col11a2 collagen, type XI, alpha 2 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: col11a2provided by ZNC
Official Full Name: collagen, type XI, alpha 2provided by ZNC
Primary source: ZFIN:ZDB-GENE-000208-23
See related: Ensembl:ENSDARG00000012422 AllianceGenome:ZFIN:ZDB-GENE-000208-23
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: col11a1
Summary: Predicted to be an extracellular matrix structural constituent. Acts upstream of or within cartilage 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 immature eye; notochord; pectoral fin bud; skeletal element; and trabecular layer. Human ortholog(s) of this gene implicated in cleft palate; nonsyndromic deafness (multiple); and osteochondrodysplasia (multiple). Orthologous to human COL11A2 (collagen type XI alpha 2 chain). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: all
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Genomic context

Location:: chromosome: 19

Exon count:: 68

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	19	NC_007130.7 (7179742..7225228, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	19	NC_007130.6 (7260817..7306303, complement)

Chromosome 19 - NC_007130.7 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?

In col11a2 mutants, type II collagen is made but is prematurely degraded in maturing cartilage and ectopically expressed in the joint. These changes are correlated with increased stiffness of both bone and cartilage.
Title: The mechanical impact of col11a2 loss on joints; col11a2 mutant zebrafish show changes to joint development and function, which leads to early-onset osteoarthritis.
Data add support to the concept that collagen XI plays an important role in cartilage morphogenesis that likely extends beyond its contribution to fibrillogenesis process.
Title: Craniofacial cartilage morphogenesis requires zebrafish col11a1 activity.

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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 cartilage development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cartilage development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cartilage morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in collagen fibril organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in sensory perception of sound	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 alpha-2(XI) chain

Names: collagen XI 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_001079992.2 → NP_001073461.2 collagen alpha-2(XI) chain isoform 1 precursor

Status: VALIDATED

Source sequence(s)

FP017221, FP085392

UniProtKB/TrEMBL

A0A8M1NB54, F6NLZ6

Related

ENSDARP00000095569.4, ENSDART00000104799.5

Conserved Domains (3) summary

pfam01391
Location:573 → 630

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:29 → 218

TSPN; Thrombospondin N-terminal -like domains

pfam01410
Location:1466 → 1693

COLFI; Fibrillar collagen C-terminal domain
NM_001328265.1 → NP_001315194.1 collagen alpha-2(XI) chain isoform 2 precursor

Status: VALIDATED

Source sequence(s)

FP017221, FP085392

UniProtKB/TrEMBL

A0A8M1P8Y1, I3ISS1

Related

ENSDARP00000125963.1, ENSDART00000151138.3

Conserved Domains (3) summary

pfam01391
Location:681 → 738

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:29 → 218

TSPN; Thrombospondin N-terminal -like domains

pfam01410
Location:1574 → 1801

COLFI; Fibrillar collagen C-terminal domain

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCz11 Primary Assembly

Genomic

NC_007130.7 Reference GRCz11 Primary Assembly

Range

7179742..7225228 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005159448.4 → XP_005159505.1 collagen alpha-2(XI) chain isoform X5

UniProtKB/TrEMBL

A0A8M2B6B8

Conserved Domains (3) summary

pfam01391
Location:642 → 699

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:29 → 218

TSPN; Thrombospondin N-terminal -like domains

pfam01410
Location:1535 → 1762

COLFI; Fibrillar collagen C-terminal domain
XM_017352253.2 → XP_017207742.1 collagen alpha-2(XI) chain isoform X4

UniProtKB/TrEMBL

A0A8M1P8Y1, I3ISS1

Conserved Domains (3) summary

pfam01391
Location:681 → 738

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:29 → 218

TSPN; Thrombospondin N-terminal -like domains

pfam01410
Location:1574 → 1801

COLFI; Fibrillar collagen C-terminal domain
XM_005159450.4 → XP_005159507.1 collagen alpha-2(XI) chain isoform X6

UniProtKB/TrEMBL

A0A8M2B659, F1R5X4

Related

ENSDARP00000119303.2, ENSDART00000133179.4

Conserved Domains (3) summary

pfam01391
Location:599 → 656

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:29 → 218

TSPN; Thrombospondin N-terminal -like domains

pfam01410
Location:1492 → 1719

COLFI; Fibrillar collagen C-terminal domain
XM_009294049.3 → XP_009292324.1 collagen alpha-2(XI) chain isoform X7

UniProtKB/TrEMBL

A0A8M1NB54, F6NLZ6

Conserved Domains (3) summary

pfam01391
Location:573 → 630

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:29 → 218

TSPN; Thrombospondin N-terminal -like domains

pfam01410
Location:1466 → 1693

COLFI; Fibrillar collagen C-terminal domain
XM_005159443.3 → XP_005159500.1 collagen alpha-2(XI) chain isoform X1

See identical proteins and their annotated locations for XP_005159500.1

UniProtKB/TrEMBL

A0A8M2B5Z5

Conserved Domains (3) summary

pfam01391
Location:899 → 956

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:29 → 218

TSPN; Thrombospondin N-terminal -like domains

pfam01410
Location:1792 → 2019

COLFI; Fibrillar collagen C-terminal domain
XM_005159442.4 → XP_005159499.1 collagen alpha-2(XI) chain isoform X1

See identical proteins and their annotated locations for XP_005159499.1

UniProtKB/TrEMBL

A0A8M2B5Z5

Conserved Domains (3) summary

pfam01391
Location:899 → 956

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:29 → 218

TSPN; Thrombospondin N-terminal -like domains

pfam01410
Location:1792 → 2019

COLFI; Fibrillar collagen C-terminal domain
XM_005159445.4 → XP_005159502.1 collagen alpha-2(XI) chain isoform X3

UniProtKB/TrEMBL

A0A8M2B6G1

Conserved Domains (3) summary

pfam01391
Location:782 → 839

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:29 → 218

TSPN; Thrombospondin N-terminal -like domains

pfam01410
Location:1675 → 1902

COLFI; Fibrillar collagen C-terminal domain
XM_017352252.2 → XP_017207741.1 collagen alpha-2(XI) chain isoform X2

UniProtKB/TrEMBL

A0A8M6Z300