col2a1b collagen, type II, alpha 1b [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: col2a1bprovided by ZNC
Official Full Name: collagen, type II, alpha 1bprovided by ZNC
Primary source: ZFIN:ZDB-GENE-050302-9
See related: Ensembl:ENSDARG00000011407 AllianceGenome:ZFIN:ZDB-GENE-050302-9
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: im:6788778
Summary: Predicted to be an extracellular matrix structural constituent. Acts upstream of or within fin morphogenesis. Predicted to be located in extracellular region. Predicted to be part of collagen trimer. Predicted to be active in extracellular matrix and extracellular space. Is expressed in several structures, including axis; central nervous system; fin; head; and notochord. Human ortholog(s) of this gene implicated in Stickler syndrome (multiple); bone disease (multiple); cleft palate; eye disease (multiple); and multiple epiphyseal dysplasia with myopia and deafness. Orthologous to human COL2A1 (collagen type II alpha 1 chain). [provided by Alliance of Genome Resources, Apr 2022]
Annotation information: Annotation category: partial on reference assembly
Orthologs: all
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Genomic context

Location:: chromosome: 11

Exon count:: 50

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	11	NC_007122.7 (32007..58763, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	11	NC_007122.6 (32007..110428, complement)

Chromosome 11 - NC_007122.7 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?

Data show that both col1a1a and col2a1b were found in actinotrichia forming cells.
Title: Actinotrichia collagens and their role in fin formation.

Submit: New GeneRIF Correction

General gene information

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Markers

G45308 (e-PCR)
- UniSTS:106110

G45423 (e-PCR)
- UniSTS:106225

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 collagen fibril 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
involved_in notochord development	IBA Inferred from Biological aspect of Ancestor more info
involved_in skeletal system development	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of collagen trimer	IBA Inferred from Biological aspect of Ancestor more info
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
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 II, alpha 1b

Names: zmp:0000000538

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_001281478.1 → NP_001268407.1 collagen, type II, alpha 1b precursor

See identical proteins and their annotated locations for NP_001268407.1

Status: PROVISIONAL

Source sequence(s)

HF563617

UniProtKB/TrEMBL

L0S5L0

Related

ENSDARP00000139349.3, ENSDART00000159169.3

Conserved Domains (3) summary

pfam01391
Location:498 → 557

Collagen; Collagen triple helix repeat (20 copies)

pfam00093
Location:39 → 94

VWC; von Willebrand factor type C domain

pfam01410
Location:1260 → 1492

COLFI; Fibrillar collagen C-terminal domain