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Aliases for SP140 Gene

Aliases for SP140 Gene

  • SP140 Nuclear Body Protein 2 3 5
  • Lymphoid-Restricted Homolog Of Sp100 3 4
  • Nuclear Autoantigen Sp-140 3 4
  • Speckled 140 KDa 3 4
  • LYSP100 3 4
  • Lymphoid-Specific SP100 Homolog 3
  • Nuclear Body Protein SP140 3
  • LYSP100-A 3
  • LYSP100-B 3

External Ids for SP140 Gene

Previous GeneCards Identifiers for SP140 Gene

  • GC02P229150
  • GC02P229822
  • GC02P231054
  • GC02P231292
  • GC02P230915
  • GC02P230798
  • GC02P231090
  • GC02P222930

Summaries for SP140 Gene

Entrez Gene Summary for SP140 Gene

  • This gene encodes a member of the SP100 family of proteins, which are share common domains including an N-terminal homogeneously staining region domain followed by a SP100/autoimmune regulator/NucP41/P75/deformed epidermal autoregulatory factor domain, a plant homeobox zinc finger, and a bromodomain. The encoded protein is interferon-inducible and is expressed at high levels in the nuclei of leukocytes. Variants of this gene have been associated with multiple sclerosis, Crohn's disease, and chronic lymphocytic leukemia. Alternative splicing results in multiple variants. [provided by RefSeq, Aug 2016]

GeneCards Summary for SP140 Gene

SP140 (SP140 Nuclear Body Protein) is a Protein Coding gene. Diseases associated with SP140 include Primary Biliary Cirrhosis and Crohn's Disease. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and chromatin binding. An important paralog of this gene is SP140L.

UniProtKB/Swiss-Prot for SP140 Gene

  • Component of the nuclear body, also known as nuclear domain 10, PML oncogenic domain, and KR body (PubMed:8910577). May be involved in the pathogenesis of acute promyelocytic leukemia and viral infection (PubMed:8910577). May play a role in chromatin-mediated regulation of gene expression although it does not bind to histone H3 tails (PubMed:24267382).

Additional gene information for SP140 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SP140 Gene

Genomics for SP140 Gene

Regulatory Elements for SP140 Gene

Enhancers for SP140 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02H230222 1.4 Ensembl ENCODE dbSUPER 10 +22.9 22876 6 HDGF PKNOX1 SIN3A BATF ZBTB40 RFX5 FOS ATF7 ETV6 RUNX3 RNU6-451P SP140 ENSG00000225963 FBXO36 SP110
GH02H230229 1.2 Ensembl ENCODE dbSUPER 9.9 +27.7 27668 1 SMARCA5 TRIM22 YBX1 ZEB2 ZNF217 JUND CBX5 TARDBP NBN ATF7 SP140 RNU6-451P SP110 GC02M230309
GH02H230656 1.9 FANTOM5 Ensembl ENCODE dbSUPER 4.5 +458.1 458104 8 HDGF PKNOX1 ATF1 ARNT YBX1 TCF12 ZNF766 GATA2 ZNF143 ZNF207 CAB39 LOC101928816 RNU6-451P ZBTB8OSP2 LINC00471 SP110 SP140 GPR55 ARMC9 SP140L
GH02H230599 1.7 FANTOM5 Ensembl ENCODE dbSUPER 5 +399.0 399011 5 HDGF FOXA2 TBL1XR1 BATF RFX5 ATF7 ETV6 RUNX3 CREM IKZF2 SLC16A14 SP140 SP110 SP140L GPR55 SP100 GC02P230588 LINC01907
GH02H230160 0.6 ENCODE 10.6 -42.4 -42423 0 CTCF ZNF654 MAX TRIM22 ZNF384 REST RAD21 KAT8 ZNF143 SMC3 SLC16A14 SP140 SP110 RNU6-451P ENSG00000283451
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SP140 on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the SP140 gene promoter:

Genomic Location for SP140 Gene

Chromosome:
2
Start:
230,202,742 bp from pter
End:
230,316,616 bp from pter
Size:
113,875 bases
Orientation:
Plus strand

Genomic View for SP140 Gene

Genes around SP140 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SP140 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SP140 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SP140 Gene

Proteins for SP140 Gene

  • Protein details for SP140 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q13342-SP140_HUMAN
    Recommended name:
    Nuclear body protein SP140
    Protein Accession:
    Q13342
    Secondary Accessions:
    • E7ESH9
    • E7EUR5
    • E9PFJ6
    • Q0VGE5
    • Q13341
    • Q3KR17
    • Q4ZG66
    • Q53TG1
    • Q6NSG4
    • Q92881
    • Q96TG3

    Protein attributes for SP140 Gene

    Size:
    867 amino acids
    Molecular mass:
    98223 Da
    Quaternary structure:
    • Interacts with PIN1.
    Miscellaneous:
    • This antigen is recognized by autoantibodies from patients with primary biliary cirrhosis.
    SequenceCaution:
    • Sequence=AAB18617.1; Type=Frameshift; Positions=862; Evidence={ECO:0000305}; Sequence=AAX93282.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SP140 Gene

    Alternative splice isoforms for SP140 Gene

neXtProt entry for SP140 Gene

Post-translational modifications for SP140 Gene

  • Phosphorylation at Thr-726 promotes binding of PIN1 and subsequent isomerization of Pro-727.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SP140 Gene

Domains & Families for SP140 Gene

Gene Families for SP140 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Suggested Antigen Peptide Sequences for SP140 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SP140: view

No data available for UniProtKB/Swiss-Prot for SP140 Gene

Function for SP140 Gene

Molecular function for SP140 Gene

UniProtKB/Swiss-Prot Function:
Component of the nuclear body, also known as nuclear domain 10, PML oncogenic domain, and KR body (PubMed:8910577). May be involved in the pathogenesis of acute promyelocytic leukemia and viral infection (PubMed:8910577). May play a role in chromatin-mediated regulation of gene expression although it does not bind to histone H3 tails (PubMed:24267382).
UniProtKB/Swiss-Prot Induction:
By gamma-interferon.

Phenotypes From GWAS Catalog for SP140 Gene

Gene Ontology (GO) - Molecular Function for SP140 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003700 transcription factor activity, sequence-specific DNA binding TAS 8695863
GO:0005515 protein binding IPI 24267382
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with SP140: view
genes like me logo Genes that share phenotypes with SP140: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for SP140 Gene

Localization for SP140 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SP140 Gene

Nucleus. Nucleus, PML body. Cytoplasm. Note=Localized to nuclear structures termed LANDS, for LYSp100-associated nuclear domains. LANDS are globular, electron-dense structures most often found in the nucleoplasm, but also found at the nuclear membrane and in the cytoplasm, suggesting that these structures may traffic between the cytoplasm and the nucleus (PubMed:8695863). Also colocalizes with PML in a subset of PML nuclear bodies (PubMed:8910577). {ECO:0000269 PubMed:8695863, ECO:0000269 PubMed:8910577}.

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 SP140 gene
Compartment Confidence
nucleus 5
mitochondrion 4
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Mitochondria (2)
  • Nucleoli fibrillar center (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SP140 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001650 fibrillar center IDA --
GO:0005634 nucleus TAS 8910577
GO:0005635 nuclear envelope TAS 8695863
GO:0005654 nucleoplasm TAS 8695863
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with SP140: view

Pathways & Interactions for SP140 Gene

SuperPathways for SP140 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SP140 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006952 defense response TAS 8910577
genes like me logo Genes that share ontologies with SP140: view

No data available for Pathways by source and SIGNOR curated interactions for SP140 Gene

Drugs & Compounds for SP140 Gene

No Compound Related Data Available

Transcripts for SP140 Gene

Unigene Clusters for SP140 Gene

SP140 nuclear body protein:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for SP140 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17a · 17b ^ 18 ^ 19 ^
SP1: - - - - - -
SP2: - - - - - - -
SP3: - - - - - - - - - -
SP4:
SP5: - - - -
SP6: -
SP7: - - -
SP8: - - -
SP9: - -

ExUns: 20 ^ 21a · 21b ^ 22 ^ 23 ^ 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30a · 30b
SP1: -
SP2: -
SP3: -
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:

Relevant External Links for SP140 Gene

GeneLoc Exon Structure for
SP140
ECgene alternative splicing isoforms for
SP140

Expression for SP140 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SP140 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SP140 Gene

This gene is overexpressed in Whole Blood (x9.0), Spleen (x8.5), and Small Intestine - Terminal Ileum (x4.6).

Protein differential expression in normal tissues from HIPED for SP140 Gene

This gene is overexpressed in Blymphocyte (38.3) and Peripheral blood mononuclear cells (21.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SP140 Gene



Protein tissue co-expression partners for SP140 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SP140 Gene:

SP140

SOURCE GeneReport for Unigene cluster for SP140 Gene:

Hs.632549

mRNA Expression by UniProt/SwissProt for SP140 Gene:

Q13342-SP140_HUMAN
Tissue specificity: High levels in spleen and peripheral blood leukocytes, much lower levels in tonsils, thymus, prostate, ovary, small intestine, and colon (PubMed:8695863, PubMed:8910577.) Very low levels in heart, brain, placenta, lung, liver, skeletal muscle, kidney, and pancreas (PubMed:8910577). Not detected in brain, liver and muscle (PubMed:8695863).

Evidence on tissue expression from TISSUES for SP140 Gene

  • Blood(2.2)
genes like me logo Genes that share expression patterns with SP140: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SP140 Gene

Orthologs for SP140 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SP140 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SP140 34
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SP140 34 33
  • 73.78 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SP140 33
  • 72.22 (n)
SP140L 34
  • 34 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Sp140 16 34 33
  • 69 (n)
AC125149.1 34
  • 61 (a)
OneToMany
AC125149.2 34
  • 59 (a)
OneToMany
AC132444.5 34
  • 46 (a)
OneToMany
A530032D15Rik 34
  • 34 (a)
OneToMany
AC133103.1 34
  • 33 (a)
OneToMany
C130026I21Rik 34
  • 32 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Sp140 33
  • 65.16 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 47 (a)
ManyToMany
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 20 (a)
OneToMany
zebrafish
(Danio rerio)
Actinopterygii BX569789.2 34
  • 33 (a)
ManyToMany
zgc:113411 34
  • 24 (a)
ManyToMany
BX569789.4 34
  • 22 (a)
ManyToMany
Species where no ortholog for SP140 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • chicken (Gallus gallus)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SP140 Gene

ENSEMBL:
Gene Tree for SP140 (if available)
TreeFam:
Gene Tree for SP140 (if available)

Paralogs for SP140 Gene

Paralogs for SP140 Gene

Pseudogenes.org Pseudogenes for SP140 Gene

genes like me logo Genes that share paralogs with SP140: view

Variants for SP140 Gene

Sequence variations from dbSNP and Humsavar for SP140 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs397515361 Pathogenic 230,212,372(-) ATGCC(-/C)AGCCT intron-variant, reference, frameshift-variant
rs397515362 Pathogenic 230,216,888(-) TTTTT(-/C)AGCAC intron-variant, reference, frameshift-variant
rs397515569 Pathogenic 230,213,018(-) TGCTT(-/GGTGCTT)CCTAT intron-variant, reference, frameshift-variant, utr-variant-5-prime
rs397515570 Pathogenic 230,212,971(-) CCCCA(-/A)CTGGC intron-variant, reference, frameshift-variant, utr-variant-5-prime
rs397515571 Pathogenic 230,212,345(-) CAAGG(-/G)TAACA intron-variant, splice-donor-variant

Structural Variations from Database of Genomic Variants (DGV) for SP140 Gene

Variant ID Type Subtype PubMed ID
dgv4180n100 CNV loss 25217958
esv2721594 CNV deletion 23290073
esv29172 CNV loss 19812545
esv3433395 CNV duplication 20981092
esv3594598 CNV loss 21293372
esv3594600 CNV loss 21293372
nsv584666 CNV gain 21841781
nsv584667 CNV loss 21841781
nsv961934 CNV duplication 23825009
nsv998291 CNV gain 25217958

Variation tolerance for SP140 Gene

Residual Variation Intolerance Score: 88.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.39; 71.09% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SP140 Gene

Human Gene Mutation Database (HGMD)
SP140
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SP140

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SP140 Gene

Disorders for SP140 Gene

MalaCards: The human disease database

(3) MalaCards diseases for SP140 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
primary biliary cirrhosis
  • biliary liver cirrhosis
crohn's disease
  • crohn disease
chronic lymphocytic leukemia
  • b-cell chronic lymphocytic leukemia
- elite association - COSMIC cancer census association via MalaCards
Search SP140 in MalaCards View complete list of genes associated with diseases

Relevant External Links for SP140

Genetic Association Database (GAD)
SP140
Human Genome Epidemiology (HuGE) Navigator
SP140
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SP140
genes like me logo Genes that share disorders with SP140: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SP140 Gene

Publications for SP140 Gene

  1. LYSP100-associated nuclear domains (LANDs): description of a new class of subnuclear structures and their relationship to PML nuclear bodies. (PMID: 8695863) Dent AL … Staudt LM (Blood 1996) 2 3 4 22 60
  2. Identification and characterization of a leukocyte-specific component of the nuclear body. (PMID: 8910577) Bloch DB … Bloch KD (The Journal of biological chemistry 1996) 2 3 4 22 60
  3. Implication of the lymphocyte-specific nuclear body protein Sp140 in an innate response to human immunodeficiency virus type 1. (PMID: 12368356) Madani N … Kabat D (Journal of virology 2002) 2 3 22 60
  4. Structure of human Sp140 PHD finger: an atypical fold interacting with Pin1. (PMID: 24267382) Zucchelli C … Musco G (The FEBS journal 2014) 3 4 60
  5. Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis. (PMID: 21833088) International Multiple Sclerosis Genetics Consortium … Compston A (Nature 2011) 3 45 60

Products for SP140 Gene

  • Addgene plasmids for SP140

Sources for SP140 Gene

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