SPECC1 sperm antigen with calponin homology and coiled-coil domains 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SPECC1provided by HGNC
Official Full Name: sperm antigen with calponin homology and coiled-coil domains 1provided by HGNC
Primary source: HGNC:HGNC:30615
See related: Ensembl:ENSG00000128487 MIM:608793; AllianceGenome:HGNC:30615
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: NSP; NSP5; CYTSB; HCMOGT1; HCMOGT-1
Summary: The protein encoded by this gene belongs to the cytospin-A family. It is localized in the nucleus, and highly expressed in testis and some cancer cell lines. A chromosomal translocation involving this gene and platelet-derived growth factor receptor, beta gene (PDGFRB) may be a cause of juvenile myelomonocytic leukemia. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2011]
Expression: Broad expression in brain (RPKM 6.4), testis (RPKM 6.0) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17p11.2

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (20009359..20319026)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (19958073..20267692)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (19912672..20222339)

Chromosome 17 - NC_000017.11 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: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

NSP 5a3a induces apoptosis in Head and Neck cell line HN30 through p73-DAXX and TRAF2-TRADD.
Title: A novel dual signaling axis for NSP 5a3a induced apoptosis in head and neck carcinoma.
NSP 5a3a's novel interaction with B23 and ribonuclear protein hnRNP-L implicates NSP 5a3a in cellular processes such as ribosome biogenesis and rRNA transcription .
Title: NSP 5a3a's link to nuclear-cyto proteins B23 and hnRNP-L between normal and aberrant breast cell lines.
Loss of NSP 5a3a is associated with head and neck carcinoma.
Title: NSP 5a3a: a potential novel cancer target in head and neck carcinoma.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
PCR and fluoresecne in situ hybridization shows that HCMOGT-1 is a novel fusion partner to PDGFRB in juvenile myelomonocytic leukemia with t(5;17)(q33;p11.2).
Title: HCMOGT-1 is a novel fusion partner to PDGFRB in juvenile myelomonocytic leukemia with t(5;17)(q33;p11.2).

Submit: New GeneRIF Correction

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

EBI GWAS Catalog

Description
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. 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

RH26729 (e-PCR)
- UniSTS:86545

G32683 (e-PCR)
- UniSTS:117265

RH123322 (e-PCR)
- UniSTS:135699

RH64978 (e-PCR)
- UniSTS:87329

RH71161 (e-PCR)
- UniSTS:85557

D1S1425 (e-PCR)
- UniSTS:149621

RH64975 (e-PCR)
- UniSTS:41077

SGC33585 (e-PCR)
- UniSTS:17784

SGC31181 (e-PCR)
- UniSTS:21636

SGC33556 (e-PCR)
- UniSTS:20108

STS-R89252 (e-PCR)
- UniSTS:21392

RH65077 (e-PCR)
- UniSTS:84373

SHGC-58566 (e-PCR)
- UniSTS:94401

SHGC-106909 (e-PCR)
- UniSTS:183018

A009N28 (e-PCR)
- UniSTS:37358

RH27079 (e-PCR)
- UniSTS:88062

Gene Ontology Provided by GOA

Process	Evidence Code	Pubs
involved_in actin cytoskeleton organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in associative learning	IEA Inferred from Electronic Annotation more info
involved_in blastocyst development	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in apical part of cell	IEA Inferred from Electronic Annotation more info
located_in cytosol	IDA Inferred from Direct Assay more info
located_in fibrillar center	IDA Inferred from Direct Assay more info
part_of filamentous actin	IBA Inferred from Biological aspect of Ancestor more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in membrane	IEA Inferred from Electronic Annotation more info
is_active_in microtubule organizing center	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: cytospin-B

Names: cytokinesis and spindle organization B; nuclear structure protein 5; sperm antigen HCMOGT-1; sperm antigen with calponin-like and coiled coil domains 1; structure protein NSP5a3a; structure protein NSP5a3b; structure protein NSP5b3a; structure protein NSP5b3b

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_029768.3 RefSeqGene

Range

5002..314669

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001033553.3 → NP_001028725.1 cytospin-B isoform 1

See identical proteins and their annotated locations for NP_001028725.1

Status: REVIEWED

Source sequence(s)

AC004702, AC007963, AC008088

Consensus CDS

CCDS32590.1

UniProtKB/Swiss-Prot

B4DHH0, B7WNS8, Q5IBP1, Q5IBP2, Q5IBP3, Q5IBP4, Q5M772, Q5M773, Q5M774, Q5M775, Q86XT8, Q8N4U4, Q8WU84, Q9HCQ3

UniProtKB/TrEMBL

A0A7I2V486

Related

ENSP00000261503.5, ENST00000261503.9

Conserved Domains (2) summary

TIGR04523
Location:367 → 771

Mplasa_alph_rch; helix-rich Mycoplasma protein

cd21257
Location:956 → 1067

CH_CYTSB; calponin homology (CH) domain found in cytospin-B
NM_001033554.3 → NP_001028726.1 cytospin-B isoform 4

See identical proteins and their annotated locations for NP_001028726.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) contains alternate exons at both the 5' and 3' ends compared to variant 1. This results in a shorter isoform (4, also known as NSP5alpha3alpha) with distinct N- and C- termini compared to isoform 1.

Source sequence(s)

AC004702, AI950511, AK304186, AY816326, BC033618, BC037532, BP309862, CN361555, DC336225

Consensus CDS

CCDS45628.1

UniProtKB/TrEMBL

A0A7P0T9K0

Related

ENSP00000378896.3, ENST00000395525.7

Conserved Domains (1) summary

cl09111
Location:555 → 650

Prefoldin; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits ...
NM_001033555.3 → NP_001028727.1 cytospin-B isoform 2

See identical proteins and their annotated locations for NP_001028727.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) contains an alternate 5' terminal exon compared to variant 1. This results in a shorter isoform (2, also known as NSP5alpha3beta) with a distinct N-terminus compared to isoform 1.

Source sequence(s)

AC008088, AK301318, AK304186, AY816327, AY816329, BP309862, CA427363, DC336225

Consensus CDS

CCDS42281.1

UniProtKB/TrEMBL

B4E2A4

Related

ENSP00000378901.2, ENST00000395530.6

Conserved Domains (3) summary

cd00014
Location:885 → 985

CH; Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like ...

pfam04156
Location:64 → 179

IncA; IncA protein

cl09111
Location:555 → 650

Prefoldin; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits ...
NM_001243438.2 → NP_001230367.1 cytospin-B isoform 5

Status: REVIEWED

Description

Transcript Variant: This variant (5) contains alternate exons at both the 5' and 3' ends, and uses an alternate donor splice site at the penultimate exon compared to variant 1. This results in a shorter isoform (5) with distinct N- and C- termini compared to isoform 1.

Source sequence(s)

AC004702, AI950511, AK304186, BC033618, BC037532, BC050058, BP309862, CN361555, DC336225

Consensus CDS

CCDS58531.1

UniProtKB/TrEMBL

A0A7P0T9K0

Related

ENSP00000378893.2, ENST00000395522.6

Conserved Domains (1) summary

cl09111
Location:555 → 650

Prefoldin; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits ...
NM_001243439.2 → NP_001230368.1 cytospin-B isoform 1

See identical proteins and their annotated locations for NP_001230368.1

Status: REVIEWED

Description

Transcript Variant: This variant (6) contains an alternate 5' terminal non-coding exon compared to variant 1. Variants 1 and 6 encode the same isoform (1).

Source sequence(s)

AC008088, AK295093, AK301318, AK304186, AY816329, BP309862, CA427363, DA058164

Consensus CDS

CCDS32590.1

UniProtKB/Swiss-Prot

B4DHH0, B7WNS8, Q5IBP1, Q5IBP2, Q5IBP3, Q5IBP4, Q5M772, Q5M773, Q5M774, Q5M775, Q86XT8, Q8N4U4, Q8WU84, Q9HCQ3

UniProtKB/TrEMBL

A0A7I2V486

Related

ENSP00000378898.4, ENST00000395527.9

Conserved Domains (2) summary

TIGR04523
Location:367 → 771

Mplasa_alph_rch; helix-rich Mycoplasma protein

cd21257
Location:956 → 1067

CH_CYTSB; calponin homology (CH) domain found in cytospin-B
NM_001386077.2 → NP_001373006.1 cytospin-B isoform 6

Status: REVIEWED

Source sequence(s)

AC004702, AC007963, AC008088

Consensus CDS

CCDS92279.1

UniProtKB/TrEMBL

B4DW07, J3KSG2

Related

ENSP00000462471.2, ENST00000581399.6

Conserved Domains (2) summary

COG1196
Location:2 → 113

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

cd21257
Location:296 → 407

CH_CYTSB; calponin homology (CH) domain found in cytospin-B
NM_001386078.2 → NP_001373007.1 cytospin-B isoform 7

Status: REVIEWED

Source sequence(s)

AC004702, AC005730, AC007963, AC008088

Consensus CDS

CCDS92274.1

UniProtKB/TrEMBL

J3KRB9

Related

ENSP00000461918.2, ENST00000583528.6

Conserved Domains (2) summary

COG1196
Location:142 → 277

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

cd21257
Location:462 → 573

CH_CYTSB; calponin homology (CH) domain found in cytospin-B
NM_001386079.1 → NP_001373008.1 cytospin-B isoform 8

Status: REVIEWED

Source sequence(s)

AC004702, AC005730, AC007963

Consensus CDS

CCDS92278.1

UniProtKB/TrEMBL

A0A7P0TAS3, J3KRD8, J3KS18, J3KTI9, J3QRQ9, J3QS22

Related

ENSP00000506319.1, ENST00000681202.1

Conserved Domains (1) summary

TIGR02168
Location:370 → 726

SMC_prok_B; chromosome segregation protein SMC, common bacterial type
NM_001386080.1 → NP_001373009.1 cytospin-B isoform 9

Status: REVIEWED

Source sequence(s)

AC004702, AC005730, AC007963, AC008088

UniProtKB/TrEMBL

B4DIW7

Related

ENST00000678651.1

Conserved Domains (2) summary

TIGR02168
Location:146 → 502

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

cd21257
Location:732 → 843

CH_CYTSB; calponin homology (CH) domain found in cytospin-B
NM_001386081.1 → NP_001373010.1 cytospin-B isoform 10

Status: REVIEWED

Source sequence(s)

AC004702, AC005730, AC007963, AC008088

Consensus CDS

CCDS92275.1

UniProtKB/TrEMBL

A0A7I2V486, A0A7P0TBP2

Related

ENSP00000506699.1, ENST00000680019.1

Conserved Domains (2) summary

TIGR04523
Location:367 → 771

Mplasa_alph_rch; helix-rich Mycoplasma protein

cl00030
Location:956 → 1019

CH_SF; calponin homology (CH) domain superfamily
NM_001386082.1 → NP_001373011.1 cytospin-B isoform 11

Status: REVIEWED

Source sequence(s)

AC004702, AC005730, AC007963, AC008088

Consensus CDS

CCDS92276.1

UniProtKB/TrEMBL

A0A7I2V416, A0A7I2V451

Related

ENSP00000503509.1, ENST00000678019.1

Conserved Domains (2) summary

TIGR04523
Location:367 → 771

Mplasa_alph_rch; helix-rich Mycoplasma protein

cl00030
Location:956 → 1047

CH_SF; calponin homology (CH) domain superfamily
NM_001386083.2 → NP_001373012.2 cytospin-B isoform 1

Status: REVIEWED

Source sequence(s)

AC004702, AC005730, AC007963, AC008088

Consensus CDS

CCDS32590.1

UniProtKB/Swiss-Prot

B4DHH0, B7WNS8, Q5IBP1, Q5IBP2, Q5IBP3, Q5IBP4, Q5M772, Q5M773, Q5M774, Q5M775, Q86XT8, Q8N4U4, Q8WU84, Q9HCQ3

UniProtKB/TrEMBL

A0A7I2V486

Related

ENSP00000504211.1, ENST00000679255.1

Conserved Domains (2) summary

TIGR04523
Location:367 → 771

Mplasa_alph_rch; helix-rich Mycoplasma protein

cd21257
Location:956 → 1067

CH_CYTSB; calponin homology (CH) domain found in cytospin-B
NM_001386084.1 → NP_001373013.1 cytospin-B isoform 13

Status: REVIEWED

Source sequence(s)

AC004702, AC005730, AC007963

UniProtKB/TrEMBL

J3KRD8, J3KS18, J3KTI9, J3QRQ9, J3QS22

Conserved Domains (1) summary

TIGR02168
Location:378 → 734

SMC_prok_B; chromosome segregation protein SMC, common bacterial type
NM_001386085.1 → NP_001373014.1 cytospin-B isoform 14

Status: REVIEWED

Source sequence(s)

AC004702, AC005730, AC007963, AC008088

Consensus CDS

CCDS92277.1

UniProtKB/TrEMBL

A0A7I2V451, A0A7I2YQJ3

Related

ENSP00000503774.1, ENST00000679048.1

Conserved Domains (2) summary

TIGR04523
Location:367 → 771

Mplasa_alph_rch; helix-rich Mycoplasma protein

cl00030
Location:956 → 1028

CH_SF; calponin homology (CH) domain superfamily
NM_152904.4 → NP_690868.3 cytospin-B isoform 3

See identical proteins and their annotated locations for NP_690868.3

Status: REVIEWED

Description

Transcript Variant: This variant (3) contains an alternate 3' terminal exon compared to variant 1. This results in a shorter isoform (3, also known as NSP5beta3alpha) with a distinct C-terminus compared to isoform 1.

Source sequence(s)

AC004702, AI950511, AK295093, AK304186, AY816328, BC033618, BC037532, BP309862, CN361555

Consensus CDS

CCDS42280.1

UniProtKB/TrEMBL

J3KRD8, J3KS18, J3KTI9, J3QRQ9, J3QS22

Related

ENSP00000378900.3, ENST00000395529.7

Conserved Domains (1) summary

cl09111
Location:636 → 731

Prefoldin; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits ...