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    SP110 SP110 nuclear body protein [ Homo sapiens (human) ]

    Gene ID: 3431, updated on 28-Jun-2021

    Summary

    Official Symbol
    SP110provided by HGNC
    Official Full Name
    SP110 nuclear body proteinprovided by HGNC
    Primary source
    HGNC:HGNC:5401
    See related
    Ensembl:ENSG00000135899 MIM:604457
    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
    IPR1; VODI; IFI41; IFI75
    Summary
    The nuclear body is a multiprotein complex that may have a role in the regulation of gene transcription. This gene is a member of the SP100/SP140 family of nuclear body proteins and encodes a leukocyte-specific nuclear body component. The protein can function as an activator of gene transcription and may serve as a nuclear hormone receptor coactivator. In addition, it has been suggested that the protein may play a role in ribosome biogenesis and in the induction of myeloid cell differentiation. Alternative splicing has been observed for this gene and three transcript variants, encoding distinct isoforms, have been identified. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in spleen (RPKM 11.2), lymph node (RPKM 10.7) and 24 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See SP110 in Genome Data Viewer
    Location:
    2q37.1
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (230165186..230225729, complement)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (231029902..231090351, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene solute carrier family 16 member 14 Neighboring gene uncharacterized LOC107985995 Neighboring gene uncharacterized LOC107985997 Neighboring gene SP140 nuclear body protein Neighboring gene SP140 nuclear body protein like Neighboring gene uncharacterized LOC105373925 Neighboring gene uncharacterized LOC101928816 Neighboring gene SP100 nuclear antigen Neighboring gene RNA, 7SL, cytoplasmic 834, pseudogene

    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?

    Phenotypes

    Associated conditions

    Description Tests
    A genome-wide association study identifies multiple susceptibility loci for chronic lymphocytic leukemia.
    GeneReviews: Not available
    A genome-wide association study identifies six susceptibility loci for chronic lymphocytic leukemia.
    GeneReviews: Not available
    Common variation at 6p21.31 (BAK1) influences the risk of chronic lymphocytic leukemia.
    GeneReviews: Not available
    Genome-wide association study identifies multiple risk loci for chronic lymphocytic leukemia.
    GeneReviews: Not available
    Hepatic veno-occlusive disease-immunodeficiency syndrome Compare labs
    Mycobacterium tuberculosis, susceptibility to
    MedGen: C1834752 OMIM: 607948 GeneReviews: Not available
    Compare labs
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    GeneReviews: Not available

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Infectious wild type HIV-1 production is enhanced by 293T cells over-expressing SP110 PubMed
    Knockdown of SP110 nuclear body protein by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat Microarray analysis indicates HIV-1 Tat upregulates the interferon-responsive gene expression of many proteins, including IFI41, in immature dendritic cells, an effect that likely facilitates the expansion of HIV-1 infection PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ22835

    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
    PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 

    General protein information

    Preferred Names
    sp110 nuclear body protein
    Names
    interferon-induced protein 41, 30kD
    interferon-induced protein 41/75
    interferon-induced protein 75, 52kD
    phosphoprotein 41
    phosphoprotein 75
    speckled 110 kDa
    transcriptional coactivator Sp110

    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_008295.1 RefSeqGene

      Range
      3327..56194
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_109

    mRNA and Protein(s)

    1. NM_001185015.2NP_001171944.1  sp110 nuclear body protein isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (d) has an alternate 5' sequence, lacks multiple 3' exons and has an alternate 3' exon, compared to variant c. The resulting protein (isoform d) has a longer N-terminus and a shorter and distinct C-terminus when it is compared to isoform c.
      Source sequence(s)
      AC009950, AK301097, BC019059
      Consensus CDS
      CCDS54435.1
      UniProtKB/Swiss-Prot
      Q9HB58
      Related
      ENSP00000439558.1, ENST00000540870.5
      Conserved Domains (2) summary
      pfam01342
      Location:465540
      SAND; SAND domain
      pfam03172
      Location:17110
      Sp100; Sp100 domain
    2. NM_001378442.1NP_001365371.1  sp110 nuclear body protein isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC009950
      Conserved Domains (4) summary
      cd15626
      Location:542583
      PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
      pfam01342
      Location:465538
      SAND; SAND domain
      pfam03172
      Location:14112
      HSR; HSR domain
      cl02556
      Location:574733
      Bromodomain; Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
    3. NM_001378443.1NP_001365372.1  sp110 nuclear body protein isoform f

      Status: REVIEWED

      Source sequence(s)
      AC009950
      Conserved Domains (4) summary
      cd15626
      Location:536577
      PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
      pfam01342
      Location:459532
      SAND; SAND domain
      pfam03172
      Location:8106
      HSR; HSR domain
      cl02556
      Location:568727
      Bromodomain; Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
    4. NM_001378444.1NP_001365373.1  sp110 nuclear body protein isoform g

      Status: REVIEWED

      Source sequence(s)
      AC009950
      Conserved Domains (4) summary
      cd05501
      Location:607707
      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 ...
      cd15626
      Location:542583
      PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
      pfam01342
      Location:465538
      SAND; SAND domain
      pfam03172
      Location:14112
      HSR; HSR domain
    5. NM_001378445.1NP_001365374.1  sp110 nuclear body protein isoform h

      Status: REVIEWED

      Source sequence(s)
      AC009950
      Conserved Domains (4) summary
      cd15626
      Location:542583
      PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
      pfam01342
      Location:465538
      SAND; SAND domain
      pfam03172
      Location:14112
      HSR; HSR domain
      cl02556
      Location:574683
      Bromodomain; Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
    6. NM_001378446.1NP_001365375.1  sp110 nuclear body protein isoform i

      Status: REVIEWED

      Source sequence(s)
      AC009950
      Conserved Domains (4) summary
      cd15626
      Location:542583
      PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
      pfam01342
      Location:465538
      SAND; SAND domain
      pfam03172
      Location:14112
      HSR; HSR domain
      cl02556
      Location:574636
      Bromodomain; Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
    7. NM_001378447.1NP_001365376.1  sp110 nuclear body protein isoform j

      Status: REVIEWED

      Source sequence(s)
      AC009950
      Conserved Domains (2) summary
      pfam01342
      Location:409484
      SAND; SAND domain
      pfam03172
      Location:8106
      HSR; HSR domain
    8. NM_004509.5NP_004500.4  sp110 nuclear body protein isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (a) lacks an internal alternate exon in the 3' coding region, compared to variant c. The resulting protein (isoform a) has a truncated bromodomain region when it is compared to isoform c.
      Source sequence(s)
      AC009950
      Consensus CDS
      CCDS2474.1
      Related
      ENSP00000351488.4, ENST00000358662.9
      Conserved Domains (5) summary
      cd15626
      Location:536577
      PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
      pfam01342
      Location:463532
      SAND; SAND domain
      pfam03172
      Location:8106
      HSR; HSR domain
      pfam05110
      Location:171380
      AF-4; AF-4 proto-oncoprotein
      cl02556
      Location:568677
      Bromodomain; Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
    9. NM_004510.4NP_004501.4  sp110 nuclear body protein isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (b) uses an alternate exon for the 3' coding region and 3' UTR, as compared to variant c. The encoded protein (isoform b) has a shorter and distinct C-terminus and lacks the bromodomain when it is compared to isoform c.
      Source sequence(s)
      AC009950
      Consensus CDS
      CCDS2476.1
      Related
      ENSP00000258382.5, ENST00000258382.10
      Conserved Domains (3) summary
      pfam01342
      Location:463534
      SAND; SAND domain
      pfam03172
      Location:8106
      HSR; HSR domain
      pfam05110
      Location:171380
      AF-4; AF-4 proto-oncoprotein
    10. NM_080424.4NP_536349.3  sp110 nuclear body protein isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (c) represents the longest transcript and it encodes the longest protein (isoform c).
      Source sequence(s)
      AC009950, AK026488, AL832300, DB474530, L22343
      Consensus CDS
      CCDS2475.1
      Related
      ENSP00000258381.6, ENST00000258381.11
      Conserved Domains (4) summary
      cd05501
      Location:601701
      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 ...
      cd15626
      Location:536577
      PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
      pfam01342
      Location:459532
      SAND; SAND domain
      pfam03172
      Location:8106
      HSR; HSR domain

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

    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
      230165186..230225729 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024452850.1XP_024308618.1  sp110 nuclear body protein isoform X8

      Conserved Domains (4) summary
      cd15626
      Location:492533
      PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
      pfam01342
      Location:415488
      SAND; SAND domain
      pfam03172
      Location:14112
      HSR; HSR domain
      cl02556
      Location:524586
      Bromodomain; Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
    2. XM_011511091.3XP_011509393.1  sp110 nuclear body protein isoform X6

      Conserved Domains (4) summary
      cd15626
      Location:542583
      PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
      pfam01342
      Location:465538
      SAND; SAND domain
      pfam03172
      Location:17110
      Sp100; Sp100 domain
      cl02556
      Location:574660
      Bromodomain; Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
    3. XM_011511090.3XP_011509392.1  sp110 nuclear body protein isoform X5

      Conserved Domains (4) summary
      cd15626
      Location:492533
      PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
      pfam01342
      Location:415488
      SAND; SAND domain
      pfam03172
      Location:17110
      Sp100; Sp100 domain
      cl02556
      Location:524683
      Bromodomain; Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
    4. XM_017003968.2XP_016859457.1  sp110 nuclear body protein isoform X1

      Conserved Domains (4) summary
      cd15626
      Location:542583
      PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
      pfam01342
      Location:465538
      SAND; SAND domain
      pfam03172
      Location:14112
      HSR; HSR domain
      cl02556
      Location:574733
      Bromodomain; Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
    5. XM_011511092.3XP_011509394.1  sp110 nuclear body protein isoform X9

      Conserved Domains (3) summary
      cd15626
      Location:333374
      PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
      pfam01342
      Location:256329
      SAND; SAND domain
      cl02556
      Location:365524
      Bromodomain; Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
    6. XM_017003969.1XP_016859458.1  sp110 nuclear body protein isoform X10

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