Col17a1 collagen type XVII alpha 1 chain [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Col17a1provided by RGD
Official Full Name: collagen type XVII alpha 1 chainprovided by RGD
Primary source: RGD:1311130
See related: EnsemblRapid:ENSRNOG00000012110 AllianceGenome:RGD:1311130
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 enable heparin binding activity. Predicted to be an extracellular matrix structural constituent conferring tensile strength. Predicted to be involved in extracellular matrix organization and hemidesmosome assembly. Predicted to be located in membrane. Predicted to be part of collagen trimer. Predicted to be active in collagen-containing extracellular matrix; extracellular space; and hemidesmosome. Human ortholog(s) of this gene implicated in epithelial recurrent erosion dystrophy and junctional epidermolysis bullosa. Orthologous to human COL17A1 (collagen type XVII alpha 1 chain). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Thymus (RPKM 71.6), Kidney (RPKM 42.5) and 5 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q54

Exon count:: 54

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (256472648..256518857, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (246530589..246577559, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (267416681..267465049, complement)

Chromosome 1 - NC_086019.1 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?

Junctional Epidermolysis Bullosa in Sprague Dawley Rats Caused by a Frameshift Mutation of Col17a1 Gene.
Title: Junctional Epidermolysis Bullosa in Sprague Dawley Rats Caused by a Frameshift Mutation of Col17a1 Gene.

Submit: New GeneRIF Correction

General gene information

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Markers

RH133997 (e-PCR)
- UniSTS:217279

RH143451 (e-PCR)
- UniSTS:232698

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
enables heparin binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in biological_process	ND No biological Data available more info
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in hemidesmosome assembly	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of collagen trimer	IEA Inferred from Electronic Annotation more info
is_active_in collagen-containing extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
is_active_in hemidesmosome	IBA Inferred from Biological aspect of Ancestor more info
located_in hemidesmosome	ISO Inferred from Sequence Orthology more info
located_in membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: collagen alpha-1(XVII) chain

Names: collagen, type XVII, alpha 1; procollagen, type XVII, 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_001415840.1 → NP_001402769.1 collagen alpha-1(XVII) chain isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000001

UniProtKB/TrEMBL

A0A0G2K449

Related

ENSRNOP00000072907.1, ENSRNOT00000084851.3
NM_001415841.1 → NP_001402770.1 collagen alpha-1(XVII) chain isoform 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000001

UniProtKB/TrEMBL

D3ZSH7

Related

ENSRNOP00000016645.6, ENSRNOT00000016645.8

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_086019.1 Reference GRCr8

Range

256472648..256518857 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001106366.1: Suppressed sequence

Description

NM_001106366.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.