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SP140 SP140 nuclear body protein [ Homo sapiens (human) ]

Gene ID: 11262, updated on 23-Oct-2022

Summary

Official Symbol
SP140provided by HGNC
Official Full Name
SP140 nuclear body proteinprovided by HGNC
Primary source
HGNC:HGNC:17133
See related
Ensembl:ENSG00000079263 MIM:608602; AllianceGenome:HGNC:17133
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
LYSP100; LYSP100-A; LYSP100-B
Summary
This gene encodes a member of the SP100 family of proteins, which are share common domains including an N-terminal homogeneously staining region domain followed by a SP100/autoimmune regulator/NucP41/P75/deformed epidermal autoregulatory factor domain, a plant homeobox zinc finger, and a bromodomain. The encoded protein is interferon-inducible and is expressed at high levels in the nuclei of leukocytes. Variants of this gene have been associated with multiple sclerosis, Crohn's disease, and chronic lymphocytic leukemia. Alternative splicing results in multiple variants. [provided by RefSeq, Aug 2016]
Expression
Biased expression in lymph node (RPKM 12.2), spleen (RPKM 7.6) and 10 other tissues See more
Orthologs
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Genomic context

See SP140 in Genome Data Viewer
Location:
2q37.1
Exon count:
35
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (230186151..230316571)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (230708861..230796327)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (231090451..231177930)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene solute carrier family 16 member 14 Neighboring gene uncharacterized LOC107985995 Neighboring gene RNY4 pseudogene 19 Neighboring gene SP110 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

EBI GWAS Catalog

Description
A genome-wide association study identifies multiple susceptibility loci for chronic lymphocytic leukemia.
EBI GWAS Catalog
A genome-wide association study identifies six susceptibility loci for chronic lymphocytic leukemia.
EBI GWAS Catalog
Common variation at 6p21.31 (BAK1) influences the risk of chronic lymphocytic leukemia.
EBI GWAS Catalog
Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.
EBI GWAS Catalog
Genome-wide association study identifies multiple risk loci for chronic lymphocytic leukemia.
EBI GWAS Catalog
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
EBI GWAS Catalog
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
EBI GWAS Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Vif vif Wild-type HIV-1 Vif binds to the carboxyl-terminal region of Sp140 between amino acids 527-836, while Vif mutants with deletions of amino acids 12-23, 43-59, 73-87 or 97-112 are strongly inhibited in their binding to Sp140 PubMed
vif HIV-1 Vif may enhance the cytosolic retention of Sp140 PubMed
vif Specific binding of HIV-1 Vif to Sp140 was identified using a yeast two-hybrid screen of a human lymphocyte cDNA library and verified by co-immunoprecipitation 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

  • MGC126440

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
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in defense response TAS
Traceable Author Statement
more info
PubMed 
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 PML body IEA
Inferred from Electronic Annotation
more info
 
located_in fibrillar center IDA
Inferred from Direct Assay
more info
 
located_in mitochondrion 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
nuclear body protein SP140
Names
lymphoid-restricted homolog of Sp100
lymphoid-specific SP100 homolog
nuclear autoantigen Sp-140
speckled 140 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_051286.2 RefSeqGene

    Range
    44587..132066
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001005176.3NP_001005176.1  nuclear body protein SP140 isoform 2

    See identical proteins and their annotated locations for NP_001005176.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks multiple 3' exons, and has an alternate 3' sequence, as compared to variant 1. The encoded isoform 2 is much shorter and has a distinct C-terminus, as compared to isoform 1.
    Source sequence(s)
    AA741304, AK301267, BC070160
    Consensus CDS
    CCDS33392.1
    UniProtKB/Swiss-Prot
    Q13342
    UniProtKB/TrEMBL
    B4DVW8
    Related
    ENSP00000362749.3, ENST00000373645.3
    Conserved Domains (1) summary
    pfam03172
    Location:42135
    Sp100; Sp100 domain
  2. NM_001278451.2NP_001265380.1  nuclear body protein SP140 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AC009949, BC105960, DC391925, U36499
    Consensus CDS
    CCDS63150.1
    UniProtKB/Swiss-Prot
    Q13342
    Related
    ENSP00000398210.3, ENST00000420434.7
    Conserved Domains (4) summary
    cd05501
    Location:730833
    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:665706
    PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
    pfam01342
    Location:558633
    SAND; SAND domain
    pfam03172
    Location:42135
    Sp100; Sp100 domain
  3. NM_001278452.2NP_001265381.1  nuclear body protein SP140 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks two alternate in-frame exons compared to variant 1. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AC009949, BC105744, DC391925, U36499
    Consensus CDS
    CCDS63151.1
    UniProtKB/Swiss-Prot
    Q13342
    UniProtKB/TrEMBL
    Q0VGE4
    Related
    ENSP00000342096.6, ENST00000343805.10
    Conserved Domains (5) summary
    cd05501
    Location:697800
    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 ...
    PHA03169
    Location:202419
    PHA03169; hypothetical protein; Provisional
    cd15626
    Location:632673
    PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
    pfam01342
    Location:525600
    SAND; SAND domain
    pfam03172
    Location:42135
    Sp100; Sp100 domain
  4. NM_001278453.2NP_001265382.1  nuclear body protein SP140 isoform 5

    See identical proteins and their annotated locations for NP_001265382.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks three alternate in-frame exons and uses an alternate in-frame splice junction at the 3' end of an exon compared to variant 1. The resulting isoform (5) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AC009949, AC009950, DC391925, U36499, U63420
    Consensus CDS
    CCDS63149.1
    UniProtKB/Swiss-Prot
    Q13342
    Related
    ENSP00000393618.3, ENST00000417495.7
    Conserved Domains (4) summary
    cd05501
    Location:643746
    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:578619
    PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
    pfam01342
    Location:471546
    SAND; SAND domain
    pfam03172
    Location:42135
    Sp100; Sp100 domain
  5. NM_007237.5NP_009168.4  nuclear body protein SP140 isoform 1

    See identical proteins and their annotated locations for NP_009168.4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC009949, AK301267, BC038091, BC105960, U36500
    Consensus CDS
    CCDS42831.1
    UniProtKB/Swiss-Prot
    Q13342, Q96TG3
    UniProtKB/TrEMBL
    B4DVW8, Q8IWJ1
    Related
    ENSP00000375899.3, ENST00000392045.8
    Conserved Domains (4) summary
    cd05501
    Location:757860
    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:692733
    PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
    pfam01342
    Location:585660
    SAND; SAND domain
    pfam03172
    Location:42135
    Sp100; Sp100 domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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
    230186151..230316571
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047443073.1XP_047299029.1  nuclear body protein SP140 isoform X7

  2. XM_011510517.4XP_011508819.1  nuclear body protein SP140 isoform X7

    See identical proteins and their annotated locations for XP_011508819.1

    Conserved Domains (4) summary
    cd05501
    Location:737840
    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:672713
    PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
    pfam01342
    Location:565640
    SAND; SAND domain
    pfam03172
    Location:22115
    Sp100; Sp100 domain
  3. XM_006712223.4XP_006712286.1  nuclear body protein SP140 isoform X1

    Conserved Domains (4) summary
    cd15626
    Location:692733
    PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
    pfam01342
    Location:585660
    SAND; SAND domain
    pfam03172
    Location:42135
    Sp100; Sp100 domain
    cl02556
    Location:757838
    Bromodomain; Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
  4. XM_047443077.1XP_047299033.1  nuclear body protein SP140 isoform X21

  5. XM_011510518.3XP_011508820.1  nuclear body protein SP140 isoform X7

    See identical proteins and their annotated locations for XP_011508820.1

    Conserved Domains (4) summary
    cd05501
    Location:737840
    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:672713
    PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
    pfam01342
    Location:565640
    SAND; SAND domain
    pfam03172
    Location:22115
    Sp100; Sp100 domain
  6. XM_011510516.2XP_011508818.1  nuclear body protein SP140 isoform X5

    Conserved Domains (4) summary
    cd05501
    Location:748851
    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:692726
    PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
    pfam01342
    Location:585660
    SAND; SAND domain
    pfam03172
    Location:42135
    Sp100; Sp100 domain
  7. XM_011510515.2XP_011508817.1  nuclear body protein SP140 isoform X3

    Conserved Domains (4) summary
    cd05501
    Location:751854
    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:686727
    PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
    pfam01342
    Location:579654
    SAND; SAND domain
    pfam03172
    Location:42135
    Sp100; Sp100 domain
  8. XM_005246254.3XP_005246311.1  nuclear body protein SP140 isoform X13

    Conserved Domains (4) summary
    cd05501
    Location:723826
    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:658699
    PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
    pfam01342
    Location:551626
    SAND; SAND domain
    pfam03172
    Location:42135
    Sp100; Sp100 domain
  9. XM_011510519.2XP_011508821.1  nuclear body protein SP140 isoform X9

    Conserved Domains (4) summary
    cd05501
    Location:730833
    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:665706
    PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
    pfam01342
    Location:558633
    SAND; SAND domain
    pfam03172
    Location:42135
    Sp100; Sp100 domain
  10. XM_005246256.3XP_005246313.1  nuclear body protein SP140 isoform X20

    Conserved Domains (4) summary
    cd05501
    Location:696799
    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:631672
    PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
    pfam01342
    Location:524599
    SAND; SAND domain
    pfam03172
    Location:42135
    Sp100; Sp100 domain
  11. XM_047443078.1XP_047299034.1  nuclear body protein SP140 isoform X24

  12. XM_005246255.3XP_005246312.1  nuclear body protein SP140 isoform X16

    Conserved Domains (4) summary
    cd05501
    Location:707810
    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:642683
    PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
    pfam01342
    Location:535610
    SAND; SAND domain
    pfam03172
    Location:42135
    Sp100; Sp100 domain
  13. XM_047443076.1XP_047299032.1  nuclear body protein SP140 isoform X19

  14. XM_017003252.2XP_016858741.1  nuclear body protein SP140 isoform X28

  15. XM_005246253.3XP_005246310.1  nuclear body protein SP140 isoform X8

    Conserved Domains (5) summary
    cd05501
    Location:731834
    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 ...
    PHA03169
    Location:202453
    PHA03169; hypothetical protein; Provisional
    cd15626
    Location:666707
    PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
    pfam01342
    Location:559634
    SAND; SAND domain
    pfam03172
    Location:42135
    Sp100; Sp100 domain
  16. XM_017003240.2XP_016858729.1  nuclear body protein SP140 isoform X12

  17. XM_017003249.2XP_016858738.1  nuclear body protein SP140 isoform X26

  18. XM_005246252.3XP_005246309.1  nuclear body protein SP140 isoform X2

    Conserved Domains (4) summary
    cd05501
    Location:754857
    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:689730
    PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
    pfam01342
    Location:582657
    SAND; SAND domain
    pfam03172
    Location:42135
    Sp100; Sp100 domain
  19. XM_047443072.1XP_047299028.1  nuclear body protein SP140 isoform X6

  20. XM_017003239.2XP_016858728.1  nuclear body protein SP140 isoform X4

  21. XM_017003243.2XP_016858732.1  nuclear body protein SP140 isoform X15

  22. XM_047443074.1XP_047299030.1  nuclear body protein SP140 isoform X11

  23. XM_017003248.2XP_016858737.1  nuclear body protein SP140 isoform X23

  24. XM_047443079.1XP_047299035.1  nuclear body protein SP140 isoform X25

  25. XM_017003245.2XP_016858734.1  nuclear body protein SP140 isoform X17

  26. XM_011510520.2XP_011508822.1  nuclear body protein SP140 isoform X10

    Conserved Domains (4) summary
    cd05501
    Location:728831
    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:663704
    PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
    pfam01342
    Location:556631
    SAND; SAND domain
    pfam03172
    Location:42135
    Sp100; Sp100 domain
  27. XM_017003242.2XP_016858731.1  nuclear body protein SP140 isoform X14

  28. XM_017003247.2XP_016858736.1  nuclear body protein SP140 isoform X22

  29. XM_017003246.2XP_016858735.1  nuclear body protein SP140 isoform X18

  30. XM_017003250.2XP_016858739.1  nuclear body protein SP140 isoform X27

  31. XM_047443080.1XP_047299036.1  nuclear body protein SP140 isoform X29

  32. XM_047443081.1XP_047299037.1  nuclear body protein SP140 isoform X31

  33. XM_017003253.2XP_016858742.1  nuclear body protein SP140 isoform X30

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    230708861..230796327
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)