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

Gene ID: 25434, updated on 30-Sep-2021

Summary

Official Symbol
Sparcl1provided by RGD
Official Full Name
SPARC like 1provided by RGD
Primary source
RGD:2531
See related
EnsemblRapid:ENSRNOG00000015093
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
putative extracellular matrix glycoprotein that binds calcium and plays an important role in the developing brain [RGD, Feb 2006]
Expression
Biased expression in Brain (RPKM 2934.0), Heart (RPKM 1217.6) and 4 other tissues See more
Orthologs
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Genomic context

See Sparcl1 in Genome Data Viewer
Location:
14p22
Exon count:
11
Annotation release Status Assembly Chr Location
108 current 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_051349.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC108352697 Neighboring gene dentin matrix acidic phosphoprotein 1 Neighboring gene dentin sialophosphoprotein Neighboring gene secretory calcium-binding phosphoprotein proline-glutamine rich 1-like Neighboring gene nudix hydrolase 9 Neighboring gene hydroxysteroid (17-beta) dehydrogenase 11

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

General gene information

Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables calcium ion binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
enables collagen binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables extracellular matrix binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
involved_in anatomical structure development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 
located_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
PubMed 
located_in extracellular space IEA
Inferred from Electronic Annotation
more info
 
is_active_in glutamatergic synapse EXP
Inferred from Experiment
more info
PubMed 
located_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 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
 
located_in glutamatergic synapse ISO
Inferred from Sequence Orthology
more info
 
located_in synapse IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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)

  1. NM_012946.2NP_037078.2  SPARC-like protein 1 precursor

    Status: PROVISIONAL

    Source sequence(s)
    JACYVU010000248
    Related
    ENSRNOP00000020357.6, ENSRNOT00000020357.7
    Conserved Domains (3) summary
    cd16236
    Location:485625
    EFh_SPARC_SPARCL1; EF-hand, extracellular calcium-binding (EC) motif, found in secreted protein, acidic and rich in cysteine-like 1 (SPARCL1)
    NF033845
    Location:95402
    MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB
    cl00097
    Location:403482
    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 ...

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 108 details...Open this link in a new tab

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

Reference mRatBN7.2 Primary Assembly

Genomic

  1. NC_051349.1 Reference mRatBN7.2 Primary Assembly

    Range
    5632816..5663866
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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