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Col12a1 collagen type XII alpha 1 chain [ Rattus norvegicus (Norway rat) ]

Gene ID: 25683, updated on 18-Apr-2019

Summary

Official Symbol
Col12a1provided by RGD
Official Full Name
collagen type XII alpha 1 chainprovided by RGD
Primary source
RGD:2374
See related
Ensembl:ENSRNOG00000058470
Gene type
protein coding
RefSeq status
MODEL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
may mediate interactions between extracellular matrix molecules and cells [RGD, Feb 2006]
Expression
Biased expression in Kidney (RPKM 392.9), Adrenal (RPKM 291.6) and 7 other tissues See more
Orthologs

Genomic context

See Col12a1 in Genome Data Viewer
Location:
8q31
Exon count:
64
Annotation release Status Assembly Chr Location
106 current Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (87042820..87150701, complement)
104 previous assembly Rnor_5.0 (GCF_000001895.4) 8 NC_005107.3 (86584555..86701809, complement)

Chromosome 8 - NC_005107.4Genomic Context describing neighboring genes Neighboring gene dynein light chain 1-like Neighboring gene similar to 40S ribosomal protein S3a (V-fos transformation effector protein) Neighboring gene uncharacterized LOC103690438 Neighboring gene protein transport protein Sec61 subunit gamma pseudogene

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

Gene Ontology Provided by RGD

Function Evidence Code Pubs
extracellular matrix structural constituent TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
cell adhesion IEA
Inferred from Electronic Annotation
more info
 
collagen fibril organization IEA
Inferred from Electronic Annotation
more info
 
endodermal cell differentiation IEA
Inferred from Electronic Annotation
more info
 
endodermal cell differentiation ISO
Inferred from Sequence Orthology
more info
PubMed 
Component Evidence Code Pubs
collagen type XII trimer IDA
Inferred from Direct Assay
more info
PubMed 
collagen type XII trimer IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
collagen alpha-1(XII) chain; LOW QUALITY PROTEIN: collagen alpha-1(XII) chain
Names
collagen, type XII, alpha 1
procollagen, type XII, alpha 1

NCBI Reference Sequences (RefSeq)

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_005107.4 Reference Rnor_6.0 Primary Assembly

    Range
    87042820..87150701 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017596099.1XP_017451588.1  LOW QUALITY PROTEIN: collagen alpha-1(XII) chain isoform X1

    Related
    ENSRNOP00000075422.1, ENSRNOT00000077071.1

Alternate Rn_Celera

Genomic

  1. AC_000076.1 Alternate Rn_Celera

    Range
    80273757..80389987 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_001060689.6XP_001060689.2  collagen alpha-1(XII) chain isoform X2

    Conserved Domains (6) summary
    pfam01391
    Location:27652892
    Collagen; Collagen triple helix repeat (20 copies)
    smart00060
    Location:14741548
    FN3; Fibronectin type 3 domain
    smart00210
    Location:25212713
    TSPN; Thrombospondin N-terminal -like domains
    cd00063
    Location:724805
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    cd01482
    Location:11981361
    vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...
    pfam00041
    Location:17561836
    fn3; Fibronectin type III domain
  2. XM_008757826.2XP_008756048.1  collagen alpha-1(XII) chain isoform X3

    Conserved Domains (6) summary
    pfam01391
    Location:17061734
    Collagen; Collagen triple helix repeat (20 copies)
    smart00060
    Location:310384
    FN3; Fibronectin type 3 domain
    smart00210
    Location:13571549
    TSPN; Thrombospondin N-terminal -like domains
    cd00063
    Location:9551034
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    cd01482
    Location:34197
    vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...
    pfam00041
    Location:592672
    fn3; Fibronectin type III domain
  3. XM_008757825.2XP_008756047.1  collagen alpha-1(XII) chain isoform X1

    Conserved Domains (6) summary
    pfam01391
    Location:28032930
    Collagen; Collagen triple helix repeat (20 copies)
    smart00060
    Location:15121586
    FN3; Fibronectin type 3 domain
    smart00210
    Location:25592751
    TSPN; Thrombospondin N-terminal -like domains
    cd00063
    Location:762843
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    cd01482
    Location:12361399
    vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...
    pfam00041
    Location:17941874
    fn3; Fibronectin type III domain
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