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Col16a1 collagen type XVI alpha 1 chain [ Rattus norvegicus (Norway rat) ]

Gene ID: 366474, updated on 2-Oct-2018

Summary

Official Symbol
Col16a1provided by RGD
Official Full Name
collagen type XVI alpha 1 chainprovided by RGD
Primary source
RGD:1310982
See related
Ensembl:ENSRNOG00000031475
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Expression
Biased expression in Uterus (RPKM 172.2), Lung (RPKM 121.7) and 8 other tissues See more
Orthologs

Genomic context

See Col16a1 in Genome Data Viewer
Location:
5q36
Exon count:
73
Annotation release Status Assembly Chr Location
106 current Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (148257030..148311645)
104 previous assembly Rnor_5.0 (GCF_000001895.4) 5 NC_005104.3 (151976106..152030103)

Chromosome 5 - NC_005104.4Genomic Context describing neighboring genes Neighboring gene SPOC domain containing 1 Neighboring gene adhesion G protein-coupled receptor B2 Neighboring gene penta-EF hand domain containing 1 Neighboring gene hypocretin receptor 1

Genomic regions, transcripts, and products

Expression

  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Pathways from BioSystems

General gene information

Markers

Homology

Clone Names

  • MGC109452

Gene Ontology Provided by RGD

Function Evidence Code Pubs
extracellular matrix structural constituent IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integrin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integrin binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell adhesion ISO
Inferred from Sequence Orthology
more info
 
cell adhesion mediated by integrin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell adhesion mediated by integrin ISO
Inferred from Sequence Orthology
more info
 
cellular response to amino acid stimulus IEA
Inferred from Electronic Annotation
more info
 
cellular response to amino acid stimulus ISO
Inferred from Sequence Orthology
more info
 
extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integrin activation IEA
Inferred from Electronic Annotation
more info
 
integrin activation ISO
Inferred from Sequence Orthology
more info
 
positive regulation of focal adhesion assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of focal adhesion assembly ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

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

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.

mRNA and Protein(s)

  1. NM_001302967.1NP_001289896.1  collagen alpha-1(XVI) chain precursor

    See identical proteins and their annotated locations for NP_001289896.1

    Status: VALIDATED

    Source sequence(s)
    AABR07050014, AABR07050015
    Conserved Domains (2) summary
    pfam01391
    Location:10831136
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:50231
    TSPN; Thrombospondin N-terminal -like domains

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

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

Reference Rnor_6.0 Primary Assembly

Genomic

  1. NC_005104.4 Reference Rnor_6.0 Primary Assembly

    Range
    148257030..148311645
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006238953.3XP_006239015.1  collagen alpha-1(XVI) chain isoform X6

    Conserved Domains (2) summary
    pfam01391
    Location:10521105
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:56237
    TSPN; Thrombospondin N-terminal -like domains
  2. XM_008764158.2XP_008762380.1  collagen alpha-1(XVI) chain isoform X1

    See identical proteins and their annotated locations for XP_008762380.1

    Conserved Domains (2) summary
    pfam01391
    Location:11041157
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:56237
    TSPN; Thrombospondin N-terminal -like domains
  3. XM_006238946.3XP_006239008.1  collagen alpha-1(XVI) chain isoform X1

    See identical proteins and their annotated locations for XP_006239008.1

    Conserved Domains (2) summary
    pfam01391
    Location:11041157
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:56237
    TSPN; Thrombospondin N-terminal -like domains
  4. XM_006238948.3XP_006239010.1  collagen alpha-1(XVI) chain isoform X3

    Conserved Domains (2) summary
    pfam01391
    Location:10891142
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:56237
    TSPN; Thrombospondin N-terminal -like domains
  5. XM_006238950.3XP_006239012.1  collagen alpha-1(XVI) chain isoform X4

    Conserved Domains (2) summary
    pfam01391
    Location:10881141
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:56237
    TSPN; Thrombospondin N-terminal -like domains
  6. XM_006238947.3XP_006239009.1  collagen alpha-1(XVI) chain isoform X2

    Related
    ENSRNOP00000058947.2, ENSRNOT00000067663.2
    Conserved Domains (2) summary
    pfam01391
    Location:10981151
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:50231
    TSPN; Thrombospondin N-terminal -like domains
  7. XM_006238951.3XP_006239013.1  collagen alpha-1(XVI) chain isoform X5

    See identical proteins and their annotated locations for XP_006239013.1

    Conserved Domains (2) summary
    pfam01391
    Location:10831136
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:50231
    TSPN; Thrombospondin N-terminal -like domains

Alternate Rn_Celera

Genomic

  1. AC_000073.1 Alternate Rn_Celera

    Range
    140857544..140910551
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001015033.2: Suppressed sequence

    Description
    NM_001015033.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
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