col15a1a collagen, type XV, alpha 1a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: col15a1aprovided by ZNC
Official Full Name: collagen, type XV, alpha 1aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-080918-1
See related: AllianceGenome:ZFIN:ZDB-GENE-080918-1
Gene type: protein coding
RefSeq status: MODEL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: cb605; col15a1; col115a1; col15a1l; sb:cb605
Summary: Acts upstream of or within notochord cell differentiation and skeletal muscle tissue development. Predicted to be part of collagen trimer. Is expressed in several structures, including axial mesoderm; central nervous system; chordo neural hinge; integument; and pectoral fin. Orthologous to human COL15A1 (collagen type XV alpha 1 chain). [provided by Alliance of Genome Resources, Dec 2024]
Annotation information: Annotation category: partial on reference assembly
Orthologs: all
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Genomic context

Location:: chromosome: 24

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	24	NC_007135.7 (46468..59903)
105	previous assembly	GRCz10 (GCF_000002035.5)	24	NC_007135.6 (56926..69612, complement)

Chromosome 24 - NC_007135.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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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?

Collagen XV is required for notochord differentiation and muscle development in the zebrafish embryo and it interplays with Shh signalling.
Title: Collagen XV, a novel factor in zebrafish notochord differentiation and muscle development.

Submit: New GeneRIF Correction

General gene information

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Markers

Z9851 (e-PCR)
- UniSTS:18277

Z8382 (e-PCR)
- UniSTS:19354

G39850 (e-PCR)
- UniSTS:2997

Homology

NCBI Orthologs

Orthologs from OrthoDB

Gene Ontology Provided by ZFIN

Process	Evidence Code	Pubs
acts_upstream_of_or_within notochord cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within skeletal muscle tissue development	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of collagen trimer	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: collagen alpha-1(XVIII) chain

Names: collagen XV alpha 1; collagen, type XV, alpha 1, like

NCBI Reference Sequences (RefSeq)

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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_007135.7 Reference GRCz11 Primary Assembly

Range

46468..59903

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_068217290.1 → XP_068073391.1 collagen alpha-1(XVIII) chain

UniProtKB/TrEMBL

A0A8M9P6B2

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001080091.1: Suppressed sequence

Description

NM_001080091.1: This RefSeq was suppressed temporarily based on the calculation that the encoded protein was shorter than proteins from the putative ortholog from human: COL18A1 (GeneID:80781).