col12a1b collagen, type XII, alpha 1b [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: col12a1bprovided by ZNC
Official Full Name: collagen, type XII, alpha 1bprovided by ZNC
Primary source: ZFIN:ZDB-GENE-120215-116
See related: Ensembl:ENSDARG00000019601 AllianceGenome:ZFIN:ZDB-GENE-120215-116
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: col12a1; si:ch211-106k22.1
Summary: Acts upstream of or within regeneration and regulation of axon regeneration. Predicted to be located in extracellular region. Predicted to be part of collagen trimer. Predicted to be active in collagen-containing extracellular matrix and extracellular space. Human ortholog(s) of this gene implicated in Ullrich congenital muscular dystrophy. Orthologous to human COL12A1 (collagen type XII alpha 1 chain). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: all
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Genomic context

Location:: chromosome: 20

Exon count:: 79

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	20	NC_007131.7 (49450996..49683978, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	20	NC_007131.6 (49647149..49869321, complement)

Chromosome 20 - NC_007131.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

Wnt/beta-catenin signaling induces expression of col12a1a/b and deposition of Collagen XII, which is necessary for axons to actively navigate the non-neural lesion site environment.
Title: Wnt signaling controls pro-regenerative Collagen XII in functional spinal cord regeneration in zebrafish.

Submit: New GeneRIF Correction

General gene information

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Markers

G45965 (e-PCR)
- UniSTS:106767

z44227 (e-PCR), detects polymorphism
- UniSTS:238496

fk68d06.x1 (e-PCR)
- UniSTS:201414

Homology

NCBI Orthologs

Orthologs from OrthoDB

Gene Ontology Provided by ZFIN

Process	Evidence Code	Pubs
involved_in endodermal cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regeneration	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within regulation of axon regeneration	IGI Inferred from Genetic Interaction more info	PubMed

Component	Evidence Code	Pubs
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

General protein information

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Preferred Names: collagen alpha-1(XII) chain; collagen, type XII, alpha 1b

Names: collagen, type XII, alpha 1

NCBI Reference Sequences (RefSeq)

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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_007131.7 Reference GRCz11 Primary Assembly

Range

49450996..49683978 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017352646.2 → XP_017208135.2 collagen alpha-1(XII) chain isoform X3

UniProtKB/TrEMBL

A0A8M6Z3F3

Related

ENSDARP00000009356.7, ENSDART00000025926.9

Conserved Domains (7) summary

pfam01391
Location:3351 → 3401

Collagen; Collagen triple helix repeat (20 copies)

smart00060
Location:1568 → 1646

FN3; Fibronectin type 3 domain

smart00210
Location:3062 → 3256

TSPN; Thrombospondin N-terminal -like domains

cd00063
Location:2658 → 2735

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cd01482
Location:1199 → 1362

vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...

pfam00041
Location:1751 → 1829

fn3; Fibronectin type III domain

cl21522
Location:1478 → 1559

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
XM_017352645.2 → XP_017208134.2 collagen alpha-1(XII) chain isoform X2

UniProtKB/TrEMBL

A0A8M6YWS8

Conserved Domains (7) summary

pfam01391
Location:3355 → 3405

Collagen; Collagen triple helix repeat (20 copies)

smart00060
Location:1568 → 1646

FN3; Fibronectin type 3 domain

smart00210
Location:3066 → 3260

TSPN; Thrombospondin N-terminal -like domains

cd00063
Location:2662 → 2739

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cd01482
Location:1199 → 1362

vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...

pfam00041
Location:1758 → 1836

fn3; Fibronectin type III domain

cl21522
Location:1478 → 1559

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
XM_017352648.2 → XP_017208137.2 collagen alpha-1(XII) chain isoform X5

UniProtKB/TrEMBL

A0A8M6Z2U2

Conserved Domains (7) summary

pfam01391
Location:3177 → 3227

Collagen; Collagen triple helix repeat (20 copies)

smart00060
Location:1568 → 1646

FN3; Fibronectin type 3 domain

smart00210
Location:2888 → 3082

TSPN; Thrombospondin N-terminal -like domains

cd00063
Location:2484 → 2561

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cd01482
Location:1199 → 1362

vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...

pfam00041
Location:1758 → 1836

fn3; Fibronectin type III domain

cl21522
Location:1478 → 1559

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
XM_017352644.2 → XP_017208133.2 collagen alpha-1(XII) chain isoform X1

UniProtKB/TrEMBL

A0A8M6YUY1

Conserved Domains (7) summary

pfam01391
Location:3358 → 3408

Collagen; Collagen triple helix repeat (20 copies)

smart00060
Location:1568 → 1646

FN3; Fibronectin type 3 domain

smart00210
Location:3069 → 3263

TSPN; Thrombospondin N-terminal -like domains

cd00063
Location:2665 → 2742

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cd01482
Location:1199 → 1362

vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...

pfam00041
Location:1758 → 1836

fn3; Fibronectin type III domain

cl21522
Location:1478 → 1559

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
XM_021468712.1 → XP_021324387.1 collagen alpha-1(XII) chain isoform X6

UniProtKB/TrEMBL

A0A8M9P340

Conserved Domains (7) summary

pfam01391
Location:2192 → 2242

Collagen; Collagen triple helix repeat (20 copies)

smart00060
Location:402 → 480

FN3; Fibronectin type 3 domain

smart00210
Location:1903 → 2097

TSPN; Thrombospondin N-terminal -like domains

cd00063
Location:1499 → 1576

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cd01482
Location:33 → 196

vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...

pfam00041
Location:592 → 670

fn3; Fibronectin type III domain

cl21522
Location:312 → 393

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
XM_017352647.2 → XP_017208136.2 collagen alpha-1(XII) chain isoform X4

UniProtKB/TrEMBL

A0A8M6YUB5

Conserved Domains (7) summary

pfam01391
Location:3358 → 3408

Collagen; Collagen triple helix repeat (20 copies)

smart00060
Location:1568 → 1646

FN3; Fibronectin type 3 domain

smart00210
Location:3069 → 3263

TSPN; Thrombospondin N-terminal -like domains

cd00063
Location:2665 → 2742

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cd01482
Location:1199 → 1362

vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...

pfam00041
Location:1758 → 1836

fn3; Fibronectin type III domain

cl21522
Location:1478 → 1559

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...