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

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; AllianceGenome:HGNC:5401
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: all
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Genomic context

Location:: 2q37.1

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (230165186..230225636, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (230648299..230708761, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (231029902..231090351, complement)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Transcriptional regulators SP110 and SP140 modulate inflammatory response genes in Mycobacterium tuberculosis-infected human macrophages.
Title: Transcriptional regulators SP110 and SP140 modulate inflammatory response genes in Mycobacterium tuberculosis-infected human macrophages.
Epigenetic regulation of Fructose-1,6-bisphosphatase 1 by host transcription factor Speckled 110 kDa during hepatitis B virus infection.
Title: Epigenetic regulation of Fructose-1,6-bisphosphatase 1 by host transcription factor Speckled 110 kDa during hepatitis B virus infection.
Polymorphisms in the ASAP1 and SP110 Genes and Its Association with the Susceptibility to Pulmonary Tuberculosis in a Mongolian Population.
Title: Polymorphisms in the ASAP1 and SP110 Genes and Its Association with the Susceptibility to Pulmonary Tuberculosis in a Mongolian Population.
HSP60, SP110 and TNF-alpha expression in Chlamydia pneumoniae-positive versus Chlamydia pneumoniae-negative atherosclerotic plaques.
Title: HSP60, SP110 and TNF-α expression in Chlamydia pneumoniae-positive versus Chlamydia pneumoniae-negative atherosclerotic plaques.
Novel Missense Mutation inSP110Associated with Combined Immunodeficiency and Advanced Liver Disease Without VOD.
Title: Novel Missense Mutation inSP110Associated with Combined Immunodeficiency and Advanced Liver Disease Without VOD.
Results suggest that the SP110 variants have a role in controlling genetic susceptibility to latent and active tuberculosis (TB) infection in Taiwan. Additionally, the SP110 rs9061 SNP is shown to be associated with plasma TNFalpha levels in LTBI individuals. These data suggest that the identified SP110 SNPs may serve as a biomarker for latent and active TB infection in Taiwan.
Title: SP110 Polymorphisms Are Genetic Markers for Vulnerability to Latent and Active Tuberculosis Infection in Taiwan.
TNF-alpha -308G>A (rs1800629) showed no association with susceptibility to pulmonary tuberculosis and spinal tuberculosis patients in southern China.
Title: Polymorphisms in the SP110 and TNF-α Gene and Susceptibility to Pulmonary and Spinal Tuberculosis among Southern Chinese Population.
SP110 polymorphism is associated with tuberculosis.
Title: SP110 and PMP22 polymorphisms are associated with tuberculosis risk in a Chinese-Tibetan population.
Data suggest that Sp110 is sumoylated, de-sumoylated, and then released from the promyelocytic leukemia nuclear bodies in hepatocytes infected with HBV (hepatitis B virus); Sp110 differentially regulates several direct target genes of HBx, a viral co-factor; these mechanisms may be involved in evasion of host immune response by HBV. (Sp110 = Speckled 110 kDa; HBx = hepatitis B virus protein X)
Title: Host transcription factor Speckled 110 kDa (Sp110), a nuclear body protein, is hijacked by hepatitis B virus protein X for viral persistence.
Using mouse models and genetic characteristics of human patients the role of SP110b was studied to determine its role in controlling host immunity and susceptibility to TB by modulating nuclear factor-kappaB (NF-kappaB) activity resulting in down regulation of TNF-alpha production and upregulation of NF-kappaB-induced antipoptotic gene expression suppressing IFN-gamma-mediated monocyte and/or macrophage cell death.
Title: SP110b Controls Host Immunity and Susceptibility to Tuberculosis.

Submit: New GeneRIF Correction See all GeneRIFs (31)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Hepatic veno-occlusive disease-immunodeficiency syndrome MedGen: C1856128 OMIM: 235550 GeneReviews: Hepatic Veno-Occlusive Disease with Immunodeficiency	not available
Mycobacterium tuberculosis, susceptibility to MedGen: C1834752 OMIM: 607948 GeneReviews: Not available	not available

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-85063 (e-PCR)
- UniSTS:103448

G09664 (e-PCR)
- UniSTS:75613

RH78723 (e-PCR)
- UniSTS:53138

RH66657 (e-PCR)
- UniSTS:35551

SGC32635 (e-PCR)
- UniSTS:31464

RH45567 (e-PCR)
- UniSTS:63213

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 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

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
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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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)

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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

NG_008295.1 RefSeqGene

Range

3327..56194

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_109

mRNA and Protein(s)

NM_001185015.2 → NP_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/TrEMBL

G5E9C0

Related

ENSP00000439558.1, ENST00000540870.5

Conserved Domains (2) summary

pfam01342
Location:465 → 540

SAND; SAND domain

pfam03172
Location:17 → 110

Sp100; Sp100 domain
NM_001378442.1 → NP_001365371.1 sp110 nuclear body protein isoform 3

Status: REVIEWED

Source sequence(s)

AC009950

Conserved Domains (4) summary

cd15626
Location:542 → 583

PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components

pfam01342
Location:465 → 538

SAND; SAND domain

pfam03172
Location:14 → 112

HSR; HSR domain

cl02556
Location:574 → 733

Bromodomain; Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
NM_001378443.1 → NP_001365372.1 sp110 nuclear body protein isoform f

Status: REVIEWED

Source sequence(s)

AC009950

Conserved Domains (4) summary

cd15626
Location:536 → 577

PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components

pfam01342
Location:459 → 532

SAND; SAND domain

pfam03172
Location:8 → 106

HSR; HSR domain

cl02556
Location:568 → 727

Bromodomain; Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
NM_001378444.1 → NP_001365373.1 sp110 nuclear body protein isoform g

Status: REVIEWED

Source sequence(s)

AC009950

Conserved Domains (4) summary

cd05501
Location:607 → 707

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:542 → 583

PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components

pfam01342
Location:465 → 538

SAND; SAND domain

pfam03172
Location:14 → 112

HSR; HSR domain
NM_001378445.1 → NP_001365374.1 sp110 nuclear body protein isoform h

Status: REVIEWED

Source sequence(s)

AC009950

Conserved Domains (4) summary

cd15626
Location:542 → 583

PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components

pfam01342
Location:465 → 538

SAND; SAND domain

pfam03172
Location:14 → 112

HSR; HSR domain

cl02556
Location:574 → 683

Bromodomain; Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
NM_001378446.1 → NP_001365375.1 sp110 nuclear body protein isoform i

Status: REVIEWED

Source sequence(s)

AC009950

UniProtKB/TrEMBL

A0A8V8TLE9

Conserved Domains (4) summary

cd15626
Location:542 → 583

PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components

pfam01342
Location:465 → 538

SAND; SAND domain

pfam03172
Location:14 → 112

HSR; HSR domain

cl02556
Location:574 → 636

Bromodomain; Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
NM_001378447.1 → NP_001365376.1 sp110 nuclear body protein isoform j

Status: REVIEWED

Source sequence(s)

AC009950

UniProtKB/TrEMBL

A0A8V8TMX7

Related

ENSP00000513567.1, ENST00000698103.1

Conserved Domains (2) summary

pfam01342
Location:409 → 484

SAND; SAND domain

pfam03172
Location:8 → 106

HSR; HSR domain
NM_004509.5 → NP_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

UniProtKB/Swiss-Prot

B4DVI4, F5H1M1, Q14976, Q14977, Q53TG2, Q8WUZ6, Q9HB58, Q9HCT8

Related

ENSP00000351488.4, ENST00000358662.9

Conserved Domains (5) summary

cd15626
Location:536 → 577

PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components

pfam01342
Location:463 → 532

SAND; SAND domain

pfam03172
Location:8 → 106

HSR; HSR domain

pfam05110
Location:171 → 380

AF-4; AF-4 proto-oncoprotein

cl02556
Location:568 → 677

Bromodomain; Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
NM_004510.4 → NP_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

UniProtKB/TrEMBL

G5E9C0

Related

ENSP00000258382.5, ENST00000258382.10

Conserved Domains (3) summary

pfam01342
Location:463 → 534

SAND; SAND domain

pfam03172
Location:8 → 106

HSR; HSR domain

pfam05110
Location:171 → 380

AF-4; AF-4 proto-oncoprotein
NM_080424.4 → NP_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:601 → 701

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:536 → 577

PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components

pfam01342
Location:459 → 532

SAND; SAND domain

pfam03172
Location:8 → 106

HSR; HSR domain

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

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

230165186..230225636 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_024452850.2 → XP_024308618.1 sp110 nuclear body protein isoform X5

UniProtKB/TrEMBL

A0A8V8TMX7

Conserved Domains (4) summary

cd15626
Location:492 → 533

PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components

pfam01342
Location:415 → 488

SAND; SAND domain

pfam03172
Location:14 → 112

HSR; HSR domain

cl02556
Location:524 → 586

Bromodomain; Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
XM_011511090.4 → XP_011509392.1 sp110 nuclear body protein isoform X2

Conserved Domains (4) summary

cd15626
Location:492 → 533

PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components

pfam01342
Location:415 → 488

SAND; SAND domain

pfam03172
Location:17 → 110

Sp100; Sp100 domain

cl02556
Location:524 → 683

Bromodomain; Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
XM_011511091.4 → XP_011509393.1 sp110 nuclear body protein isoform X3

Conserved Domains (4) summary

cd15626
Location:542 → 583

PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components

pfam01342
Location:465 → 538

SAND; SAND domain

pfam03172
Location:17 → 110

Sp100; Sp100 domain

cl02556
Location:574 → 660

Bromodomain; Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
XM_017003968.3 → XP_016859457.1 sp110 nuclear body protein isoform X1

Conserved Domains (4) summary

cd15626
Location:542 → 583

PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components

pfam01342
Location:465 → 538

SAND; SAND domain

pfam03172
Location:14 → 112

HSR; HSR domain

cl02556
Location:574 → 733

Bromodomain; Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
XM_011511092.4 → XP_011509394.1 sp110 nuclear body protein isoform X7

Conserved Domains (3) summary

cd15626
Location:333 → 374

PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components

pfam01342
Location:256 → 329

SAND; SAND domain

cl02556
Location:365 → 524

Bromodomain; Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
XM_047444121.1 → XP_047300077.1 sp110 nuclear body protein isoform X6

UniProtKB/TrEMBL

A0A8V8TMX7, A0A8V8TN67

Related

ENSP00000513564.1, ENST00000698100.1
XM_047444120.1 → XP_047300076.1 sp110 nuclear body protein isoform X4

UniProtKB/TrEMBL

A0A8V8TLE9
XM_017003969.2 → XP_016859458.1 sp110 nuclear body protein isoform X8

UniProtKB/TrEMBL

A0A8V8TMX7

Alternate T2T-CHM13v2.0

Genomic

NC_060926.1 Alternate T2T-CHM13v2.0

Range

230648299..230708761 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054341727.1 → XP_054197702.1 sp110 nuclear body protein isoform X5

UniProtKB/TrEMBL

A0A8V8TMX7
XM_054341724.1 → XP_054197699.1 sp110 nuclear body protein isoform X2
XM_054341725.1 → XP_054197700.1 sp110 nuclear body protein isoform X3
XM_054341723.1 → XP_054197698.1 sp110 nuclear body protein isoform X1
XM_054341729.1 → XP_054197704.1 sp110 nuclear body protein isoform X7
XM_054341728.1 → XP_054197703.1 sp110 nuclear body protein isoform X6

UniProtKB/TrEMBL

A0A8V8TMX7
XM_054341726.1 → XP_054197701.1 sp110 nuclear body protein isoform X4

UniProtKB/TrEMBL

A0A8V8TLE9
XM_054341730.1 → XP_054197705.1 sp110 nuclear body protein isoform X8

UniProtKB/TrEMBL

A0A8V8TMX7