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    SPARCL1 SPARC like 1 [ Homo sapiens (human) ]

    Gene ID: 8404, updated on 27-Nov-2024

    Summary

    Official Symbol
    SPARCL1provided by HGNC
    Official Full Name
    SPARC like 1provided by HGNC
    Primary source
    HGNC:HGNC:11220
    See related
    Ensembl:ENSG00000152583 MIM:606041; AllianceGenome:HGNC:11220
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SC1; MAST9; PIG33; MAST 9
    Summary
    Predicted to enable calcium ion binding activity; collagen binding activity; and extracellular matrix binding activity. Predicted to be involved in regulation of synapse organization. Located in extracellular space. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in brain (RPKM 777.2), endometrium (RPKM 500.6) and 20 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See SPARCL1 in Genome Data Viewer
    Location:
    4q22.1
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (87473335..87529376, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (90802350..90858405, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (88394487..88450528, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:88343613-88344547 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:88345091-88345594 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:88345595-88346096 Neighboring gene nudix hydrolase 9 Neighboring gene secretory calcium-binding phosphoprotein proline-glutamine rich 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:88432037-88432537 Neighboring gene uncharacterized LOC124900729 Neighboring gene NANOG hESC enhancer GRCh37_chr4:88441567-88442068 Neighboring gene dentin sialophosphoprotein Neighboring gene uncharacterized LOC105377323 Neighboring gene dentin matrix acidic phosphoprotein 1

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    A genome-wide association study identifies new susceptibility loci for esophageal adenocarcinoma and Barrett's esophagus.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IBA
    Inferred from Biological aspect of Ancestor
    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
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in regulation of synapse organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in signal transduction IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in synaptic membrane adhesion IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    SPARC-like protein 1
    Names
    SPARC-like 1 (hevin)
    high endothelial venule protein
    proliferation-inducing protein 33

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001128310.3NP_001121782.1  SPARC-like protein 1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_001121782.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1). Variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      BC022484, DC403565, DC421365, X86693
      Consensus CDS
      CCDS3622.1
      UniProtKB/Swiss-Prot
      B4E2Z0, E7ESU2, Q14515, Q14800
      UniProtKB/TrEMBL
      Q8N4S1
      Related
      ENSP00000414856.1, ENST00000418378.5
      Conserved Domains (3) summary
      cd00252
      Location:514662
      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:513648
      SPARC_Ca_bdg; Secreted protein acidic and rich in cysteine Ca binding region
      cl00097
      Location:433512
      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 ...
    2. NM_001291976.2NP_001278905.1  SPARC-like protein 1 isoform 2

      See identical proteins and their annotated locations for NP_001278905.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. Variants 3 and 4 encode the same isoform (2), which has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AK316533, AL833430, DA283085, DC403565, X86693
      Consensus CDS
      CCDS77939.1
      UniProtKB/TrEMBL
      B7ZB68
      Related
      ENSP00000422903.1, ENST00000503414.5
      Conserved Domains (3) summary
      cd00252
      Location:389537
      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:388523
      SPARC_Ca_bdg; Secreted protein acidic and rich in cysteine Ca binding region
      cl00097
      Location:308387
      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 ...
    3. NM_001291977.2NP_001278906.1  SPARC-like protein 1 isoform 2

      See identical proteins and their annotated locations for NP_001278906.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. Variants 3 and 4 encode the same isoform (2), which has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AK304494, DC403565, X86693
      Consensus CDS
      CCDS77939.1
      UniProtKB/TrEMBL
      B7ZB68
      Conserved Domains (3) summary
      cd00252
      Location:389537
      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:388523
      SPARC_Ca_bdg; Secreted protein acidic and rich in cysteine Ca binding region
      cl00097
      Location:308387
      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 ...
    4. NM_004684.6NP_004675.3  SPARC-like protein 1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_004675.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      AK304494, BC022484, BC033721, DA283085, DC403565, X86693
      Consensus CDS
      CCDS3622.1
      UniProtKB/Swiss-Prot
      B4E2Z0, E7ESU2, Q14515, Q14800
      UniProtKB/TrEMBL
      Q8N4S1
      Related
      ENSP00000282470.6, ENST00000282470.11
      Conserved Domains (3) summary
      cd00252
      Location:514662
      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:513648
      SPARC_Ca_bdg; Secreted protein acidic and rich in cysteine Ca binding region
      cl00097
      Location:433512
      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: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      87473335..87529376 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      90802350..90858405 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)