Col28a1 collagen type XXVIII alpha 1 chain [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Col28a1provided by RGD
Official Full Name: collagen type XXVIII alpha 1 chainprovided by RGD
Primary source: RGD:1564680
See related: EnsemblRapid:ENSRNOG00000033618 AllianceGenome:RGD:1564680
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
Also known as: RGD1564680
Summary: Predicted to be an extracellular matrix structural constituent. Predicted to be involved in extracellular matrix organization. Predicted to be located in basement membrane. Predicted to be part of collagen trimer. Predicted to be active in extracellular matrix and extracellular space. Orthologous to human COL28A1 (collagen type XXVIII alpha 1 chain). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Muscle (RPKM 7.2), Adrenal (RPKM 5.8) and 8 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 4q21

Exon count:: 35

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (37036303..37189435, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (36069980..36223128, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (34048074..34198558, complement)

Chromosome 4 - NC_086022.1 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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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
enables serine-type endopeptidase inhibitor activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in collagen fibril organization	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in basement membrane	ISO Inferred from Sequence Orthology more info
part_of collagen type V trimer	IBA Inferred from Biological aspect of Ancestor 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

General protein information

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Preferred Names: collagen alpha-1(XXVIII) chain; collagen type XXVIII alpha 1 chain

Names: collagen, type XXVIII, 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_001431719.1 → NP_001418648.1 collagen type XXVIII alpha 1 chain precursor

Status: VALIDATED

Source sequence(s)

JAXUCZ010000004

UniProtKB/TrEMBL

D3ZN64

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_086022.1 Reference GRCr8

Range

37036303..37189435 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039108604.2 → XP_038964532.1 collagen alpha-1(XXVIII) chain isoform X1

Related

ENSRNOP00000046298.6, ENSRNOT00000045270.7

Conserved Domains (5) summary

cd00109
Location:1086 → 1139

KU; BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.

cd01450
Location:47 → 212

vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

pfam09606
Location:387 → 636

Med15; ARC105 or Med15 subunit of Mediator complex non-fungal

pfam00092
Location:799 → 974

VWA; von Willebrand factor type A domain

pfam01391
Location:263 → 321

Collagen; Collagen triple helix repeat (20 copies)
XM_039108605.1 → XP_038964533.1 collagen alpha-1(XXVIII) chain isoform X2

Conserved Domains (4) summary

cd00109
Location:850 → 903

KU; BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.

pfam09606
Location:151 → 400

Med15; ARC105 or Med15 subunit of Mediator complex non-fungal

pfam00092
Location:563 → 738

VWA; von Willebrand factor type A domain

pfam01391
Location:41 → 84

Collagen; Collagen triple helix repeat (20 copies)