hapln1a hyaluronan and proteoglycan link protein 1a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: hapln1aprovided by ZNC
Official Full Name: hyaluronan and proteoglycan link protein 1aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-050302-175
See related: Ensembl:ENSDARG00000089769 AllianceGenome:ZFIN:ZDB-GENE-050302-175
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: crtl1; hapln1; fc26f11; fc37g04; fc50e12; fc55h01; wu:fc26f11; wu:fc37g04; wu:fc50e12; wu:fc55h01
Summary: Predicted to enable hyaluronic acid binding activity. Acts upstream of or within extracellular matrix organization involved in endocardium development and fin regeneration. Predicted to be located in plasma membrane. Predicted to be active in extracellular space; perineuronal net; and synapse. Is expressed in several structures, including adaxial cell; cardiovascular system; hypochord; pharyngeal arch; and rhombomere. Orthologous to human HAPLN1 (hyaluronan and proteoglycan link protein 1). [provided by Alliance of Genome Resources, Jan 2025]
Orthologs: all
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Genomic context

Location:: chromosome: 5

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	5	NC_007116.7 (46490621..46505702, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	5	NC_007116.6 (45890468..45905549, complement)

Chromosome 5 - NC_007116.7 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?

hapln1 Defines an Epicardial Cell Subpopulation Required for Cardiomyocyte Expansion During Heart Morphogenesis and Regeneration.
Title: hapln1 Defines an Epicardial Cell Subpopulation Required for Cardiomyocyte Expansion During Heart Morphogenesis and Regeneration.
Asymmetric Hapln1a drives regionalized cardiac ECM expansion and promotes heart morphogenesis in zebrafish development.
Title: Asymmetric Hapln1a drives regionalized cardiac ECM expansion and promotes heart morphogenesis in zebrafish development.
Hapln1a-ECM stabilizes the secreted growth factor Semaphorin3d (Sema3d), which has been independently shown to mediate Cx43 dependent phenotypes during regeneration.
Title: Cx43-Dependent Skeletal Phenotypes Are Mediated by Interactions between the Hapln1a-ECM and Sema3d during Fin Regeneration.
Hapln1a has a critical role in connexin43-dependent growth and patterning in the regenerating fin skeleton
Title: Hapln1a is required for connexin43-dependent growth and patterning in the regenerating fin skeleton.
The cloning and characterization of crtl1 and its expression during embryogenesis are reported.
Title: Molecular cloning and developmental expression of a hyaluronan and proteoglycan link protein gene, crtl1/hapln1, in zebrafish.

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General gene information

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Markers

fb17d05.y1 (e-PCR)
- UniSTS:190213

fc26f11.x1 (e-PCR)
- UniSTS:193322

fc26f11.x1 (e-PCR)
- UniSTS:193323

fc50e12 (e-PCR)
- UniSTS:189272

fc37g04.x1 (e-PCR)
- UniSTS:188071

fc55h01 (e-PCR)
- UniSTS:189369

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables hyaluronic acid binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in central nervous system development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within extracellular matrix organization involved in endocardium development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within fin regeneration	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within fin regeneration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in skeletal system development	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	IEA Inferred from Electronic Annotation more info
is_active_in perineuronal net	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
is_active_in synapse	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: hyaluronan and proteoglycan link protein 1a

Names: hyaluronan proteoglycan link protein 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_001007790.2 → NP_001007791.2 hyaluronan and proteoglycan link protein 1a isoform 1 precursor

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

BX465199, EH448450

UniProtKB/TrEMBL

A0A8M1N3M4, Q1LXE1

Related

ENSDARP00000109404.2, ENSDART00000122966.4

Conserved Domains (4) summary

cd05877
Location:33 → 132

Ig_LP_like; Immunoglobulin (Ig)-like domain of human cartilage link protein (LP)

smart00410
Location:29 → 130

IG_like; Immunoglobulin like

cd03518
Location:141 → 235

Link_domain_HAPLN_module_1; Link_domain_HAPLN_module_1; this link domain is found in the first link module of proteins similar to the vertebrate HAPLN (hyaluronan/HA and proteoglycan binding link) protein family which includes cartilage link protein. The link domain is a HA-binding ...

cd03519
Location:241 → 332

Link_domain_HAPLN_module_2; Link_domain_HAPLN_module_2; this link domain is found in the second link module of proteins similar to the vertebrate HAPLN (hyaluronan/HA and proteoglycan binding link) protein family which includes cartilage link protein. The link domain is a ...
NM_001313730.1 → NP_001300659.1 hyaluronan and proteoglycan link protein 1a isoform 2 precursor

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. It encodes isoform 2, which is shorter than isoform 1.

Source sequence(s)

BX465199, EH448450

UniProtKB/TrEMBL

A0A8M1P2I9, B3DIH3

Related

ENSDARP00000136494.1, ENSDART00000166907.2

Conserved Domains (4) summary

cd05877
Location:33 → 134

Ig_LP_like; Immunoglobulin (Ig)-like domain of human cartilage link protein (LP)

smart00410
Location:29 → 130

IG_like; Immunoglobulin like

cd03518
Location:133 → 227

Link_domain_HAPLN_module_1; Link_domain_HAPLN_module_1; this link domain is found in the first link module of proteins similar to the vertebrate HAPLN (hyaluronan/HA and proteoglycan binding link) protein family which includes cartilage link protein. The link domain is a HA-binding ...

cd03519
Location:233 → 324

Link_domain_HAPLN_module_2; Link_domain_HAPLN_module_2; this link domain is found in the second link module of proteins similar to the vertebrate HAPLN (hyaluronan/HA and proteoglycan binding link) protein family which includes cartilage link protein. The link domain is a ...