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

Gene ID: 92521, updated on 1-Jun-2020

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
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; 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

Genomic context

See SPECC1 in Genome Data Viewer
Location:
17p11.2
Exon count:
19
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 17 NC_000017.11 (20009301..20319026)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (19912649..20218072)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene unc-51 like autophagy activating kinase 2 Neighboring gene tRNA-Gly (anticodon CCC) 3-1 Neighboring gene A-kinase anchoring protein 10 Neighboring gene uncharacterized LOC100131943 Neighboring gene uncharacterized LOC105371579 Neighboring gene RNA, U6 small nuclear 258, pseudogene Neighboring gene potassium channel tetramerization domain containing 9 pseudogene 1 Neighboring gene RNA, U6 small nuclear 1057, pseudogene Neighboring gene coiled-coil domain containing 144C, pseudogene Neighboring gene RNA, U6 small nuclear 467, pseudogene Neighboring gene UPF3A pseudogene 2

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

NHGRI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ36955

Gene Ontology Provided by GOA

Process Evidence Code Pubs
actin cytoskeleton organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
 
fibrillar center IDA
Inferred from Direct Assay
more info
 
filamentous actin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
membrane IEA
Inferred from Electronic Annotation
more info
 
microtubule organizing center IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
cytospin-B
Names
NSP5
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)

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_029768.2 RefSeqGene

    Range
    5001..310424
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001033553.2NP_001028725.1  cytospin-B isoform 1

    See identical proteins and their annotated locations for NP_001028725.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1, also known as NSP5beta3beta). Variants 1 and 6 encode the same isoform.
    Source sequence(s)
    AK295093, AK301318, AK304186, AY816329, BP309862, CA427363
    Consensus CDS
    CCDS32590.1
    UniProtKB/Swiss-Prot
    Q5M775
    UniProtKB/TrEMBL
    A0A024QYY9, B4DW07, B4E2A4
    Related
    ENSP00000261503.5, ENST00000261503.9
    Conserved Domains (4) summary
    cd00014
    Location:9661066
    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 ...
    TIGR04523
    Location:367771
    Mplasa_alph_rch; helix-rich Mycoplasma protein
    pfam04156
    Location:145260
    IncA; IncA protein
    cl09111
    Location:636731
    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 ...
  2. NM_001033554.3NP_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/Swiss-Prot
    Q5M775
    UniProtKB/TrEMBL
    B4E2A4
    Related
    ENSP00000378896.3, ENST00000395525.7
    Conserved Domains (1) summary
    cl09111
    Location:555650
    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 ...
  3. NM_001033555.3NP_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/Swiss-Prot
    Q5M775
    UniProtKB/TrEMBL
    B4DW07, B4E2A4
    Related
    ENSP00000378901.2, ENST00000395530.6
    Conserved Domains (3) summary
    cd00014
    Location:885985
    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:64179
    IncA; IncA protein
    cl09111
    Location:555650
    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 ...
  4. NM_001243438.2NP_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/Swiss-Prot
    Q5M775
    UniProtKB/TrEMBL
    B4E2A4
    Related
    ENSP00000378893.2, ENST00000395522.6
    Conserved Domains (1) summary
    cl09111
    Location:555650
    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 ...
  5. NM_001243439.2NP_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
    Q5M775
    UniProtKB/TrEMBL
    A0A024QYY9, B4DW07, B4E2A4
    Related
    ENSP00000378898.4, ENST00000395527.8
    Conserved Domains (4) summary
    cd00014
    Location:9661066
    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 ...
    TIGR04523
    Location:367771
    Mplasa_alph_rch; helix-rich Mycoplasma protein
    pfam04156
    Location:145260
    IncA; IncA protein
    cl09111
    Location:636731
    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 ...
  6. NM_152904.4NP_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/Swiss-Prot
    Q5M775
    UniProtKB/TrEMBL
    B4E2A4
    Related
    ENSP00000378900.3, ENST00000395529.7
    Conserved Domains (1) summary
    cl09111
    Location:636731
    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 ...

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p13 Primary Assembly

    Range
    20009301..20319026
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017025319.1XP_016880808.1  cytospin-B isoform X3

  2. XM_017025320.1XP_016880809.1  cytospin-B isoform X4

    Conserved Domains (4) summary
    TIGR04523
    Location:367771
    Mplasa_alph_rch; helix-rich Mycoplasma protein
    pfam04156
    Location:145260
    IncA; IncA protein
    cl00030
    Location:9831027
    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 ...
    cl09111
    Location:636731
    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 ...
  3. XM_017025325.1XP_016880814.1  cytospin-B isoform X9

    UniProtKB/Swiss-Prot
    Q5M775
    Conserved Domains (1) summary
    cl09111
    Location:636731
    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 ...
  4. XM_017025318.1XP_016880807.1  cytospin-B isoform X2

  5. XM_017025317.1XP_016880806.1  cytospin-B isoform X1

  6. XM_017025324.1XP_016880813.1  cytospin-B isoform X7

  7. XM_017025323.1XP_016880812.1  cytospin-B isoform X7

  8. XM_017025322.1XP_016880811.1  cytospin-B isoform X6

  9. XM_011524075.2XP_011522377.1  cytospin-B isoform X8

    See identical proteins and their annotated locations for XP_011522377.1

    Conserved Domains (1) summary
    cl09111
    Location:636731
    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 ...
  10. XM_017025321.1XP_016880810.1  cytospin-B isoform X5

  11. XM_005256860.2XP_005256917.1  cytospin-B isoform X10

    Conserved Domains (2) summary
    cd00014
    Location:306406
    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 ...
    pfam04871
    Location:27109
    Uso1_p115_C; Uso1 / p115 like vesicle tethering protein, C terminal region

RNA

  1. XR_001752682.1 RNA Sequence

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