) chain isoform X8

    10. XM_047441815.1XP_047297771.1  collagen alpha-6(IV) chain isoform X6

    RNA

    1. XR_001755650.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      106593205..106877000 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054326445.1XP_054182420.1  collagen alpha-6(IV) chain isoform X4

    2. XM_054326443.1XP_054182418.1  collagen alpha-6(IV) chain isoform X2

    3. XM_054326442.1XP_054182417.1  collagen alpha-6(IV) chain isoform X1

    4. XM_054326444.1XP_054182419.1  collagen alpha-6(IV) chain isoform X3

    5. XM_054326450.1XP_054182425.1  collagen alpha-6(IV) chain isoform X9

    6. XM_054326448.1XP_054182423.1  collagen alpha-6(IV) chain isoform X7

    7. XM_054326446.1XP_054182421.1  collagen alpha-6(IV) chain isoform X5

    8. XM_054326451.1XP_054182426.1  collagen alpha-6(IV) chain isoform X10

    9. XM_054326449.1XP_054182424.1  collagen alpha-6(IV) chain isoform X8

    10. XM_054326447.1XP_054182422.1  collagen alpha-6(IV) chain isoform X6

    RNA

    1. XR_008485449.1 RNA Sequence