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

Gene ID: 25434, updated on 3-Jan-2019

Summary

Official Symbol
Sparcl1provided by RGD
Official Full Name
SPARC like 1provided by RGD
Primary source
RGD:2531
See related
Ensembl: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

Genomic context

See Sparcl1 in Genome Data Viewer
Location:
14p22
Exon count:
11
Annotation release Status Assembly Chr Location
106 current Rnor_6.0 (GCF_000001895.5) 14 NC_005113.4 (6994261..7025309)
104 previous assembly Rnor_5.0 (GCF_000001895.4) 14 NC_005113.3 (6985394..7016296)

Chromosome 14 - NC_005113.4Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC108352697 Neighboring gene dentin matrix acidic phosphoprotein 1 Neighboring gene dentin sialophosphoprotein Neighboring gene uncharacterized LOC103692564 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 FunctionsWhat's a GeneRIF?

General gene information

Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
calcium ion binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
collagen binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
collagen binding IEA
Inferred from Electronic Annotation
more info
 
extracellular matrix binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
regulation of synapse organization EXP
Inferred from Experiment
more info
PubMed 
regulation of synapse organization IDA
Inferred from Direct Assay
more info
PubMed 
signal transduction IEA
Inferred from Electronic Annotation
more info
 
synaptic membrane adhesion IEA
Inferred from Electronic Annotation
more info
 
synaptic membrane adhesion ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
collagen-containing extracellular matrix IEA
Inferred from Electronic Annotation
more info
 
extracellular matrix of synaptic cleft IDA
Inferred from Direct Assay
more info
PubMed 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular space IEA
Inferred from Electronic Annotation
more info
 
glutamatergic synapse EXP
Inferred from Experiment
more info
PubMed 
glutamatergic synapse IDA
Inferred from Direct Assay
more info
PubMed 
glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
 
glutamatergic synapse ISO
Inferred from Sequence Orthology
more info
 
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)

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

    See identical proteins and their annotated locations for NP_037078.1

    Status: PROVISIONAL

    Source sequence(s)
    U27562
    UniProtKB/Swiss-Prot
    P24054
    Related
    ENSRNOP00000020357.5, ENSRNOT00000020357.6
    Conserved Domains (3) summary
    cd00252
    Location:484632
    SPARC_EC; SPARC_EC; extracellular Ca2+ binding domain (containing 2 EF-hand motifs) of SPARC and related proteins (QR1, SC1/hevin, testican and tsc-36/FRP). SPARC (BM-40) is a multifunctional glycoprotein, a matricellular protein, that functions to regulate ...
    pfam10591
    Location:483618
    SPARC_Ca_bdg; Secreted protein acidic and rich in cysteine Ca binding region
    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 106 details...Open this link in a new tab

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

Reference Rnor_6.0 Primary Assembly

Genomic

  1. NC_005113.4 Reference Rnor_6.0 Primary Assembly

    Range
    6994261..7025309
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate Rn_Celera

Genomic

  1. AC_000082.1 Alternate Rn_Celera

    Range
    5771812..5802805
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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