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COL6A6 collagen type VI alpha 6 chain [ Homo sapiens (human) ]

Gene ID: 131873, updated on 5-May-2024

Summary

Official Symbol
COL6A6provided by HGNC
Official Full Name
collagen type VI alpha 6 chainprovided by HGNC
Primary source
HGNC:HGNC:27023
See related
Ensembl:ENSG00000206384 MIM:616613; AllianceGenome:HGNC:27023
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
Summary
This gene encodes a large protein that contains multiple von Willebrand factor domains and forms a component of the basal lamina of epithelial cells. This protein may regulate epithelial cell-fibronectin interactions. Variation in this gene may be implicated in skin diseases. [provided by RefSeq, May 2017]
Expression
Biased expression in lung (RPKM 3.3), fat (RPKM 0.9) and 7 other tissues See more
Orthologs
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Genomic context

Location:
3q22.1
Exon count:
45
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (130516720..130677042)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (133260574..133420884)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (130236021..130395886)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATP5MC2 pseudogene 5 Neighboring gene collagen type VI alpha 5 chain Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:130126750-130127949 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:130161092-130161649 Neighboring gene MPRA-validated peak4833 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14733 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:130297667-130297916 Neighboring gene phosphoinositide-3-kinase regulatory subunit 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20523 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14734 Neighboring gene uncharacterized LOC107986023 Neighboring gene RN7SK pseudogene 212

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?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General protein information

Preferred Names
collagen alpha-6(VI) chain
Names
collagen, type VI, alpha 6

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_054914.1 RefSeqGene

    Range
    5469..165334
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001102608.3NP_001096078.1  collagen alpha-6(VI) chain precursor

    See identical proteins and their annotated locations for NP_001096078.1

    Status: REVIEWED

    Source sequence(s)
    AC093006, AC117398, AC128683
    Consensus CDS
    CCDS46911.1
    UniProtKB/Swiss-Prot
    A6NMZ7, A7DZQ0, A7DZQ1, A7DZQ2, Q69YT0
    Related
    ENSP00000351310.6, ENST00000358511.11
    Conserved Domains (6) summary
    pfam01391
    Location:14581515
    Collagen; Collagen triple helix repeat (20 copies)
    smart00327
    Location:12061345
    VWA; von Willebrand factor (vWF) type A domain
    COG2304
    Location:435593
    YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]
    cd01450
    Location:19642142
    vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    pfam00092
    Location:622790
    VWA; von Willebrand factor type A domain
    cl00057
    Location:26192
    vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    130516720..130677042
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017005713.3XP_016861202.1  collagen alpha-6(VI) chain isoform X2

    UniProtKB/Swiss-Prot
    A6NMZ7, A7DZQ0, A7DZQ1, A7DZQ2, Q69YT0
    Conserved Domains (6) summary
    pfam01391
    Location:14581515
    Collagen; Collagen triple helix repeat (20 copies)
    smart00327
    Location:12061345
    VWA; von Willebrand factor (vWF) type A domain
    COG2304
    Location:435593
    YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]
    cd01450
    Location:19642142
    vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    pfam00092
    Location:622790
    VWA; von Willebrand factor type A domain
    cl00057
    Location:26192
    vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
  2. XM_017005711.3XP_016861200.1  collagen alpha-6(VI) chain isoform X2

    UniProtKB/Swiss-Prot
    A6NMZ7, A7DZQ0, A7DZQ1, A7DZQ2, Q69YT0
    Conserved Domains (6) summary
    pfam01391
    Location:14581515
    Collagen; Collagen triple helix repeat (20 copies)
    smart00327
    Location:12061345
    VWA; von Willebrand factor (vWF) type A domain
    COG2304
    Location:435593
    YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]
    cd01450
    Location:19642142
    vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    pfam00092
    Location:622790
    VWA; von Willebrand factor type A domain
    cl00057
    Location:26192
    vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
  3. XM_011512426.4XP_011510728.1  collagen alpha-6(VI) chain isoform X2

    See identical proteins and their annotated locations for XP_011510728.1

    UniProtKB/Swiss-Prot
    A6NMZ7, A7DZQ0, A7DZQ1, A7DZQ2, Q69YT0
    Conserved Domains (6) summary
    pfam01391
    Location:14581515
    Collagen; Collagen triple helix repeat (20 copies)
    smart00327
    Location:12061345
    VWA; von Willebrand factor (vWF) type A domain
    COG2304
    Location:435593
    YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]
    cd01450
    Location:19642142
    vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    pfam00092
    Location:622790
    VWA; von Willebrand factor type A domain
    cl00057
    Location:26192
    vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
  4. XM_005247121.6XP_005247178.1  collagen alpha-6(VI) chain isoform X2

    See identical proteins and their annotated locations for XP_005247178.1

    UniProtKB/Swiss-Prot
    A6NMZ7, A7DZQ0, A7DZQ1, A7DZQ2, Q69YT0
    Conserved Domains (6) summary
    pfam01391
    Location:14581515
    Collagen; Collagen triple helix repeat (20 copies)
    smart00327
    Location:12061345
    VWA; von Willebrand factor (vWF) type A domain
    COG2304
    Location:435593
    YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]
    cd01450
    Location:19642142
    vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    pfam00092
    Location:622790
    VWA; von Willebrand factor type A domain
    cl00057
    Location:26192
    vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
  5. XM_011512424.3XP_011510726.1  collagen alpha-6(VI) chain isoform X1

    See identical proteins and their annotated locations for XP_011510726.1

    Conserved Domains (6) summary
    pfam01391
    Location:14741531
    Collagen; Collagen triple helix repeat (20 copies)
    smart00327
    Location:12221361
    VWA; von Willebrand factor (vWF) type A domain
    COG2304
    Location:451609
    YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]
    cd01450
    Location:19802158
    vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    pfam00092
    Location:638806
    VWA; von Willebrand factor type A domain
    cl00057
    Location:42208
    vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
  6. XM_011512431.3XP_011510733.1  collagen alpha-6(VI) chain isoform X3

    Conserved Domains (5) summary
    pfam01391
    Location:14741531
    Collagen; Collagen triple helix repeat (20 copies)
    smart00327
    Location:12221361
    VWA; von Willebrand factor (vWF) type A domain
    COG2304
    Location:451609
    YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]
    pfam00092
    Location:638806
    VWA; von Willebrand factor type A domain
    cl00057
    Location:42208
    vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
  7. XM_017005716.2XP_016861205.1  collagen alpha-6(VI) chain isoform X4

  8. XM_011512432.3XP_011510734.1  collagen alpha-6(VI) chain isoform X5

    Conserved Domains (5) summary
    pfam01391
    Location:14741531
    Collagen; Collagen triple helix repeat (20 copies)
    smart00327
    Location:12221361
    VWA; von Willebrand factor (vWF) type A domain
    COG2304
    Location:451609
    YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]
    pfam00092
    Location:638806
    VWA; von Willebrand factor type A domain
    cl00057
    Location:42208
    vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
  9. XM_017005712.3XP_016861201.1  collagen alpha-6(VI) chain isoform X2

    UniProtKB/Swiss-Prot
    A6NMZ7, A7DZQ0, A7DZQ1, A7DZQ2, Q69YT0
    Conserved Domains (6) summary
    pfam01391
    Location:14581515
    Collagen; Collagen triple helix repeat (20 copies)
    smart00327
    Location:12061345
    VWA; von Willebrand factor (vWF) type A domain
    COG2304
    Location:435593
    YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]
    cd01450
    Location:19642142
    vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    pfam00092
    Location:622790
    VWA; von Willebrand factor type A domain
    cl00057
    Location:26192
    vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
  10. XM_047447448.1XP_047303404.1  collagen alpha-6(VI) chain isoform X2

    UniProtKB/Swiss-Prot
    A6NMZ7, A7DZQ0, A7DZQ1, A7DZQ2, Q69YT0
  11. XM_047447445.1XP_047303401.1  collagen alpha-6(VI) chain isoform X2

    UniProtKB/Swiss-Prot
    A6NMZ7, A7DZQ0, A7DZQ1, A7DZQ2, Q69YT0
  12. XM_047447447.1XP_047303403.1  collagen alpha-6(VI) chain isoform X2

    UniProtKB/Swiss-Prot
    A6NMZ7, A7DZQ0, A7DZQ1, A7DZQ2, Q69YT0
  13. XM_017005714.3XP_016861203.1  collagen alpha-6(VI) chain isoform X2

    UniProtKB/Swiss-Prot
    A6NMZ7, A7DZQ0, A7DZQ1, A7DZQ2, Q69YT0
    Conserved Domains (6) summary
    pfam01391
    Location:14581515
    Collagen; Collagen triple helix repeat (20 copies)
    smart00327
    Location:12061345
    VWA; von Willebrand factor (vWF) type A domain
    COG2304
    Location:435593
    YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]
    cd01450
    Location:19642142
    vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    pfam00092
    Location:622790
    VWA; von Willebrand factor type A domain
    cl00057
    Location:26192
    vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
  14. XM_047447446.1XP_047303402.1  collagen alpha-6(VI) chain isoform X2

    UniProtKB/Swiss-Prot
    A6NMZ7, A7DZQ0, A7DZQ1, A7DZQ2, Q69YT0

RNA

  1. XR_924103.3 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    133260574..133420884
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054345237.1XP_054201212.1  collagen alpha-6(VI) chain isoform X2

  2. XM_054345236.1XP_054201211.1  collagen alpha-6(VI) chain isoform X2

  3. XM_054345240.1XP_054201215.1  collagen alpha-6(VI) chain isoform X2

  4. XM_054345241.1XP_054201216.1  collagen alpha-6(VI) chain isoform X2

  5. XM_054345233.1XP_054201208.1  collagen alpha-6(VI) chain isoform X1

  6. XM_054345244.1XP_054201219.1  collagen alpha-6(VI) chain isoform X3

  7. XM_054345245.1XP_054201220.1  collagen alpha-6(VI) chain isoform X4

  8. XM_054345246.1XP_054201221.1  collagen alpha-6(VI) chain isoform X5

  9. XM_054345234.1XP_054201209.1  collagen alpha-6(VI) chain isoform X2

  10. XM_054345243.1XP_054201218.1  collagen alpha-6(VI) chain isoform X2

  11. XM_054345238.1XP_054201213.1  collagen alpha-6(VI) chain isoform X2

  12. XM_054345242.1XP_054201217.1  collagen alpha-6(VI) chain isoform X2

  13. XM_054345239.1XP_054201214.1  collagen alpha-6(VI) chain isoform X2

  14. XM_054345235.1XP_054201210.1  collagen alpha-6(VI) chain isoform X2

RNA

  1. XR_008486657.1 RNA Sequence