col11a1b collagen, type XI, alpha 1b [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: col11a1bprovided by ZNC
Official Full Name: collagen, type XI, alpha 1bprovided by ZNC
Primary source: ZFIN:ZDB-GENE-070912-607
See related: Ensembl:ENSDARG00000009014 AllianceGenome:ZFIN:ZDB-GENE-070912-607
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: si:dkey-87l9.2
Summary: Predicted to enable heparin binding activity. Predicted to be an extracellular matrix structural constituent conferring tensile strength. Acts upstream of or within notochord development. Predicted to be located in extracellular region. 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 axis; cranial cartilage; nervous system; notochord; and otic vesicle. Human ortholog(s) of this gene implicated in Marshall syndrome; Stickler syndrome 2; autosomal dominant nonsyndromic deafness; and fibrochondrogenesis 1. Orthologous to human COL11A1 (collagen type XI alpha 1 chain). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs: all
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Genomic context

Location:: chromosome: 2

Exon count:: 67

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	2	NC_007113.7 (15389941..15562886, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	2	NC_007113.6 (15720603..15894296, complement)

Chromosome 2 - NC_007113.7 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 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?

Submit: New GeneRIF Correction

General gene information

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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 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
acts_upstream_of_or_within notochord development	IMP Inferred from Mutant Phenotype more info	PubMed

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
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 XI, alpha 1b

Names: novel collagen protein

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_001184954.1 → NP_001171883.1 collagen, type XI, alpha 1b precursor

See identical proteins and their annotated locations for NP_001171883.1

Status: PROVISIONAL

Source sequence(s)

GQ485665

UniProtKB/TrEMBL

A0A8M1NUN5, D6MUD3

Related

ENSDARP00000049588.6, ENSDART00000049589.9

Conserved Domains (3) summary

pfam01391
Location:628 → 686

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:43 → 233

TSPN; Thrombospondin N-terminal -like domains

pfam01410
Location:1587 → 1813

COLFI; Fibrillar collagen C-terminal domain