SP100 SP100 nuclear antigen [Homo sapiens (human)] - Gene

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: mouse all
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Genomic context

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_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

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?

Histone lactylation-boosted ALKBH3 potentiates tumor progression and diminished promyelocytic leukemia protein nuclear condensates by m1A demethylation of SP100A.
Title: Histone lactylation-boosted ALKBH3 potentiates tumor progression and diminished promyelocytic leukemia protein nuclear condensates by m1A demethylation of SP100A.
PML Body Component Sp100A Restricts Wild-Type Herpes Simplex Virus 1 Infection.
Title: PML Body Component Sp100A Restricts Wild-Type Herpes Simplex Virus 1 Infection.
significant genetic predisposition to the sp100 autoantibody, but not the gp210 autoantibody, subphenotype in primary biliary cholangitis patients
Title: Genome-wide Association Studies of Specific Antinuclear Autoantibody Subphenotypes in Primary Biliary Cholangitis.
Findings demonstrated that spheroids from pancreatic cancer cells caused circular defects in lymphatic endothelial monolayers. These CCIDs in pancreatic cancer were partly regulated by S100P.
Title: S100P regulates the collective invasion of pancreatic cancer cells into the lymphatic endothelial monolayer.
The cellular nuclear domain 10 (ND10) complex plays an important role in suppressing HHV-6A lytic replication and the silencing of the virus genome in latently infected cells.
Title: The ND10 Complex Represses Lytic Human Herpesvirus 6A Replication and Promotes Silencing of the Viral Genome.
the ND10 bodies become viral replication compartments, and ICP0, a viral E3 ligase, degrades both PML and SP100. The amounts of PML and SP100 and the number of ND10 structures increase in cells exposed to IFN-beta.
Title: The SP100 component of ND10 enhances accumulation of PML and suppresses replication and the assembly of HSV replication compartments.
that Sp100 represses viral transcription and replication in differentiated cells
Title: Sp100 colocalizes with HPV replication foci and restricts the productive stage of the infectious cycle.
Data suggest that nuclear antigen Sp100C is a multifaceted histone H3 methylation and phosphorylation sensor.
Title: Multifaceted Histone H3 Methylation and Phosphorylation Readout by the Plant Homeodomain Finger of Human Nuclear Antigen Sp100C.
These results suggest that high-risk human papillomavirus 31 target interferon kappa to prevent Sp100 expression and identify Sp100 as an interferon-stimulated gene with anti-human papillomavirus activity.
Title: Interferon Kappa Inhibits Human Papillomavirus 31 Transcription by Inducing Sp100 Proteins.
PML, hDaxx and Sp100 primarily act as cellular restriction factors during lytic human cytomegalovirus replication and during the dynamic process of reactivation but do not serve as key determinants for the establishment of latency.
Title: Contribution of the Major ND10 Proteins PML, hDaxx and Sp100 to the Regulation of Human Cytomegalovirus Latency and Lytic Replication in the Monocytic Cell Line THP-1.

Submit: New GeneRIF Correction See all GeneRIFs (34)

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

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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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH93607 (e-PCR)
- UniSTS:84503

D8S2279 (e-PCR)
- UniSTS:473907

SHGC-144697 (e-PCR)
- UniSTS:172362

D2S2641 (e-PCR)
- UniSTS:11877

RH70945 (e-PCR)
- UniSTS:78966

WIAF-2192 (e-PCR)
- UniSTS:12177

RH68107 (e-PCR)
- UniSTS:67994

REN30944 (e-PCR)
- UniSTS:355744

GDB:335751 (e-PCR)
- UniSTS:156601

PMC56901P1 (e-PCR)
- UniSTS:273357

PMC56901P2 (e-PCR)
- UniSTS:273358

D2S2624 (e-PCR)
- UniSTS:29403

MARC_26602-26603:1033757772:1 (e-PCR)
- UniSTS:269038

SHGC-60177 (e-PCR)
- UniSTS:51702

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	IC Inferred by Curator more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II-specific DNA-binding transcription factor binding	IPI Inferred from Physical Interaction 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
enables protein homodimerization activity	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 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 more info	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

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Preferred Names: nuclear autoantigen Sp-100

Names: SP100-HMG nuclear autoantigen; nuclear dot-associated Sp100 protein; speckled 100 kDa

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_029842.1 RefSeqGene

Range

5046..134451

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001080391.2 → NP_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:773 → 874

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:704 → 745

PHD_TIF1_like; PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar proteins

pfam01342
Location:600 → 675

SAND; SAND domain

pfam03172
Location:52 → 146

Sp100; Sp100 domain
NM_001206701.2 → NP_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:600 → 675

SAND; SAND domain

pfam03172
Location:52 → 146

Sp100; Sp100 domain
NM_001206702.2 → NP_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:49 → 147

HSR; HSR domain
NM_001206703.2 → NP_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:27 → 121

Sp100; Sp100 domain
NM_001206704.2 → NP_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:17 → 111

Sp100; Sp100 domain
NM_003113.4 → NP_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:769 → 818

HMG_box; HMG (high mobility group) box

pfam01342
Location:600 → 675

SAND; SAND domain

pfam03172
Location:52 → 146

Sp100; Sp100 domain

cl00082
Location:699 → 752

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 ...