col1a1b collagen, type I, alpha 1b [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: col1a1bprovided by ZNC
Official Full Name: collagen, type I, alpha 1bprovided by ZNC
Primary source: ZFIN:ZDB-GENE-030131-4400
See related: Ensembl:ENSDARG00000035809 AllianceGenome:ZFIN:ZDB-GENE-030131-4400
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: col1a3; fj59a10; alpha3(I); hm:zeh0348; wu:fa95h05; wu:fd02a10; wu:fj59a10
Summary: Predicted to be an extracellular matrix structural constituent conferring tensile strength. Acts upstream of or within skeletal system development. Predicted to be located in extracellular region. Predicted to be part of collagen trimer. Predicted to be active in collagen-containing extracellular matrix; cytoplasm; and extracellular space. Is expressed in several structures, including corneal epithelium; integument; muscle; osteoblast; and trunk. Used to study osteogenesis imperfecta. Human ortholog(s) of this gene implicated in several diseases, including Ehlers-Danlos syndrome arthrochalasia type 1; aggressive periodontitis; bone disease (multiple); cutaneous leishmaniasis; and dentinogenesis imperfecta. Orthologous to human COL1A1 (collagen type I alpha 1 chain). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs: all
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Genomic context

Location:: chromosome: 12

Exon count:: 51

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	12	NC_007123.7 (3095699..3133481, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	12	NC_007123.6 (3060961..3098764, complement)

Chromosome 12 - NC_007123.7 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: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

A novel de novo mutation in COL1A1 leading to osteogenesis imperfecta confirmed by zebrafish model.
Title: A novel de novo mutation in COL1A1 leading to osteogenesis imperfecta confirmed by zebrafish model.
Even though in adult bone, skin and scales equal amounts of a1(col1a1a) a2(col1a2) and a3(col1a2)chains are present, the presented data suggest a tissue-specific stoichiometry and/or post-translational modification status for collagen type I
Title: Zebrafish Collagen Type I: Molecular and Biochemical Characterization of the Major Structural Protein in Bone and Skin.

Submit: New GeneRIF Correction

General gene information

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Markers

fd02a05.x1 (e-PCR)
- UniSTS:204040

fd02a10.x1 (e-PCR)
- UniSTS:194860

z99209 (e-PCR), detects polymorphism
- UniSTS:238904

fb11f11.x1 (e-PCR)
- UniSTS:202848

fl01f09.x1 (e-PCR)
- UniSTS:201846

fj23f03.y1 (e-PCR)
- UniSTS:198831

AI331969 (e-PCR)
- UniSTS:206789

fj59a10.x1 (e-PCR)
- UniSTS:199627

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables extracellular matrix structural constituent	IEA Inferred from Electronic Annotation more info
enables extracellular matrix structural constituent conferring tensile strength	IBA Inferred from Biological aspect of Ancestor more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
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
acts_upstream_of_or_within skeletal system development	IMP Inferred from Mutant Phenotype more info	PubMed

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 cytoplasm	IBA Inferred from Biological aspect of Ancestor 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, type I, alpha 1b

Names: collagen, type I, alpha 3

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_201478.1 → NP_958886.1 collagen, type I, alpha 1b precursor

See identical proteins and their annotated locations for NP_958886.1

Status: PROVISIONAL

Source sequence(s)

BC058045

UniProtKB/TrEMBL

Q6PEI9

Related

ENSDARP00000003038.8, ENSDART00000015092.9

Conserved Domains (3) summary

pfam01391
Location:433 → 491

Collagen; Collagen triple helix repeat (20 copies)

smart00214
Location:33 → 88

VWC; von Willebrand factor (vWF) type C domain

pfam01410
Location:1215 → 1448

COLFI; Fibrillar collagen C-terminal domain

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

NC_007123.7 Reference GRCz11 Primary Assembly

Range

3095699..3133481 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005155976.5 → XP_005156033.1 collagen, type I, alpha 1b isoform X1

UniProtKB/TrEMBL

A0A8M2B227

Conserved Domains (3) summary

pfam01391
Location:432 → 490

Collagen; Collagen triple helix repeat (20 copies)

smart00214
Location:33 → 88

VWC; von Willebrand factor (vWF) type C domain

pfam01410
Location:1214 → 1447

COLFI; Fibrillar collagen C-terminal domain