Vcan versican [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Vcanprovided by RGD
Official Full Name: versicanprovided by RGD
Primary source: RGD:619940
See related: Ensembl:ENSRNOG00000029212 AllianceGenome:RGD:619940
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Cspg2
Summary: Predicted to enable protein phosphatase binding activity. Involved in axon regeneration. Located in cell surface and perineuronal net. Is active in synapse. Biomarker of myocardial infarction. Human ortholog(s) of this gene implicated in intracranial aneurysm. Orthologous to human VCAN (versican). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Heart (RPKM 115.3), Uterus (RPKM 98.0) and 8 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 2q12

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	2	NC_086020.1 (22497035..22595955, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	2	NC_051337.1 (20761718..20860637, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	2	NC_005101.4 (18490102..18587340, complement)

Chromosome 2 - NC_086020.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The synthesis and secretion of versican isoform V3 by mammalian cells: A role for N-linked glycosylation.
Title: The synthesis and secretion of versican isoform V3 by mammalian cells: A role for N-linked glycosylation.
mRNAs of the versican gene with exon 8beta are predicted to be constitutively degraded by nonsense-mediated RNA decay.
Title: Expression of a novel versican variant in dorsal root ganglia from spared nerve injury rats.
Versican localizes to the nucleus in proliferating mesenchymal cells and suggest role in mitotic spindle organization during cell division.
Title: Versican localizes to the nucleus in proliferating mesenchymal cells.
V3 expression reprograms arterial smooth muscle cells promoting differentiated and anti-inflammatory phenotypes.
Title: Expression of V3 Versican by Rat Arterial Smooth Muscle Cells Promotes Differentiated and Anti-inflammatory Phenotypes.
A neuronal origin for versican V2 was found in C-fiber nociceptors.
Title: Neuronally produced versican V2 renders C-fiber nociceptors IB4 -positive.
These results indicate that V3 expression by arterial smooth muscle cells creates a microenvironment resistant to monocyte adhesion via differentially regulating multiple signaling pathways.
Title: Expression of versican V3 by arterial smooth muscle cells alters tumor growth factor β (TGFβ)-, epidermal growth factor (EGF)-, and nuclear factor κB (NFκB)-dependent signaling pathways, creating a microenvironment that resists monocyte adhesion.
miR-143 specifically binds to the 3'-untranslated region of versican mRNA.
Title: Repression of versican expression by microRNA-143.
Significant increases in versican mRNA occurred at 4 & 14 days after traumatic brain injury, but no changes were seen in neurocan, aggrecan, or phosphacan
Title: Traumatic brain injury results in disparate regions of chondroitin sulfate proteoglycan expression that are temporally limited.
Data show that GDNF hyperalgesia is mediated by PLCgamma, MAPK/ERK, PI3K, CDK5 and Src signaling pathways, is dependent on versican, and inviolves non-peptidergic nociceptors.
Title: GDNF hyperalgesia is mediated by PLCgamma, MAPK/ERK, PI3K, CDK5 and Src family kinase signaling and dependent on the IB4-binding protein versican.
Brevican deposition is elevated in response to progressive gray matter injury, whereas diminished versican expression may be associated with deep cerebral white matter injury.
Title: Versican and brevican are expressed with distinct pathology in neonatal hypoxic-ischemic injury.

Submit: New GeneRIF Correction See all GeneRIFs (22)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Cspg2 (e-PCR), detects polymorphism
- UniSTS:141425

Cspg2 (e-PCR), detects polymorphism
- UniSTS:141427

Cspg2 (e-PCR), detects polymorphism
- UniSTS:141431

Cspg2 (e-PCR), detects polymorphism
- UniSTS:141433

RH134008 (e-PCR)
- UniSTS:217290

RH143691 (e-PCR)
- UniSTS:232937

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables carbohydrate binding	IEA Inferred from Electronic Annotation more info
enables hyaluronic acid binding	IEA Inferred from Electronic Annotation more info
enables low-density lipoprotein particle binding	TAS Traceable Author Statement more info	PubMed
enables protein phosphatase binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in axon regeneration	IEP Inferred from Expression Pattern more info	PubMed
involved_in cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in central nervous system development	IBA Inferred from Biological aspect of Ancestor more info
involved_in glial cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in glial cell migration	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within heart development	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of neuroblast proliferation	IBA Inferred from Biological aspect of Ancestor more info
involved_in skeletal system development	IBA Inferred from Biological aspect of Ancestor more info
involved_in ureteric bud development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
located_in collagen-containing extracellular matrix	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular matrix	ISO Inferred from Sequence Orthology more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
located_in extracellular region	ISO Inferred from Sequence Orthology more info
located_in extracellular region	ISS Inferred from Sequence or Structural Similarity more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in interphotoreceptor matrix	IEA Inferred from Electronic Annotation more info
is_active_in perineuronal net	IBA Inferred from Biological aspect of Ancestor more info
located_in perineuronal net	IDA Inferred from Direct Assay more info	PubMed
located_in photoreceptor outer segment	IEA Inferred from Electronic Annotation more info
is_active_in synapse	EXP Inferred from Experiment more info	PubMed
is_active_in synapse	IBA Inferred from Biological aspect of Ancestor more info
is_active_in synapse	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: versican core protein

Names: GHAP; PG-M; chondroitin sulfate proteoglycan 2 (versican); chondroitin sulfate proteoglycan core protein 2; glial hyaluronate-binding protein; large fibroblast proteoglycan

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_001170558.1 → NP_001164029.1 versican core protein isoform 1 precursor

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1, also referred to as V0).

Source sequence(s)

AF062402, AF072892, AY007691, JAXUCZ010000002

UniProtKB/TrEMBL

D4A8Y6

Related

ENSRNOP00000045935.5, ENSRNOT00000045532.7

Conserved Domains (7) summary

cd05901
Location:36 → 151

Ig_Versican; Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), versican

cd00033
Location:3257 → 3313

CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system

cd03588
Location:3130 → 3253

CLECT_CSPGs; C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core proteins

smart00410
Location:30 → 147

IG_like; Immunoglobulin like

cd00054
Location:3088 → 3124

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

cd03517
Location:150 → 244

Link_domain_CSPGs_modules_1_3; Link_domain_CSPGs_modules_1_3; this extracellular link domain is found in the first and third link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan. In addition, it is found in the first link module of three other CSPGs: ...

cd03520
Location:251 → 346

Link_domain_CSPGs_modules_2_4; Link_domain_CSPGs_modules_2_4; this link domain is found in the second and fourth link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan and, in the second link module of three other CSPGs: versican, neurocan, and brevican. The ...
NM_001170559.1 → NP_001164030.1 versican core protein isoform 4 precursor

See identical proteins and their annotated locations for NP_001164030.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) lacks two alternate in-frame exons, compared to variant 1, resulting in a shorter protein (isoform 4, also referred to as V3), compared to isoform 1.

Source sequence(s)

AF072892, AY007691

UniProtKB/TrEMBL

A6I4N1

Related

ENSRNOP00000062961.3, ENSRNOT00000063821.4

Conserved Domains (7) summary

cd05901
Location:36 → 151

Ig_Versican; Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), versican

cd00033
Location:555 → 611

CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system

smart00410
Location:30 → 147

IG_like; Immunoglobulin like

cd00054
Location:386 → 422

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

cd03517
Location:150 → 244

Link_domain_CSPGs_modules_1_3; Link_domain_CSPGs_modules_1_3; this extracellular link domain is found in the first and third link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan. In addition, it is found in the first link module of three other CSPGs: ...

cd03520
Location:251 → 346

Link_domain_CSPGs_modules_2_4; Link_domain_CSPGs_modules_2_4; this link domain is found in the second and fourth link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan and, in the second link module of three other CSPGs: versican, neurocan, and brevican. The ...

cl02432
Location:428 → 551

CLECT; C-type lectin (CTL)/C-type lectin-like (CTLD) domain
NM_001170560.1 → NP_001164031.1 versican core protein isoform 3 precursor

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks an alternate in-frame exon, compared to variant 1, resulting in a shorter protein (isoform 3, also referred to as V2), compared to isoform 1.

Source sequence(s)

AF062402, AF072892, AY007691, JAXUCZ010000002

UniProtKB/TrEMBL

D3Z9N6

Related

ENSRNOP00000058873.3, ENSRNOT00000067456.5

Conserved Domains (8) summary

cd05901
Location:36 → 151

Ig_Versican; Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), versican

cd00033
Location:1521 → 1577

CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system

cd03588
Location:1394 → 1517

CLECT_CSPGs; C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core proteins

smart00410
Location:30 → 147

IG_like; Immunoglobulin like

cd00054
Location:1352 → 1388

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

cd03517
Location:150 → 244

Link_domain_CSPGs_modules_1_3; Link_domain_CSPGs_modules_1_3; this extracellular link domain is found in the first and third link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan. In addition, it is found in the first link module of three other CSPGs: ...

cd03520
Location:251 → 346

Link_domain_CSPGs_modules_2_4; Link_domain_CSPGs_modules_2_4; this link domain is found in the second and fourth link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan and, in the second link module of three other CSPGs: versican, neurocan, and brevican. The ...

pfam05109
Location:766 → 1193

Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
NM_053663.1 → NP_446115.1 versican core protein isoform 2 precursor

See identical proteins and their annotated locations for NP_446115.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1, resulting in a shorter protein (isoform 2, also referred to as V1), compared to isoform 1.

Source sequence(s)

CH473955

UniProtKB/Swiss-Prot

O08592, O88564, Q9ERB4, Q9R1K4

UniProtKB/TrEMBL

A0A0G2K944, A6I4N2

Related

ENSRNOP00000074854.2, ENSRNOT00000088313.2

Conserved Domains (7) summary

cd05901
Location:36 → 151

Ig_Versican; Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), versican

cd00033
Location:2291 → 2347

CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system

cd03588
Location:2164 → 2287

CLECT_CSPGs; C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core proteins

smart00410
Location:30 → 147

IG_like; Immunoglobulin like

cd00054
Location:2122 → 2158

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

cd03517
Location:150 → 244

Link_domain_CSPGs_modules_1_3; Link_domain_CSPGs_modules_1_3; this extracellular link domain is found in the first and third link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan. In addition, it is found in the first link module of three other CSPGs: ...

cd03520
Location:251 → 346

Link_domain_CSPGs_modules_2_4; Link_domain_CSPGs_modules_2_4; this link domain is found in the second and fourth link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan and, in the second link module of three other CSPGs: versican, neurocan, and brevican. The ...