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    SP100 SP100 nuclear antigen [ Homo sapiens (human) ]

    Gene ID: 6672, updated on 31-Mar-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
    NEW
    Try the new Gene table
    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_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (230416201..230545606)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (230899281..231028667)
    105.20220307 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
    • 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

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables chromo shadow domain binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables kinase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein dimerization activity IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein domain specific binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    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 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 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 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 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 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_2023_10

    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)