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SPOCK3 SPARC (osteonectin), cwcv and kazal like domains proteoglycan 3 [ Homo sapiens (human) ]

Gene ID: 50859, updated on 2-Nov-2024

Summary

Official Symbol
SPOCK3provided by HGNC
Official Full Name
SPARC (osteonectin), cwcv and kazal like domains proteoglycan 3provided by HGNC
Primary source
HGNC:HGNC:13565
See related
Ensembl:ENSG00000196104 MIM:607989; AllianceGenome:HGNC:13565
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
TES-3; TICN3; HSAJ1454
Summary
This gene encodes a member of a novel family of calcium-binding proteoglycan proteins that contain thyroglobulin type-1 and Kazal-like domains. The encoded protein and may play a role in adult T-cell leukemia by inhibiting the activity of membrane-type matrix metalloproteinases. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Oct 2011]
Expression
Biased expression in brain (RPKM 28.5), prostate (RPKM 28.2) and 2 other tissues See more
Orthologs
NEW
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Genomic context

See SPOCK3 in Genome Data Viewer
Location:
4q32.3
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (166733384..167234945, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (170090608..170592260, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (167654535..168155645, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377521 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:166888016-166889215 Neighboring gene Sharpr-MPRA regulatory region 2915 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:166963784-166964983 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22120 Neighboring gene tolloid like 1 Neighboring gene RNA, 5S ribosomal pseudogene 170 Neighboring gene Sharpr-MPRA regulatory region 13283 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_75833 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_75852 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_75875 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_75970 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_75989 Neighboring gene Sharpr-MPRA regulatory region 523 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_76035 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:167491405-167492062 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:167490745-167491404 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22121 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:167636733-167637577 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:167637578-167638421 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:167642620-167643500 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22122 Neighboring gene NANOG hESC enhancer GRCh37_chr4:167796983-167797484 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15787 Neighboring gene RNA, 5S ribosomal pseudogene 171 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22123 Neighboring gene RNA, 7SL, cytoplasmic 776, pseudogene Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:168508591-168509790 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_76084 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_76088 Neighboring gene PHB1 pseudogene 14

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues 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
Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients.
EBI GWAS Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog

Pathways from PubChem

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 IEA
Inferred from Electronic Annotation
more info
 
enables glycosaminoglycan binding IEA
Inferred from Electronic Annotation
more info
 
enables metalloendopeptidase inhibitor activity IDA
Inferred from Direct Assay
more info
PubMed 
enables metalloendopeptidase inhibitor activity TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
located_in extracellular matrix IDA
Inferred from Direct Assay
more info
PubMed 
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
 
located_in extracellular space IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
testican-3
Names
SPARC/osteonectin, cwcv and kazal like domains proteoglycan 3
sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 3

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.

Genomic

  1. NG_030414.1 RefSeqGene

    Range
    5097..506207
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001040159.2NP_001035249.1  testican-3 isoform 1 precursor

    See identical proteins and their annotated locations for NP_001035249.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) lacks an alternate in-frame exon compared to variant 2. The resulting isoform (1) has the same N- and C-termini but is shorter compared to isoform 2.
    Source sequence(s)
    AC020599, BC003017
    Consensus CDS
    CCDS34095.1
    UniProtKB/TrEMBL
    B4DFW5
    Related
    ENSP00000350153.4, ENST00000357545.9
    Conserved Domains (3) summary
    smart00280
    Location:137180
    KAZAL; Kazal type serine protease inhibitors
    cd00191
    Location:313377
    TY; Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases
    cd16239
    Location:198310
    EFh_SPARC_TICN3; EF-hand, extracellular calcium-binding (EC) motif, found in testican-3 (TICN3)
  2. NM_001204352.2NP_001191281.1  testican-3 isoform 3

    See identical proteins and their annotated locations for NP_001191281.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an exon, includes an alternate exon in the 5' coding region, and uses an alternate start codon, compared to variant 2. The encoded isoform (3) is shorter and has a distinct N-terminus, compared to isoform 2.
    Source sequence(s)
    AC020599, AK295015, BI603782
    Consensus CDS
    CCDS56344.1
    UniProtKB/TrEMBL
    B4DI52
    Related
    ENSP00000411344.2, ENST00000421836.6
    Conserved Domains (4) summary
    smart00280
    Location:89132
    KAZAL; Kazal type serine protease inhibitors
    cd00191
    Location:265329
    TY; Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases
    cd00252
    Location:149268
    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:148255
    SPARC_Ca_bdg; Secreted protein acidic and rich in cysteine Ca binding region
  3. NM_001204353.1NP_001191282.1  testican-3 isoform 4

    See identical proteins and their annotated locations for NP_001191282.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, lacks two exons and uses a downstream, in-frame start codon, compared to variant 2. The encoded isoform (4) has a shorter N-terminus, compared to isoform 2.
    Source sequence(s)
    AC020599, AK295407
    Consensus CDS
    CCDS56343.1
    UniProtKB/TrEMBL
    B4DI52
    Related
    ENSP00000444789.1, ENST00000541354.5
    Conserved Domains (4) summary
    smart00280
    Location:2063
    KAZAL; Kazal type serine protease inhibitors
    cd00191
    Location:196260
    TY; Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases
    cd00252
    Location:80199
    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:79186
    SPARC_Ca_bdg; Secreted protein acidic and rich in cysteine Ca binding region
  4. NM_001204354.2NP_001191283.1  testican-3 isoform 5

    See identical proteins and their annotated locations for NP_001191283.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks two consecutive exons and uses a downstream, in-frame start codon, compared to variant 2. The encoded isoform (5) has a shorter N-terminus, compared to isoform 2.
    Source sequence(s)
    AC020599, AK091078, AK295414
    Consensus CDS
    CCDS75207.1
    UniProtKB/TrEMBL
    A0A0A0MTJ2, B4DI52
    Related
    ENSP00000441396.2, ENST00000535728.5
    Conserved Domains (4) summary
    smart00280
    Location:4891
    KAZAL; Kazal type serine protease inhibitors
    cd00191
    Location:224288
    TY; Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases
    cd00252
    Location:108227
    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:107214
    SPARC_Ca_bdg; Secreted protein acidic and rich in cysteine Ca binding region
  5. NM_001204355.2NP_001191284.1  testican-3 isoform 6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks three consecutive coding exons and uses an alternate start codon, compared to variant 2. The encoded isoform (6) is shorter and has a distinct N-terminus, compared to isoform 2.
    Source sequence(s)
    AC020599, AK295281, BI603782
    UniProtKB/TrEMBL
    B4DI52
    Conserved Domains (4) summary
    smart00280
    Location:4487
    KAZAL; Kazal type serine protease inhibitors
    cd00191
    Location:220284
    TY; Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases
    cd00252
    Location:104223
    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:103210
    SPARC_Ca_bdg; Secreted protein acidic and rich in cysteine Ca binding region
  6. NM_001204356.2NP_001191285.1  testican-3 isoform 7 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) lacks two alternate in-frame exons compared to variant 2. The resulting isoform (7) has the same N- and C-termini but is shorter compared to isoform 2.
    Source sequence(s)
    AC020599, AK296291, BI603782
    Consensus CDS
    CCDS56346.1
    UniProtKB/TrEMBL
    B4DFW5
    Related
    ENSP00000426716.1, ENST00000510741.5
    Conserved Domains (3) summary
    smart00280
    Location:137180
    KAZAL; Kazal type serine protease inhibitors
    cd00191
    Location:273337
    TY; Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases
    cd00252
    Location:195276
    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 ...
  7. NM_001204358.2NP_001191287.1  testican-3 isoform 9 precursor

    See identical proteins and their annotated locations for NP_001191287.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) lacks an alternate in-frame exon and differs in the 3' UTR and coding sequence compared to variant 2. The resulting isoform (9, also known as N-TES) has a shorter and distinct C-terminus and lacks an alternate internal segment compared to isoform 2.
    Source sequence(s)
    AB056866, AC020599
    Consensus CDS
    CCDS56347.1
    UniProtKB/Swiss-Prot
    Q9BQ16
    Related
    ENSP00000426177.1, ENST00000512648.5
    Conserved Domains (3) summary
    smart00280
    Location:137180
    KAZAL; Kazal type serine protease inhibitors
    cd00252
    Location:197311
    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:196303
    SPARC_Ca_bdg; Secreted protein acidic and rich in cysteine Ca binding region
  8. NM_001251967.2NP_001238896.1  testican-3 isoform 11 precursor

    See identical proteins and their annotated locations for NP_001238896.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (11) lacks four consecutive coding exons but maintains the reading frame, compared to variant 2. The encoded isoform (11) is shorter than isoform 2.
    Source sequence(s)
    AC020599, AK294637, BI603782
    Consensus CDS
    CCDS58931.1
    UniProtKB/TrEMBL
    B4DI52
    Related
    ENSP00000426318.1, ENST00000512681.5
    Conserved Domains (3) summary
    cd00191
    Location:218282
    TY; Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases
    cd00252
    Location:102221
    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:101208
    SPARC_Ca_bdg; Secreted protein acidic and rich in cysteine Ca binding region
  9. NM_001430594.1NP_001417523.1  testican-3 isoform 1 precursor

    Status: REVIEWED

    Source sequence(s)
    AC010103, AC020599, AC023492, AC107210
    Related
    ENSP00000425502.1, ENST00000511269.5
  10. NM_016950.3NP_058646.2  testican-3 isoform 2 precursor

    See identical proteins and their annotated locations for NP_058646.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) encodes the longest isoform (2).
    Source sequence(s)
    AC020599, AY358973
    Consensus CDS
    CCDS54817.1
    UniProtKB/Swiss-Prot
    B2R7M7, B3KR67, B4DGK5, B4DHB4, B4DHV3, B4DI46, B4DJY3, E7EP61, F5H099, O75705, Q6UW53, Q96Q26, Q9BQ16
    UniProtKB/TrEMBL
    B4DFW5
    Related
    ENSP00000349677.3, ENST00000357154.7
    Conserved Domains (4) summary
    smart00280
    Location:140183
    KAZAL; Kazal type serine protease inhibitors
    cd00191
    Location:316380
    TY; Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases
    cd00252
    Location:200319
    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:199306
    SPARC_Ca_bdg; Secreted protein acidic and rich in cysteine Ca binding region

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
    166733384..167234945 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017008258.2XP_016863747.1  testican-3 isoform X3

    UniProtKB/TrEMBL
    B4DFW5
    Related
    ENSP00000425570.1, ENST00000504953.5
    Conserved Domains (3) summary
    smart00280
    Location:137180
    KAZAL; Kazal type serine protease inhibitors
    cd00191
    Location:313377
    TY; Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases
    cd16239
    Location:198310
    EFh_SPARC_TICN3; EF-hand, extracellular calcium-binding (EC) motif, found in testican-3 (TICN3)
  2. XM_011532018.2XP_011530320.1  testican-3 isoform X2

    See identical proteins and their annotated locations for XP_011530320.1

    UniProtKB/Swiss-Prot
    B2R7M7, B3KR67, B4DGK5, B4DHB4, B4DHV3, B4DI46, B4DJY3, E7EP61, F5H099, O75705, Q6UW53, Q96Q26, Q9BQ16
    UniProtKB/TrEMBL
    B4DFW5
    Related
    ENSP00000420920.1, ENST00000506886.5
    Conserved Domains (4) summary
    smart00280
    Location:140183
    KAZAL; Kazal type serine protease inhibitors
    cd00191
    Location:316380
    TY; Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases
    cd00252
    Location:200319
    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:199306
    SPARC_Ca_bdg; Secreted protein acidic and rich in cysteine Ca binding region

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    170090608..170592260 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054350129.1XP_054206104.1  testican-3 isoform X3

  2. XM_054350128.1XP_054206103.1  testican-3 isoform X2

    UniProtKB/Swiss-Prot
    B2R7M7, B3KR67, B4DGK5, B4DHB4, B4DHV3, B4DI46, B4DJY3, E7EP61, F5H099, O75705, Q6UW53, Q96Q26, Q9BQ16

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001204359.1: Suppressed sequence

    Description
    NM_001204359.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.