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SP100 SP100 nuclear antigen [ Homo sapiens (human) ]

Gene ID: 6672, updated on 28-Jun-2020

Summary

Official Symbol
SP100provided by HGNC
Official Full Name
SP100 nuclear antigenprovided by HGNC
Primary source
HGNC:HGNC:11206
See related
Ensembl:ENSG00000067066 MIM:604585
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
lysp100b
Summary
This gene encodes a subnuclear organelle and major component of the PML (promyelocytic leukemia)-SP100 nuclear bodies. PML and SP100 are covalently modified by the SUMO-1 modifier, which is considered crucial to nuclear body interactions. The encoded protein binds heterochromatin proteins and is thought to play a role in tumorigenesis, immunity, and gene regulation. Alternatively spliced variants have been identified for this gene; one of which encodes a high-mobility group protein. [provided by RefSeq, Aug 2011]
Expression
Ubiquitous expression in lymph node (RPKM 13.9), bone marrow (RPKM 12.8) and 25 other tissues See more
Orthologs

Genomic context

See SP100 in Genome Data Viewer
Location:
2q37.1
Exon count:
32
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (230416156..230545606)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (231280871..231410317)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene SP110 nuclear body protein Neighboring gene SP140 nuclear body protein Neighboring gene SP140 nuclear body protein like Neighboring gene uncharacterized LOC105373925 Neighboring gene uncharacterized LOC101928816 Neighboring gene RNA, 7SL, cytoplasmic 834, pseudogene Neighboring gene high mobility group box 1 pseudogene 3 Neighboring gene uncharacterized LOC112268431 Neighboring gene RNA, U6 small nuclear 451, pseudogene Neighboring gene tropomyosin 3 pseudogene 8

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?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 gp120-treated vaginal epithelial cells show downregulation of SP100 nuclear antigen (SP100) expression as compared to untreated control PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ00340, FLJ34579, DKFZp686E07254

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISM
Inferred from Sequence Model
more info
PubMed 
chromo shadow domain binding IPI
Inferred from Physical Interaction
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
kinase binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein dimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
protein domain specific binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator IDA
Inferred from Direct Assay
more info
PubMed 
interferon-gamma-mediated signaling pathway IC
Inferred by Curator
more info
PubMed 
interferon-gamma-mediated signaling pathway TAS
Traceable Author Statement
more info
 
maintenance of protein location IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of cellular component movement IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of endothelial cell migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of protein export from nucleus IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of Fas signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of angiogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of extrinsic apoptotic signaling pathway via death domain receptors IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to interferon-gamma IDA
Inferred from Direct Assay
more info
PubMed 
response to interferon-gamma IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to type I interferon IDA
Inferred from Direct Assay
more info
PubMed 
response to type I interferon IMP
Inferred from Mutant Phenotype
more info
PubMed 
telomere maintenance IMP
Inferred from Mutant Phenotype
more info
PubMed 
type I interferon signaling pathway IC
Inferred by Curator
more info
PubMed 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
colocalizes_with Mre11 complex IDA
Inferred from Direct Assay
more info
PubMed 
PML body IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nuclear body IDA
Inferred from Direct Assay
more info
 
nuclear chromosome, telomeric region HDA PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
nuclear autoantigen Sp-100
Names
SP100-HMG nuclear autoantigen
nuclear dot-associated Sp100 protein
speckled 100 kDa

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_029842.1 RefSeqGene

    Range
    5046..134451
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001080391.2NP_001073860.1  nuclear autoantigen Sp-100 isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1, also known as SP100C).
    Source sequence(s)
    AC010149, AF255565, AK160379, DA562355
    Consensus CDS
    CCDS42832.1
    UniProtKB/Swiss-Prot
    P23497
    UniProtKB/TrEMBL
    Q6ZMK3
    Related
    ENSP00000343023.4, ENST00000340126.9
    Conserved Domains (4) summary
    cd05501
    Location:773874
    Bromo_SP100C_like; Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major component of PML-SP100 nuclear bodies (NBs), which are poorly understood. It is covalently modified by SUMO-1 and may play a role in processes at the chromatin ...
    cd15541
    Location:704745
    PHD_TIF1_like; PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar proteins
    pfam01342
    Location:600675
    SAND; SAND domain
    pfam03172
    Location:52146
    Sp100; Sp100 domain
  2. NM_001206701.2NP_001193630.1  nuclear autoantigen Sp-100 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks several exons which represent the 3' coding and UTR regions of variant 1. Variant 3 represents use of an alternate transcription termination site resulting in a shorter protein (isoform 3, also known as SP100B) with a distinct C-terminus.
    Source sequence(s)
    AK293373, DA562355, L79987, U36501
    Consensus CDS
    CCDS56170.1
    UniProtKB/Swiss-Prot
    P23497
    Related
    ENSP00000386427.1, ENST00000409112.5
    Conserved Domains (2) summary
    pfam01342
    Location:600675
    SAND; SAND domain
    pfam03172
    Location:52146
    Sp100; Sp100 domain
  3. NM_001206702.1NP_001193631.1  nuclear autoantigen Sp-100 isoform 4

    See identical proteins and their annotated locations for NP_001193631.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks multiple exons which represent the 3' coding and UTR regions of variant 1. Variant 4 represents use of an alternate transcription termination site resulting in a much shorter protein (isoform 4, also known as SP100A) with a distinct C-terminus.
    Source sequence(s)
    AA810108, AK293373, BC011562, DA442074, DA562355
    Consensus CDS
    CCDS56171.1
    UniProtKB/Swiss-Prot
    P23497
    Related
    ENSP00000386404.1, ENST00000409341.5
    Conserved Domains (1) summary
    pfam03172
    Location:49147
    HSR; HSR domain
  4. NM_001206703.1NP_001193632.1  nuclear autoantigen Sp-100 isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 3' UTR and has multiple differences in the coding region, compared to variant 1. The resulting isoform (5) lacks two internal segments and has a much shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AA810108, AK293373, BC011562, DA562355
    Consensus CDS
    CCDS56172.1
    UniProtKB/Swiss-Prot
    P23497
    Related
    ENSP00000399389.2, ENST00000427101.6
    Conserved Domains (1) summary
    pfam03172
    Location:27121
    Sp100; Sp100 domain
  5. NM_001206704.1NP_001193633.1  nuclear autoantigen Sp-100 isoform 6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 5' and 3' UTRs and has multiple differences in the coding region, compared to variant 1. The resulting isoform (6) has shorter and distinct N- and C-termini, compared to isoform 1.
    Source sequence(s)
    AA810108, AK091898, AK293373, BC011562
    Consensus CDS
    CCDS56173.1
    UniProtKB/Swiss-Prot
    P23497
    Related
    ENSP00000386998.1, ENST00000409897.5
    Conserved Domains (1) summary
    pfam03172
    Location:17111
    Sp100; Sp100 domain
  6. NM_003113.4NP_003104.2  nuclear autoantigen Sp-100 isoform 2

    See identical proteins and their annotated locations for NP_003104.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks several exons which represent the 3' coding and UTR regions of variant 1. Variant 2 represents use of an alternate transcription termination site resulting in a shorter protein (isoform 2, also known as SP100-HMG) with a distinct C-terminus. Isoform 2 is identified as a high-mobility group protein.
    Source sequence(s)
    AC010149, AF056322, AI886092, AW978040, DA562355
    Consensus CDS
    CCDS2477.1
    UniProtKB/Swiss-Prot
    P23497
    Related
    ENSP00000264052.5, ENST00000264052.9
    Conserved Domains (4) summary
    pfam00505
    Location:769818
    HMG_box; HMG (high mobility group) box
    pfam01342
    Location:600675
    SAND; SAND domain
    pfam03172
    Location:52146
    Sp100; Sp100 domain
    cl00082
    Location:699752
    HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...

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_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    230416156..230545606
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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