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

Gene ID: 1288, updated on 22-Jan-2020

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
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

Genomic context

See COL4A6 in Genome Data Viewer
Location:
Xq22.3
Exon count:
50
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (108155607..108439493, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (107398837..107682704, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene proteasome 26S subunit, non-ATPase 10 Neighboring gene autophagy related 4A cysteine peptidase Neighboring gene collagen type IV alpha 5 chain Neighboring gene uncharacterized LOC101928358 Neighboring gene insulin receptor substrate 4

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
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

Homology

Clone Names

  • MGC88184

Gene Ontology Provided by GOA

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

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)

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)

mRNA and Protein(s)

  1. NM_001287758.1NP_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, AL034369, AL136080, AW082083, BG680578, CA396616, CA489342, CB050016, CN313332, CN313341, CN313343, CN313347, CN313351, CX872164, DA748513
    Consensus CDS
    CCDS76010.1
    UniProtKB/TrEMBL
    A8MXH5
    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_001287759.1NP_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)
    AL034369, AL136080, BC000874, BC144669, CB050016, CN313332, CN313347, DB260304, EU182215
    Consensus CDS
    CCDS76009.1
    UniProtKB/TrEMBL
    A0A087WZY5, A8VPY0, 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_001287760.1NP_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/Swiss-Prot
    Q14031
    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
    Q14031
    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/Swiss-Prot
    Q14031
    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: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

    Range
    108155607..108439493 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006724617.3XP_006724680.1  collagen alpha-6(IV) chain isoform X1

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

    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_011530853.3XP_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
  4. XM_011530854.2XP_011529156.1  collagen alpha-6(IV) chain isoform X4

    Conserved Domains (1) summary
    pfam01391
    Location:681740
    Collagen; Collagen triple helix repeat (20 copies)

RNA

  1. XR_001755650.1 RNA Sequence

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