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COL16A1 collagen type XVI alpha 1 chain [ Homo sapiens (human) ]

Gene ID: 1307, updated on 8-Jul-2021

Summary

Official Symbol
COL16A1provided by HGNC
Official Full Name
collagen type XVI alpha 1 chainprovided by HGNC
Primary source
HGNC:HGNC:2193
See related
Ensembl:ENSG00000084636 MIM:120326
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
447AA; FP1572
Summary
This gene encodes the alpha chain of type XVI collagen, a member of the FACIT collagen family (fibril-associated collagens with interrupted helices). Members of this collagen family are found in association with fibril-forming collagens such as type I and II, and serve to maintain the integrity of the extracellular matrix. High levels of type XVI collagen have been found in fibroblasts and keratinocytes, and in smooth muscle and amnion. [provided by RefSeq, Jul 2008]
Expression
Broad expression in ovary (RPKM 53.1), prostate (RPKM 25.7) and 20 other tissues See more
Orthologs
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Genomic context

See COL16A1 in Genome Data Viewer
Location:
1p35.2
Exon count:
74
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (31652263..31704162, complement)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (32117864..32169618, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene hypocretin receptor 1 Neighboring gene penta-EF-hand domain containing 1 Neighboring gene uncharacterized LOC105378628 Neighboring gene PEF1 and COL16A1 antisense RNA 1 Neighboring gene uncharacterized LOC101929444 Neighboring gene Sharpr-MPRA regulatory region 11964 Neighboring gene adhesion G protein-coupled receptor B2 Neighboring gene microRNA 4254

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?

Phenotypes

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2021-02-01)

ClinGen Genome Curation Page
Haploinsufficency

Dosage sensitivity unlikely (Last evaluated 2021-02-01)

ClinGen Genome Curation PagePubMed

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Component Evidence Code Pubs
part_of collagen type V trimer IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
part_of collagen type XVI trimer TAS
Traceable Author Statement
more info
PubMed 
located_in collagen-containing extracellular matrix HDA PubMed 
located_in endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
 
is_active_in extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in extracellular region TAS
Traceable Author Statement
more info
 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
collagen alpha-1(XVI) chain
Names
alpha 1 type XVI collagen
collagen XVI, alpha-1 polypeptide
collagen, type XVI, alpha 1

NCBI Reference Sequences (RefSeq)

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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_001856.4NP_001847.3  collagen alpha-1(XVI) chain precursor

    See identical proteins and their annotated locations for NP_001847.3

    Status: REVIEWED

    Source sequence(s)
    AC114488, BC064839, M92642, S57132
    Consensus CDS
    CCDS41297.1
    UniProtKB/Swiss-Prot
    Q07092
    Related
    ENSP00000362776.3, ENST00000373672.8
    Conserved Domains (2) summary
    pfam01391
    Location:756803
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:50231
    TSPN; Thrombospondin N-terminal -like domains

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    31652263..31704162 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017000339.1XP_016855828.1  collagen alpha-1(XVI) chain isoform X2

  2. XM_011540724.1XP_011539026.1  collagen alpha-1(XVI) chain isoform X6

    Conserved Domains (2) summary
    pfam01391
    Location:685744
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:50231
    TSPN; Thrombospondin N-terminal -like domains
  3. XM_011540723.1XP_011539025.1  collagen alpha-1(XVI) chain isoform X5

    Conserved Domains (2) summary
    pfam01391
    Location:756803
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:50231
    TSPN; Thrombospondin N-terminal -like domains
  4. XM_005270481.1XP_005270538.1  collagen alpha-1(XVI) chain isoform X4

    Conserved Domains (2) summary
    pfam01391
    Location:756803
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:50231
    TSPN; Thrombospondin N-terminal -like domains
  5. XM_017000338.1XP_016855827.1  collagen alpha-1(XVI) chain isoform X1

  6. XM_011540722.1XP_011539024.1  collagen alpha-1(XVI) chain isoform X3

    Conserved Domains (2) summary
    pfam01391
    Location:756803
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:50231
    TSPN; Thrombospondin N-terminal -like domains
  7. XM_011540726.3XP_011539028.1  collagen alpha-1(XVI) chain isoform X7

    Conserved Domains (2) summary
    pfam01391
    Location:585632
    Collagen; Collagen triple helix repeat (20 copies)
    cl22861
    Location:160
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
  8. XM_011540727.2XP_011539029.1  collagen alpha-1(XVI) chain isoform X8

    Conserved Domains (1) summary
    pfam01391
    Location:454501
    Collagen; Collagen triple helix repeat (20 copies)
  9. XM_017000340.2XP_016855829.1  collagen alpha-1(XVI) chain isoform X10

  10. XM_011540728.2XP_011539030.1  collagen alpha-1(XVI) chain isoform X9

    Conserved Domains (1) summary
    pfam01391
    Location:241288
    Collagen; Collagen triple helix repeat (20 copies)
  11. XM_017000341.1XP_016855830.1  collagen alpha-1(XVI) chain isoform X13

  12. XM_011540730.1XP_011539032.1  collagen alpha-1(XVI) chain isoform X12

    Related
    ENSP00000362772.3, ENST00000373668.7
    Conserved Domains (2) summary
    pfam01391
    Location:756803
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:50231
    TSPN; Thrombospondin N-terminal -like domains
  13. XM_011540729.1XP_011539031.1  collagen alpha-1(XVI) chain isoform X11

    Conserved Domains (2) summary
    pfam01391
    Location:756803
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:50231
    TSPN; Thrombospondin N-terminal -like domains

RNA

  1. XR_946546.3 RNA Sequence

  2. XR_001736981.1 RNA Sequence

  3. XR_001736982.1 RNA Sequence

  4. XR_001736984.1 RNA Sequence

  5. XR_001736983.1 RNA Sequence

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