SMOC2 SPARC related modular calcium binding 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SMOC2provided by HGNC
Official Full Name: SPARC related modular calcium binding 2provided by HGNC
Primary source: HGNC:HGNC:20323
See related: Ensembl:ENSG00000112562 MIM:607223; AllianceGenome:HGNC:20323
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: DTDP1; SMAP2; MST117; MSTP117; MSTP140; bA37D8.1; bA270C4A.1; dJ421D16.1
Summary: This gene encodes a member of the SPARC family (secreted protein acidic and rich in cysteine/osteonectin/BM-40), which are highly expressed during embryogenesis and wound healing. The gene product is a matricellular protein which promotes matrix assembly and can stimulate endothelial cell proliferation and migration, as well as angiogenic activity. Associated with pulmonary function, this secretory gene product contains a Kazal domain, two thymoglobulin type-1 domains, and two EF-hand calcium-binding domains. The encoded protein may serve as a target for controlling angiogenesis in tumor growth and myocardial ischemia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]
Expression: Broad expression in endometrium (RPKM 68.7), gall bladder (RPKM 54.9) and 18 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6q27

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (168441184..168667992)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (169784308..170014051)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (168841864..169068672)

Chromosome 6 - NC_000006.12 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: 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

FTO Positively Regulates Odontoblastic Differentiation via SMOC2 in Human Stem Cells from the Apical Papilla under Inflammatory Microenvironment.
Title: FTO Positively Regulates Odontoblastic Differentiation via SMOC2 in Human Stem Cells from the Apical Papilla under Inflammatory Microenvironment.
MicroRNA-19a-3p Acts as an Oncogene in Gastric Cancer and Exerts the Effect by Targeting SMOC2.
Title: MicroRNA-19a-3p Acts as an Oncogene in Gastric Cancer and Exerts the Effect by Targeting SMOC2.
SMOC2 promotes an epithelial-mesenchymal transition and a pro-metastatic phenotype in epithelial cells of renal cell carcinoma origin.
Title: SMOC2 promotes an epithelial-mesenchymal transition and a pro-metastatic phenotype in epithelial cells of renal cell carcinoma origin.
Prognostic and clinicopathological significance of TMEFF2, SMOC-2, and SOX17 expression in endometrial carcinoma.
Title: Prognostic and clinicopathological significance of TMEFF2, SMOC-2, and SOX17 expression in endometrial carcinoma.
The Intestinal Stem Cell Marker SMOC2 Is an Independent Prognostic Marker Associated With Better Survival in Gastric Cancer.
Title: The Intestinal Stem Cell Marker SMOC2 Is an Independent Prognostic Marker Associated With Better Survival in Gastric Cancer.
SMOC2, an intestinal stem cell marker, is an independent prognostic marker associated with better survival in colorectal cancers.
Title: SMOC2, an intestinal stem cell marker, is an independent prognostic marker associated with better survival in colorectal cancers.
Downregulation of SMOC2 expression in papillary thyroid carcinoma and its prognostic significance.
Title: Downregulation of SMOC2 expression in papillary thyroid carcinoma and its prognostic significance.
SMOC2 expression was markedly up-regulated in human liver samples with non-alcoholic fatty liver disease.
Title: Secreted modular calcium-binding protein 2 promotes high fat diet (HFD)-induced hepatic steatosis through enhancing lipid deposition, fibrosis and inflammation via targeting TGF-β1.
we conclude that SMOC-2 might be a novel endometrial cancer stem cell signature gene and therapeutic target for endometrial cancer.
Title: Targeting cancer stem cell signature gene SMOC-2 Overcomes chemoresistance and inhibits cell proliferation of endometrial carcinoma.
SMOC2 can act as an inhibitor of mineralization; there is a possible role for SMOC2 to prevent calcification disorders.
Title: SMOC2 inhibits calcification of osteoprogenitor and endothelial cells.

Submit: New GeneRIF Correction See all GeneRIFs (26)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Dentin dysplasia type I MedGen: C0399379 OMIM: 125400 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Genome-wide association study of generalized vitiligo in an isolated European founder population identifies SMOC2, in close proximity to IDDM8. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D6S992 (e-PCR)
- UniSTS:14346

D6S386 (e-PCR)
- UniSTS:47166

WI-13584 (e-PCR)
- UniSTS:41803

SHGC-144743 (e-PCR)
- UniSTS:172387

RH70362 (e-PCR)
- UniSTS:31861

G59673 (e-PCR)
- UniSTS:136827

SHGC-149927 (e-PCR)
- UniSTS:177311

RH45190 (e-PCR)
- UniSTS:6088

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	ISA Inferred from Sequence Alignment more info	PubMed
enables extracellular matrix binding	IBA Inferred from Biological aspect of Ancestor more info
enables heparin 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 extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of DNA biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA biosynthetic process	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of angiogenesis	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of angiogenesis	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of endothelial cell chemotaxis	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of endothelial cell migration	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of fibroblast growth factor receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of mitotic cell cycle	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of vascular endothelial growth factor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of vascular wound healing	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
is_active_in basement membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in cell periphery	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	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: SPARC-related modular calcium-binding protein 2

Names: SMAP-2; SMOC-2; secreted modular calcium-binding protein 2; smooth muscle associated protein 2; thyroglobulin type-1 repeat containing protein

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.

Genomic

NG_032781.1 RefSeqGene

Range

5034..231842

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001166412.2 → NP_001159884.1 SPARC-related modular calcium-binding protein 2 isoform 2 precursor

See identical proteins and their annotated locations for NP_001159884.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.

Source sequence(s)

AI032288, BC028420

Consensus CDS

CCDS55076.1

UniProtKB/Swiss-Prot

B3KPS7, Q4G169, Q5TAT7, Q5TAT8, Q86VV9, Q96SF3, Q9H1L3, Q9H1L4, Q9H3U0, Q9H3U7, Q9H4F7, Q9HCV2

Related

ENSP00000348630.3, ENST00000356284.7

Conserved Domains (4) summary

smart00280
Location:39 → 84

KAZAL; Kazal type serine protease inhibitors

cd00191
Location:215 → 281

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

pfam16597
Location:154 → 212

Thyroglob_assoc; Thyroglobulin_1 repeat associated disordered domain

cl08302
Location:352 → 410

EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
NM_022138.3 → NP_071421.1 SPARC-related modular calcium-binding protein 2 isoform 1 precursor

See identical proteins and their annotated locations for NP_071421.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AB014737, AI032288, AL136099, BC028420

Consensus CDS

CCDS5307.1

UniProtKB/Swiss-Prot

Q9H3U7

Related

ENSP00000346537.5, ENST00000354536.9

Conserved Domains (4) summary

smart00280
Location:39 → 84

KAZAL; Kazal type serine protease inhibitors

cd00191
Location:226 → 292

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

pfam16597
Location:154 → 223

Thyroglob_assoc; Thyroglobulin_1 repeat associated disordered domain

cl08302
Location:363 → 421

EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000006.12 Reference GRCh38.p14 Primary Assembly

Range

168441184..168667992

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011536066.2 → XP_011534368.1 SPARC-related modular calcium-binding protein 2 isoform X2

See identical proteins and their annotated locations for XP_011534368.1

Conserved Domains (4) summary

smart00280
Location:39 → 84

KAZAL; Kazal type serine protease inhibitors

cd00191
Location:215 → 281

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

pfam16597
Location:154 → 212

Thyroglob_assoc; Thyroglobulin_1 repeat associated disordered domain

cl08302
Location:352 → 410

EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
XM_011536065.2 → XP_011534367.1 SPARC-related modular calcium-binding protein 2 isoform X1

Conserved Domains (4) summary

smart00280
Location:39 → 84

KAZAL; Kazal type serine protease inhibitors

cd00191
Location:226 → 292

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:363 → 424

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 ...

pfam16597
Location:154 → 223

Thyroglob_assoc; Thyroglobulin_1 repeat associated disordered domain

Alternate T2T-CHM13v2.0

Genomic

NC_060930.1 Alternate T2T-CHM13v2.0

Range

169784308..170014051

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054356216.1 → XP_054212191.1 SPARC-related modular calcium-binding protein 2 isoform X2
XM_054356215.1 → XP_054212190.1 SPARC-related modular calcium-binding protein 2 isoform X1