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SP100 SP100 nuclear antigen [ Homo sapiens (human) ]

Gene ID: 6672, updated on 19-Sep-2024

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; AllianceGenome:HGNC:11206
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
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Try the new Transcript table

Genomic context

See SP100 in Genome Data Viewer
Location:
2q37.1
Exon count:
32
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (230416201..230545606)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (230899281..231028667)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (231280916..231410321)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17209 Neighboring gene SP110 nuclear body protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17210 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:231084625-231084811 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17212 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17213 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17214 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17215 Neighboring gene SP140 nuclear body protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17216 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231129497-231130018 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12408 Neighboring gene MPRA-validated peak4075 silencer Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:231176974-231178173 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12409 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17217 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17218 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231206345-231206936 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17219 Neighboring gene SP140 nuclear body protein like Neighboring gene uncharacterized LOC105373925 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12410 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17221 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17220 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17222 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17223 Neighboring gene uncharacterized LOC101928816 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17224 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17225 Neighboring gene RNA, 7SL, cytoplasmic 834, pseudogene Neighboring gene high mobility group box 1 pseudogene 3 Neighboring gene MPRA-validated peak4076 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17226 Neighboring gene uncharacterized LOC112268431 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17227 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17228 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17229 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 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

Clone Names

  • FLJ00340, FLJ34579, DKFZp686E07254

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in DNA damage response, signal transduction by p53 class mediator IDA
Inferred from Direct Assay
more info
PubMed 
involved_in maintenance of protein location IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of DNA-templated transcription IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of endothelial cell migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of protein export from nucleus IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of viral transcription IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of Fas signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of angiogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of extrinsic apoptotic signaling pathway via death domain receptors IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
involved_in response to cytokine IDA
Inferred from Direct Assay
more info
PubMed 
involved_in response to retinoic acid IDA
Inferred from Direct Assay
more info
PubMed 
involved_in response to type I interferon IDA
Inferred from Direct Assay
more info
PubMed 
involved_in response to type I interferon IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in response to type II interferon IDA
Inferred from Direct Assay
more info
PubMed 
involved_in response to type II interferon IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in retinoic acid receptor signaling pathway IC
Inferred by Curator
more info
PubMed 
involved_in telomere maintenance IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in type I interferon-mediated signaling pathway IC
Inferred by Curator
more info
PubMed 
involved_in type II interferon-mediated signaling pathway IC
Inferred by Curator
more info
PubMed 
Component Evidence Code Pubs
part_of Mre11 complex IDA
Inferred from Direct Assay
more info
PubMed 
located_in PML body IDA
Inferred from Direct Assay
more info
PubMed 
located_in chromosome, telomeric region HDA PubMed 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in nuclear body IDA
Inferred from Direct Assay
more info
 
located_in nuclear periphery IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleolus IMP
Inferred from Mutant Phenotype
more info
PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in 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)

NEW Try the new Transcript table

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_001206702.2NP_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/TrEMBL
    E9PHV6
    Related
    ENSP00000386404.1, ENST00000409341.5
    Conserved Domains (1) summary
    pfam03172
    Location:49147
    HSR; HSR domain
  4. NM_001206703.2NP_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/TrEMBL
    E9PHV6
    Related
    ENSP00000399389.2, ENST00000427101.6
    Conserved Domains (1) summary
    pfam03172
    Location:27121
    Sp100; Sp100 domain
  5. NM_001206704.2NP_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/TrEMBL
    E9PHV6
    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
    B4DDX5, B8ZZD8, E7EUA7, E9PH61, F8WFE2, O75450, P23497, Q13343, Q8TE34, Q96F70, Q96T24, Q96T95, Q9NP33, Q9UE32
    UniProtKB/TrEMBL
    Q53TD0
    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: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    230416201..230545606
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    230899281..231028667
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)