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

Summary

Official Symbol: Col12a1provided by RGD
Official Full Name: collagen type XII alpha 1 chainprovided by RGD
Primary source: RGD:2374
See related: EnsemblRapid:ENSRNOG00000058470 AllianceGenome:RGD:2374
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
Summary: Predicted to be an extracellular matrix structural constituent. Predicted to be involved in endodermal cell differentiation. Part of collagen type XII trimer. Human ortholog(s) of this gene implicated in Bethlem myopathy and Ullrich congenital muscular dystrophy 2. Orthologous to human COL12A1 (collagen type XII alpha 1 chain). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Kidney (RPKM 392.9), Adrenal (RPKM 291.6) and 7 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 8q31

Exon count:: 66

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	8	NC_086026.1 (89427834..89545886, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	8	NC_051343.1 (80547592..80665665, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	8	NC_005107.4 (87042820..87150701, complement)

Chromosome 8 - NC_086026.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Circ_001209 aggravates diabetic retinal vascular dysfunction through regulating miR-15b-5p/COL12A1.
Title: Circ_001209 aggravates diabetic retinal vascular dysfunction through regulating miR-15b-5p/COL12A1.

Submit: New GeneRIF Correction

General gene information

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Markers

BE115111 (e-PCR)
- UniSTS:248120

RH94627 (e-PCR)
- UniSTS:119875

RH132431 (e-PCR)
- UniSTS:215714

RH143456 (e-PCR)
- UniSTS:232703

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables extracellular matrix structural constituent	TAS Traceable Author Statement more info	PubMed
enables extracellular matrix structural constituent conferring tensile strength	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in angiogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in endodermal cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in endothelial cell morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in skeletal system development	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of collagen trimer	IBA Inferred from Biological aspect of Ancestor more info
part_of collagen trimer	IEA Inferred from Electronic Annotation more info
part_of collagen type XII trimer	IDA Inferred from Direct Assay more info	PubMed
is_active_in collagen-containing extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular matrix	IEA Inferred from Electronic Annotation more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: collagen alpha-1(XII) chain

Names: collagen, type XII, alpha 1; procollagen, type XII, 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)

NM_013142.1 → NP_037274.1 collagen alpha-1(XII) chain precursor

Status: VALIDATED

Source sequence(s)

JAXUCZ010000008

UniProtKB/TrEMBL

A0A8I5ZRE6

Related

ENSRNOP00000075422.3, ENSRNOT00000077071.3

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086026.1 Reference GRCr8

Range

89427834..89545886 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039082533.2 → XP_038938461.1 collagen alpha-1(XII) chain isoform X1

UniProtKB/TrEMBL

A0A0G2KAJ7, A0A8I5ZRE6

Conserved Domains (6) summary

smart00060
Location:1474 → 1548

FN3; Fibronectin type 3 domain

smart00210
Location:2521 → 2713

TSPN; Thrombospondin N-terminal -like domains

cd00063
Location:724 → 805

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:1198 → 1361

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:1387 → 1465

fn3; Fibronectin type III domain

pfam01391
Location:2766 → 2892

Collagen; Collagen triple helix repeat (20 copies)
XM_039082534.2 → XP_038938462.1 collagen alpha-1(XII) chain isoform X2

UniProtKB/TrEMBL

A6I1L5

Conserved Domains (6) summary

smart00060
Location:310 → 384

FN3; Fibronectin type 3 domain

smart00210
Location:1357 → 1549

TSPN; Thrombospondin N-terminal -like domains

cd00063
Location:955 → 1034

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:34 → 197

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:223 → 301

fn3; Fibronectin type III domain

pfam01391
Location:1706 → 1734

Collagen; Collagen triple helix repeat (20 copies)
XM_063264976.1 → XP_063121046.1 collagen alpha-1(XII) chain isoform X3

UniProtKB/TrEMBL

A6I1L5