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

Gene ID: 3431, updated on 1-Jun-2020

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

Genomic context

See SP110 in Genome Data Viewer
Location:
2q37.1
Exon count:
24
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (230165186..230225729, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (231033634..231090444, 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

NHGRI GWAS Catalog

Description
A genome-wide association study identifies multiple susceptibility loci for chronic lymphocytic leukemia.
NHGRI GWA Catalog
A genome-wide association study identifies six susceptibility loci for chronic lymphocytic leukemia.
NHGRI GWA Catalog
Common variation at 6p21.31 (BAK1) influences the risk of chronic lymphocytic leukemia.
NHGRI GWA Catalog
Genome-wide association study identifies multiple risk loci for chronic lymphocytic leukemia.
NHGRI GWA Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog

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
DNA binding IEA
Inferred from Electronic Annotation
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISM
Inferred from Sequence Model
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus TAS
Traceable Author Statement
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)

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
  3. NM_001378443.1NP_001365372.1  sp110 nuclear body protein isoform f

    Status: REVIEWED

    Source sequence(s)
    AC009950
  4. NM_001378444.1NP_001365373.1  sp110 nuclear body protein isoform g

    Status: REVIEWED

    Source sequence(s)
    AC009950
  5. NM_001378445.1NP_001365374.1  sp110 nuclear body protein isoform h

    Status: REVIEWED

    Source sequence(s)
    AC009950
  6. NM_001378446.1NP_001365375.1  sp110 nuclear body protein isoform i

    Status: REVIEWED

    Source sequence(s)
    AC009950
  7. NM_001378447.1NP_001365376.1  sp110 nuclear body protein isoform j

    Status: REVIEWED

    Source sequence(s)
    AC009950
  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, ENST00000358662.8
  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, ENST00000258382.9
  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, ENST00000258381.10

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
    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:17110
    Sp100; Sp100 domain
    cl02556
    Location:574733
    Bromodomain; 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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