Col15a1 collagen type XV alpha 1 chain [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Col15a1provided by RGD
Full Name: collagen type XV alpha 1 chainprovided by RGD
Primary source: RGD:1310820
See related: EnsemblRapid:ENSRNOG00000060381 AllianceGenome:RGD:1310820
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 conferring tensile strength. Predicted to be involved in extracellular matrix organization. Predicted to be part of collagen trimer. Predicted to be active in basement membrane and extracellular space. Orthologous to human COL15A1 (collagen type XV alpha 1 chain). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Heart (RPKM 635.6), Muscle (RPKM 370.5) and 7 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q22

Exon count:: 40

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (66297546..66403172)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (61501963..61607591)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (62840360..62950240)

Chromosome 5 - NC_086023.1 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 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?

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General gene information

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Markers

BI282987 (e-PCR)
- UniSTS:249858

RH138615 (e-PCR)
- UniSTS:220702

RH131575 (e-PCR)
- UniSTS:214858

D5Rat227 (e-PCR), detects polymorphism
- UniSTS:227925

D5Mco4 (e-PCR)
- UniSTS:240063

d5rat10 (e-PCR)
- UniSTS:122071

Gene Ontology Provided by RGD

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

Process	Evidence Code	Pubs
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in basement membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in basement membrane	ISO Inferred from Sequence Orthology more info
part_of collagen trimer	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(XV) chain

Names: collagen alpha-1(XV) chain-like; collagen, type XV, alpha 1; procollagen, type XV

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_001100535.2 → NP_001094005.1 collagen alpha-1(XV) chain precursor

See identical proteins and their annotated locations for NP_001094005.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

UniProtKB/TrEMBL

A0A0G2JV12, A6IJD6, F1LPD0

Related

ENSRNOP00000069309.2, ENSRNOT00000088385.3

Conserved Domains (3) summary

pfam01391
Location:616 → 668

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:40 → 228

TSPN; Thrombospondin N-terminal -like domains

cd00247
Location:1172 → 1338

Endostatin-like; Endostatin-like domain; the angiogenesis inhibitor endostatin is a C-terminal fragment of collagen XV/XVIII, a proteoglycan/collagen found in vessel walls and basement membranes; this domain has a compact globular fold similar to that of C-type lectins; ...