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 differe... See more...

Aliases for SPECC1 Gene

Aliases for SPECC1 Gene

  • Sperm Antigen With Calponin Homology And Coiled-Coil Domains 1 2 3 4 5
  • Cytokinesis And Spindle Organization B 2 3
  • Nuclear Structure Protein 5 3 4
  • Sperm Antigen HCMOGT-1 3 4
  • Cytospin-B 3 4
  • HCMOGT-1 2 3
  • CYTSB 3 4
  • NSP5 3 4
  • NSP 2 3
  • Sperm Antigen With Calponin-Like And Coiled Coil Domains 1 3
  • Structure Protein NSP5a3a 3
  • Structure Protein NSP5a3b 3
  • Structure Protein NSP5b3a 3
  • Structure Protein NSP5b3b 3
  • Sperm Antigen HCMOGT 1 2
  • Cytospin B 2
  • FLJ36955 2
  • HCMOGT1 3
  • SPECC1 5

External Ids for SPECC1 Gene

Previous HGNC Symbols for SPECC1 Gene

  • CYTSB

Previous GeneCards Identifiers for SPECC1 Gene

  • GC17P019931
  • GC17P019853
  • GC17P019369
  • GC17P019914

Summaries for SPECC1 Gene

Entrez Gene Summary for SPECC1 Gene

  • 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]

GeneCards Summary for SPECC1 Gene

SPECC1 (Sperm Antigen With Calponin Homology And Coiled-Coil Domains 1) is a Protein Coding gene. Diseases associated with SPECC1 include Juvenile Myelomonocytic Leukemia and Noonan Syndrome 6. An important paralog of this gene is SPECC1L.

Gene Wiki entry for SPECC1 Gene

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SPECC1 Gene

Genomics for SPECC1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SPECC1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SPECC1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SPECC1

Genomic Locations for SPECC1 Gene

Latest Assembly
chr17:20,008,865-20,319,026
(GRCh38/hg38)
Size:
310,162 bases
Orientation:
Plus strand

Previous Assembly
chr17:19,912,672-20,222,339
(GRCh37/hg19 by Entrez Gene)
Size:
309,668 bases
Orientation:
Plus strand

chr17:19,912,657-20,222,339
(GRCh37/hg19 by Ensembl)
Size:
309,683 bases
Orientation:
Plus strand

Genomic View for SPECC1 Gene

Genes around SPECC1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SPECC1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SPECC1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SPECC1 Gene

Proteins for SPECC1 Gene

  • Protein details for SPECC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5M775-CYTSB_HUMAN
    Recommended name:
    Cytospin-B
    Protein Accession:
    Q5M775
    Secondary Accessions:
    • B4DHH0
    • B7WNS8
    • Q5IBP1
    • Q5IBP2
    • Q5IBP3
    • Q5IBP4
    • Q5M772
    • Q5M773
    • Q5M774
    • Q86XT8
    • Q8N4U4
    • Q8WU84
    • Q9HCQ3

    Protein attributes for SPECC1 Gene

    Size:
    1068 amino acids
    Molecular mass:
    118585 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAH33618.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305}; Sequence=BAB16440.1; Type=Frameshift; Evidence={ECO:0000305};

    Alternative splice isoforms for SPECC1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SPECC1 Gene

Post-translational modifications for SPECC1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SPECC1 Gene

Domains & Families for SPECC1 Gene

Gene Families for SPECC1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for SPECC1 Gene

InterPro:
Blocks:
  • Calponin-like actin-binding
ProtoNet:

Suggested Antigen Peptide Sequences for SPECC1 Gene

GenScript: Design optimal peptide antigens:
  • Sperm antigen with calponin homology and coiled-coil domains 1 (CYTSB_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q5M775

UniProtKB/Swiss-Prot:

CYTSB_HUMAN :
  • Belongs to the cytospin-A family.
Family:
  • Belongs to the cytospin-A family.
genes like me logo Genes that share domains with SPECC1: view

Function for SPECC1 Gene

Phenotypes From GWAS Catalog for SPECC1 Gene

Gene Ontology (GO) - Molecular Function for SPECC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with SPECC1: view
genes like me logo Genes that share phenotypes with SPECC1: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SPECC1

Clone products for research

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SPECC1 Gene

Localization for SPECC1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SPECC1 Gene

Nucleus.
[Isoform 3]: Membrane. Lipid-anchor.
[Isoform 4]: Membrane. Lipid-anchor.
[Isoform 5]: Membrane. Lipid-anchor.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SPECC1 gene
Compartment Confidence
nucleus 5
cytosol 5
cytoskeleton 4
endoplasmic reticulum 2
plasma membrane 1
extracellular 1
mitochondrion 1
peroxisome 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Cytosol (2)
  • Nucleoli fibrillar center (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SPECC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001650 fibrillar center IDA --
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA --
GO:0005815 microtubule organizing center IBA 21873635
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with SPECC1: view

Pathways & Interactions for SPECC1 Gene

PathCards logo

SuperPathways for SPECC1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SPECC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030036 actin cytoskeleton organization IBA 21873635
genes like me logo Genes that share ontologies with SPECC1: view

No data available for Pathways by source and SIGNOR curated interactions for SPECC1 Gene

Drugs & Compounds for SPECC1 Gene

No Compound Related Data Available

Transcripts for SPECC1 Gene

mRNA/cDNA for SPECC1 Gene

15 REFSEQ mRNAs :
23 NCBI additional mRNA sequence :
51 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SPECC1

Clone products for research

Alternative Splicing Database (ASD) splice patterns (SP) for SPECC1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14
SP1: -
SP2:
SP3:
SP4: - -
SP5: -

Relevant External Links for SPECC1 Gene

GeneLoc Exon Structure for
SPECC1

Expression for SPECC1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SPECC1 Gene

Protein differential expression in normal tissues from HIPED for SPECC1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (24.1) and Lung (10.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SPECC1 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SPECC1

SOURCE GeneReport for Unigene cluster for SPECC1 Gene:

Hs.431045

mRNA Expression by UniProt/SwissProt for SPECC1 Gene:

Q5M775-CYTSB_HUMAN
Tissue specificity: Highly expressed in testis. Barely detectable in other tissues. Also highly expressed in some cancer cell lines.

Evidence on tissue expression from TISSUES for SPECC1 Gene

  • Nervous system(4.9)
  • Skin(4.4)
  • Liver(4.3)
  • Kidney(2.5)
  • Intestine(2.4)
  • Spleen(2.4)
  • Blood(2.3)
  • Lung(2.1)
genes like me logo Genes that share expression patterns with SPECC1: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for SPECC1 Gene

Orthologs for SPECC1 Gene

This gene was present in the common ancestor of animals.

Orthologs for SPECC1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SPECC1 31
  • 99 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia SPECC1 30 31
  • 85.33 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Specc1 30 17 31
  • 83.82 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Specc1 30
  • 82.73 (n)
Cow
(Bos Taurus)
Mammalia SPECC1 30 31
  • 78.67 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SPECC1 31
  • 77 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SPECC1 31
  • 77 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SPECC1 30 31
  • 72.05 (n)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia specc1 30
  • 65.36 (n)
Str.17349 30
African clawed frog
(Xenopus laevis)
Amphibia LOC398795 30
Zebrafish
(Danio rerio)
Actinopterygii specc1 30 31
  • 58.68 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta CG13366 31
  • 26 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.3677 31
  • 28 (a)
OneToMany
Species where no ortholog for SPECC1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for SPECC1 Gene

ENSEMBL:
Gene Tree for SPECC1 (if available)
TreeFam:
Gene Tree for SPECC1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SPECC1: view image

Paralogs for SPECC1 Gene

Paralogs for SPECC1 Gene

(5) SIMAP similar genes for SPECC1 Gene using alignment to 14 proteins:

  • CYTSB_HUMAN
  • F5H2Z1_HUMAN
  • J3KRB9_HUMAN
  • J3KRD8_HUMAN
  • J3KRN9_HUMAN
  • J3KS18_HUMAN
  • J3KSG2_HUMAN
  • J3KTH6_HUMAN
  • J3KTI9_HUMAN
  • J3QKL1_HUMAN
  • J3QQM0_HUMAN
  • J3QRQ9_HUMAN
  • J3QS22_HUMAN
  • J3QSD6_HUMAN

Pseudogenes.org Pseudogenes for SPECC1 Gene

genes like me logo Genes that share paralogs with SPECC1: view

Variants for SPECC1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SPECC1 Gene

SNP ID Clinical significance and condition Chr 17 pos Variation AA Info Type
873216 Benign: not specified 20,312,039(+) T/G
NM_001243439.2(SPECC1):c.3118-1937T>G
INTRON
rs2703806 - p.Met293Leu
rs35835131 - p.Asp769Asn
rs9908032 - p.Ser274Arg

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SPECC1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SPECC1 Gene

Variant ID Type Subtype PubMed ID
dgv3120n100 CNV loss 25217958
dgv566e214 CNV loss 21293372
esv2102373 CNV deletion 18987734
esv2673344 CNV deletion 23128226
esv2761953 CNV gain 21179565
esv2762522 CNV loss 21179565
esv3307298 CNV mobile element insertion 20981092
esv3423014 CNV insertion 20981092
esv3572476 CNV gain 25503493
esv3582567 CNV loss 25503493
esv3582568 CNV loss 25503493
esv3640188 CNV loss 21293372
esv3640189 CNV loss 21293372
esv3640191 CNV loss 21293372
esv3640194 CNV gain 21293372
esv3892983 CNV loss 25118596
nsv1057389 CNV loss 25217958
nsv1061317 CNV gain 25217958
nsv1064854 CNV gain 25217958
nsv2003 CNV deletion 18451855
nsv478175 CNV novel sequence insertion 20440878
nsv520772 CNV loss 19592680
nsv521025 CNV gain 19592680
nsv574581 CNV loss 21841781
nsv833394 CNV gain 17160897
nsv833395 CNV loss 17160897
nsv833396 CNV gain 17160897
nsv960437 CNV duplication 23825009

Variation tolerance for SPECC1 Gene

Residual Variation Intolerance Score: 7.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.79; 79.08% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SPECC1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SPECC1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SPECC1 Gene

Disorders for SPECC1 Gene

MalaCards: The human disease database

(13) MalaCards diseases for SPECC1 Gene - From: COP and GCD

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

CYTSB_HUMAN
  • Note=A chromosomal aberration involving CYTSB may be a cause of juvenile myelomonocytic leukemia. Translocation t(5;17)(q33;p11.2) with PDGFRB. {ECO:0000269 PubMed:15087372}.

Additional Disease Information for SPECC1

genes like me logo Genes that share disorders with SPECC1: view

No data available for Genatlas for SPECC1 Gene

Publications for SPECC1 Gene

  1. Possible functional role of NSPs in cancer. (PMID: 18763323) D'Agostino L … Giordano A (Cell cycle (Georgetown, Tex.) 2008) 2 3 23
  2. HCMOGT-1 is a novel fusion partner to PDGFRB in juvenile myelomonocytic leukemia with t(5;17)(q33;p11.2). (PMID: 15087372) Morerio C … Panarello C (Cancer research 2004) 2 3 4
  3. A gene highly expressed in tumor cells encodes novel structure proteins. (PMID: 15602574) Sang N … Giordano A (Oncogene 2004) 2 3 4
  4. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4

Products for SPECC1 Gene

Sources for SPECC1 Gene