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

    Gene ID: 131873, updated on 10-Dec-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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See COL6A6 in Genome Data Viewer
    Location:
    3q22.1
    Exon count:
    45
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (130516720..130677042)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (133260574..133420884)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    General gene information

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in cell adhesion  
    involved_in extracellular matrix organization  
    Component Evidence Code Pubs
    part_of collagen trimer  
    located_in collagen-containing extracellular matrix PubMed 
    is_active_in collagen-containing extracellular matrix  
    located_in extracellular matrix PubMed 
    located_in extracellular region  

    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_2024_08

    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

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