Col4a1 collagen type IV alpha 1 chain [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Col4a1provided by RGD
Official Full Name: collagen type IV alpha 1 chainprovided by RGD
Primary source: RGD:1307148
See related: Ensembl:ENSRNOG00000016281 AllianceGenome:RGD:1307148
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable platelet-derived growth factor binding activity. Predicted to be an extracellular matrix structural constituent conferring tensile strength. Involved in epithelial cell differentiation. Predicted to be located in extracellular region. Predicted to be part of collagen type IV trimer. Predicted to be active in basement membrane and extracellular space. Biomarker of pulmonary hypertension. Human ortholog(s) of this gene implicated in brain small vessel disease 1; myocardial infarction; and retinal arterial tortuosity. Orthologous to human COL4A1 (collagen type IV alpha 1 chain). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Lung (RPKM 831.5), Kidney (RPKM 806.3) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 16q12.5

Exon count:: 52

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	16	NC_086034.1 (84885597..84996482)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	16	NC_051351.1 (78183533..78294412)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	16	NC_005115.4 (83522162..83632153)

Chromosome 16 - NC_086034.1 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?

Hypoxia-induced upregulation of matrix metalloproteinase 9 increases basement membrane degradation by downregulating collagen type IV alpha 1 chain.
Title: Hypoxia-induced upregulation of matrix metalloproteinase 9 increases basement membrane degradation by downregulating collagen type IV alpha 1 chain.
glomerular collagen deposition and increased lipocalin-2 expression were the early signs of kidney injury.
Title: Glomerular Collagen Deposition and Lipocalin-2 Expression Are Early Signs of Renal Injury in Prediabetic Obese Rats.
PTH pretreatment prevented TGF-beta1 and high glucose-induced Smad2/3 phosphorylation and consequent upregulation of fibronectin and type IV collagen within 4 h.
Title: Parathyroid hormone inhibits TGF-β/Smad signaling and extracellular matrix proteins upregulation in rat mesangial cells.
The metabolism of individual alpha(IV) chains of Glomerular Basement Membrane is differentially regulated in diabetic conditions.
Title: Regulation of type IV collagen alpha chains of glomerular epithelial cells in diabetic conditions.

Submit: New GeneRIF Correction

General gene information

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Markers

RH129454 (e-PCR)
- UniSTS:212760

Col4a1 (e-PCR), detects polymorphism
- UniSTS:141370

Col4a1 (e-PCR), detects polymorphism
- UniSTS:496710

D0Nds29 (e-PCR), detects polymorphism
- UniSTS:141461

RH128563 (e-PCR)
- UniSTS:211871

D13S1449 (e-PCR)
- UniSTS:82630

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables extracellular matrix structural constituent	ISO Inferred from Sequence Orthology more info
enables extracellular matrix structural constituent conferring tensile strength	IBA Inferred from Biological aspect of Ancestor more info
enables extracellular matrix structural constituent conferring tensile strength	ISO Inferred from Sequence Orthology more info
enables platelet-derived growth factor binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in basement membrane organization	ISO Inferred from Sequence Orthology more info
involved_in blood vessel morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in brain development	ISO Inferred from Sequence Orthology more info
involved_in branching involved in blood vessel morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cellular response to amino acid stimulus	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within collagen-activated tyrosine kinase receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in epithelial cell differentiation	IEP Inferred from Expression Pattern more info	PubMed
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within neuromuscular junction development	ISO Inferred from Sequence Orthology more info
involved_in renal tubule morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in retinal blood vessel morphogenesis	ISO Inferred from Sequence Orthology 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 type IV trimer	ISO Inferred from Sequence Orthology more info
located_in extracellular region	TAS Traceable Author Statement more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: collagen alpha-1(IV) chain

Names: alpha 1 type IV collagen; collagen, type IV, alpha 1; procollagen, type IV, 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_001135009.1 → NP_001128481.1 collagen alpha-1(IV) chain precursor

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000016

UniProtKB/TrEMBL

F1MA59

Related

ENSRNOP00000054197.2, ENSRNOT00000057386.3

Conserved Domains (2) summary

pfam01391
Location:1088 → 1147

Collagen; Collagen triple helix repeat (20 copies)

pfam01413
Location:1556 → 1666

C4; C-terminal tandem repeated domain in type 4 procollagen