col1a1a collagen, type I, alpha 1a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: col1a1aprovided by ZNC
Official Full Name: collagen, type I, alpha 1aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-030131-9102
See related: Ensembl:ENSDARG00000012405 AllianceGenome:ZFIN:ZDB-GENE-030131-9102
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: cb21; col1a1; sb:cb21; sb:cb384; alpha1(I); wu:fa99c12; wu:fb02c06
Summary: Predicted to be an extracellular matrix structural constituent. Acts upstream of or within several processes, including bone mineralization involved in bone maturation; fin development; and fin regeneration. Located in cytoplasm. Is expressed in several structures, including head; integument; myotome; pectoral fin; and vertebra. Used to study osteogenesis imperfecta and osteogenesis imperfecta type 3. 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, Apr 2022]
Orthologs: all
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Genomic context

Location:: chromosome: 3

Exon count:: 51

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	3	NC_007114.7 (23221174..23237693)
105	previous assembly	GRCz10 (GCF_000002035.5)	3	NC_007114.6 (23090626..23107145)

Chromosome 3 - NC_007114.7 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.
Spatio-temporal expression and distribution of collagen VI during zebrafish development.
Title: Spatio-temporal expression and distribution of collagen VI during zebrafish development.
ven 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.
heterozygous chihuahua fish have phenotypic similarities to human osteogenesis imperfecta; mapping and molecular characterization of the chihuahua mutation indicates that the defect resides in the gene encoding the collagen I(alpha1) chain
Title: Radiographic analysis of zebrafish skeletal defects.

Submit: New GeneRIF Correction

General gene information

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Markers

fl13f05.x1 (e-PCR)
- UniSTS:201998

fb01h05.y1 (e-PCR)
- UniSTS:189797

fb02c06.x1 (e-PCR)
- UniSTS:202662

AI331097 (e-PCR)
- UniSTS:206802

fd22f07.y1 (e-PCR)
- UniSTS:195288

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
acts_upstream_of_or_within bone mineralization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within bone mineralization involved in bone maturation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within bone remodeling	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within collagen fibril organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within fin development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within fin morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within fin regeneration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within pectoral fin development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of ossification	IMP Inferred from Mutant Phenotype more info	PubMed
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 cytoplasm	IDA Inferred from Direct Assay more info	PubMed
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 1a

Names: chi; chihuahua; collagen, type I, alpha 1; med; microwaved

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_199214.1 → NP_954684.1 collagen, type I, alpha 1a precursor

See identical proteins and their annotated locations for NP_954684.1

Status: PROVISIONAL

Source sequence(s)

AY380817

UniProtKB/TrEMBL

Q6U1J5

Related

ENSDARP00000003177.6, ENSDART00000009393.8

Conserved Domains (3) summary

pfam01391
Location:220 → 279

Collagen; Collagen triple helix repeat (20 copies)

pfam00093
Location:33 → 88

VWC; von Willebrand factor type C domain

pfam01410
Location:1213 → 1446

COLFI; Fibrillar collagen C-terminal domain