col9a1b collagen, type IX, alpha 1b [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: col9a1bprovided by ZNC
Official Full Name: collagen, type IX, alpha 1bprovided by ZNC
Primary source: ZFIN:ZDB-GENE-040426-2410
See related: Ensembl:ENSDARG00000031483 AllianceGenome:ZFIN:ZDB-GENE-040426-2410
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: cb339; col9a1; sb:cb339; zgc:85892; wu:fa12a12; wu:fa12d02; wu:fc22c08; wu:fc38d08
Summary: Predicted to enable heparin binding activity. Predicted to be an extracellular matrix structural constituent conferring tensile strength. Predicted to be involved in extracellular matrix organization. Predicted to be part of collagen type XI trimer. Predicted to be active in collagen-containing extracellular matrix and extracellular space. Is expressed in several structures, including bone tissue; hypochord; mesenchyme derived from head mesoderm; notochord; and sensory system. Human ortholog(s) of this gene implicated in Stickler syndrome; multiple epiphyseal dysplasia 6; and osteochondrodysplasia. Orthologous to human COL9A1 (collagen type IX alpha 1 chain). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: all
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Genomic context

Location:: chromosome: 13

Exon count:: 32

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	13	NC_007124.7 (39119464..39159807, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	13	NC_007124.6 (38993574..39033917, complement)

Chromosome 13 - NC_007124.7 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 mutation of collagen IXalpha1 causes a significant reduction in the size and dramatic structural defects in collagen II-rich extracellular matrices of both embryonic finfolds and adult fins.
Title: Collagen IX is required for the integrity of collagen II fibrils and the regulation of vascular plexus formation in zebrafish caudal fins.

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General gene information

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Markers

fc02c07.x1 (e-PCR)
- UniSTS:192063

fc22c08.x1 (e-PCR)
- UniSTS:193087

fc02c07.x1 (e-PCR)
- UniSTS:192064

fa12d02.s1 (e-PCR)
- UniSTS:202341

AA494751 (e-PCR)
- UniSTS:206974

aa494751 (e-PCR)
- UniSTS:186808

fc38d08.x1 (e-PCR)
- UniSTS:188090

aa494768 (e-PCR)
- UniSTS:186812

Gene Ontology Provided by ZFIN

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

Process	Evidence Code	Pubs
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of collagen trimer	IEA Inferred from Electronic Annotation more info
part_of collagen type XI 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, type IX, alpha 1b

Names: collagen, type IX, 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_213264.2 → NP_998429.2 collagen, type IX, alpha 1b precursor

Status: VALIDATED

Source sequence(s)

BC068419, BX322620, CD777796

UniProtKB/TrEMBL

A0A8M1PPG5, B8A4T6

Related

ENSDARP00000121882.1, ENSDART00000131508.3

Conserved Domains (1) summary

pfam01391
Location:237 → 294

Collagen; Collagen triple helix repeat (20 copies)