Sparcl1 SPARC like 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Sparcl1provided by RGD
Official Full Name: SPARC like 1provided by RGD
Primary source: RGD:2531
See related: Ensembl:ENSRNOG00000015093 AllianceGenome:RGD:2531
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Sc1; Ecm2
Summary: Predicted to enable calcium ion binding activity; collagen binding activity; and extracellular matrix binding activity. Involved in regulation of synapse organization. Located in synapse. Is active in extracellular matrix of synaptic cleft and glutamatergic synapse. Orthologous to human SPARCL1 (SPARC like 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Brain (RPKM 2934.0), Heart (RPKM 1217.6) and 4 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 14p22

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	14	NC_086032.1 (5937484..5968532)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	14	NC_051349.1 (5632816..5663866)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	14	NC_005113.4 (6994261..7025309)

Chromosome 14 - NC_086032.1 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: 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?

microRNA-105-5p protects against chondrocyte injury, extracellular matrix degradation, and osteoarthritis progression by targeting SPARCL1.
Title: microRNA-105-5p protects against chondrocyte injury, extracellular matrix degradation, and osteoarthritis progression by targeting SPARCL1.
Upregulation of Hevin contributes to postoperative pain hypersensitivity by inducing neurexin1beta/neuroligin1-mediated synaptic targeting of GluA1-containing AMPA receptors in rat dorsal horn.
Title: Upregulation of Hevin contributes to postoperative pain hypersensitivity by inducing neurexin1β/neuroligin1-mediated synaptic targeting of GluA1-containing AMPA receptors in rat dorsal horn.
SC1 appears to characterize damaged striatal white matter damage after multiple types of injury
Title: SC1/hevin identifies early white matter injury after ischemia and intracerebral hemorrhage in young and aged rats.
This study discovered that hevin expression in an early responding "starburst" cell immediately adjacent to the ischemic lesion in both young adult and aged rats.
Title: SC1/hevin and reactive gliosis after transient ischemic stroke in young and aged rats.
These findings indicate that the pattern of SC1 localization coincides with synaptogenesis during rat postnatal development.
Title: Localization of the extracellular matrix protein SC1 coincides with synaptogenesis during rat postnatal development.

Submit: New GeneRIF Correction

General gene information

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Markers

RH133331 (e-PCR)
- UniSTS:216614

SPARCL1 (e-PCR)
- UniSTS:279130

D14Wox22 (e-PCR)
- UniSTS:518774

RH137752 (e-PCR)
- UniSTS:219839

AW529913 (e-PCR)
- UniSTS:261361

D21S1917 (e-PCR), detects polymorphism
- UniSTS:16372

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables calcium ion binding	IBA Inferred from Biological aspect of Ancestor more info
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables collagen binding	IBA Inferred from Biological aspect of Ancestor more info
enables extracellular matrix binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in anatomical structure development	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of synapse organization	EXP Inferred from Experiment more info	PubMed
involved_in regulation of synapse organization	IDA Inferred from Direct Assay more info	PubMed
involved_in signal transduction	IEA Inferred from Electronic Annotation more info
involved_in synaptic membrane adhesion	IEA Inferred from Electronic Annotation more info
involved_in synaptic membrane adhesion	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in collagen-containing extracellular matrix	IEA Inferred from Electronic Annotation more info
is_active_in extracellular matrix of synaptic cleft	IDA Inferred from Direct Assay more info	PubMed
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular space	IEA Inferred from Electronic Annotation more info
is_active_in glutamatergic synapse	EXP Inferred from Experiment more info	PubMed
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
is_active_in glutamatergic synapse	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: SPARC-like protein 1

Names: Extracellular matrix protein 2; SPARC-like 1 (hevin); SPARC-like 1 (mast9, hevin); matrix glycoprotein Sc1

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_012946.2 → NP_037078.2 SPARC-like protein 1 precursor

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000014

UniProtKB/TrEMBL

A6K5T4, Q6P7A8

Related

ENSRNOP00000020357.6, ENSRNOT00000020357.7

Conserved Domains (3) summary

cd16236
Location:485 → 625

EFh_SPARC_SPARCL1; EF-hand, extracellular calcium-binding (EC) motif, found in secreted protein, acidic and rich in cysteine-like 1 (SPARCL1)

NF033845
Location:95 → 402

MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

cl00097
Location:403 → 482

KAZAL_FS; Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the ...