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SP140L SP140 nuclear body protein like [ Homo sapiens (human) ]

Gene ID: 93349, updated on 5-Mar-2024

Summary

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Official Symbol
SP140Lprovided by HGNC
Official Full Name
SP140 nuclear body protein likeprovided by HGNC
Primary source
HGNC:HGNC:25105
See related
Ensembl:ENSG00000185404 MIM:617747; AllianceGenome:HGNC:25105
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nuclear body. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in lymph node (RPKM 8.7), spleen (RPKM 8.3) and 24 other tissues See more
Orthologs
all
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Genomic context

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Location:
2q37.1
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (230327193..230403732)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (230810305..230886812)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (231191908..231268447)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene solute carrier family 16 member 14 Neighboring gene uncharacterized LOC107985995 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:230932348-230933118 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17207 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17208 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:231005392-231005920 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12407 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:231044589-231045131 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17209 Neighboring gene SP110 nuclear body protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17210 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:231084625-231084811 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17212 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17213 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17214 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17215 Neighboring gene SP140 nuclear body protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17216 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231129497-231130018 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12408 Neighboring gene MPRA-validated peak4075 silencer Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:231176974-231178173 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12409 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17217 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17218 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231206345-231206936 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17219 Neighboring gene uncharacterized LOC105373925 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12410 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17221 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17220 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17222 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17223 Neighboring gene uncharacterized LOC101928816 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17224 Neighboring gene SP100 nuclear antigen Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17225 Neighboring gene RNA, 7SL, cytoplasmic 834, pseudogene Neighboring gene high mobility group box 1 pseudogene 3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. SP140L, an Evolutionarily Recent Member of the SP100 Family, Is an Autoantigen in Primary Biliary Cirrhosis. Saare M, et al. J Immunol Res, 2015. PMID 26347895, Free PMC Article
  2. A genome-wide association study of behavioral disinhibition. McGue M, et al. Behav Genet, 2013 Sep. PMID 23942779, Free PMC Article
  3. Comparison of substrate specificity of the ubiquitin ligases Nedd4 and Nedd4-2 using proteome arrays. Persaud A, et al. Mol Syst Biol, 2009. PMID 19953087, Free PMC Article
  4. Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study. Flachsbart F, et al. Mutat Res, 2010 Dec 10. PMID 20800603
  5. A census of human transcription factors: function, expression and evolution. Vaquerizas JM, et al. Nat Rev Genet, 2009 Apr. PMID 19274049

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. our results show that SP140L is phylogenetically recent member of SP100 proteins and acts as an autoantigen in primary biliary cirrhosis patients.
    Title: SP140L, an Evolutionarily Recent Member of the SP100 Family, Is an Autoantigen in Primary Biliary Cirrhosis.
  2. Observational study of gene-disease association. (HuGE Navigator)
    Title: Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study.
  3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Submit: New GeneRIF Correction

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

EBI GWAS Catalog

Description
A genome-wide association study of behavioral disinhibition.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC132667

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
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
nuclear body protein SP140-like protein
Names
SP140L-1 protein
SP140L-2 protein
SP140L-3 protein

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.

mRNA and Protein(s)

  1. NM_001308162.3 → NP_001295091.1  nuclear body protein SP140-like protein isoform 2

    See identical proteins and their annotated locations for NP_001295091.1

    Status: VALIDATED

    Source sequence(s)
    AC009949, AK023116, BX281497, DW428200, KF419365
    Consensus CDS
    CCDS77536.1
    UniProtKB/TrEMBL
    U5Y3L1
    Related
    ENSP00000243810.7, ENST00000243810.10
    Conserved Domains (4) summary
    cd05501
    Location:445 → 548
    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:380 → 421
    PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
    pfam01342
    Location:273 → 348
    SAND; SAND domain
    pfam03172
    Location:27 → 121
    Sp100; Sp100 domain

  2. NM_001308163.3 → NP_001295092.1  nuclear body protein SP140-like protein isoform 3

    See identical proteins and their annotated locations for NP_001295092.1

    Status: VALIDATED

    Source sequence(s)
    AC009949, AK023116, BX281497, DW428200, KF419366
    Consensus CDS
    CCDS77537.1
    UniProtKB/TrEMBL
    H7BYP4, U5Y3U3
    Related
    ENSP00000379811.5, ENST00000396563.8
    Conserved Domains (4) summary
    cd05501
    Location:410 → 513
    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:345 → 386
    PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
    pfam01342
    Location:261 → 313
    SAND; SAND domain
    pfam03172
    Location:27 → 121
    Sp100; Sp100 domain

  3. NM_001352892.2 → NP_001339821.1  nuclear body protein SP140-like protein isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC009949
    Conserved Domains (4) summary
    cd05501
    Location:461 → 564
    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:405 → 439
    PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
    pfam01342
    Location:298 → 373
    SAND; SAND domain
    pfam03172
    Location:49 → 147
    HSR; HSR domain

  4. NM_001352893.2 → NP_001339822.1  nuclear body protein SP140-like protein isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC009949
    Conserved Domains (4) summary
    cd05501
    Location:435 → 538
    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:370 → 411
    PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
    pfam01342
    Location:286 → 338
    SAND; SAND domain
    pfam03172
    Location:49 → 147
    HSR; HSR domain

  5. NM_001352894.2 → NP_001339823.1  nuclear body protein SP140-like protein isoform 6

    Status: VALIDATED

    Source sequence(s)
    AC009949, KF419367
    UniProtKB/TrEMBL
    U5Y1J8
    Conserved Domains (4) summary
    cd05501
    Location:401 → 504
    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:345 → 379
    PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
    pfam01342
    Location:261 → 313
    SAND; SAND domain
    pfam03172
    Location:24 → 122
    HSR; HSR domain

  6. NM_138402.6 → NP_612411.4  nuclear body protein SP140-like protein isoform 1

    See identical proteins and their annotated locations for NP_612411.4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC009949, AK023116, AU130836, BQ232706, BQ690359, CR987282, DB240458
    Consensus CDS
    CCDS46538.1
    UniProtKB/Swiss-Prot
    Q2M375, Q4ZG65, Q9BSP3, Q9H930
    Related
    ENSP00000397911.2, ENST00000415673.7
    Conserved Domains (4) summary
    cd05501
    Location:470 → 573
    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:405 → 446
    PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
    pfam01342
    Location:298 → 373
    SAND; SAND domain
    pfam03172
    Location:52 → 146
    Sp100; Sp100 domain

RNA

  1. NR_148198.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC009949

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    230327193..230403732
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047446412.1 → XP_047302368.1  nuclear body protein SP140-like protein isoform X1

  2. XM_047446413.1 → XP_047302369.1  nuclear body protein SP140-like protein isoform X2

  3. XM_006712856.2 → XP_006712919.1  nuclear body protein SP140-like protein isoform X5

    Conserved Domains (4) summary
    cd05501
    Location:426 → 529
    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:370 → 404
    PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
    pfam01342
    Location:286 → 338
    SAND; SAND domain
    pfam03172
    Location:52 → 146
    Sp100; Sp100 domain

  4. XM_047446415.1 → XP_047302371.1  nuclear body protein SP140-like protein isoform X4

  5. XM_047446416.1 → XP_047302372.1  nuclear body protein SP140-like protein isoform X6

  6. XM_047446414.1 → XP_047302370.1  nuclear body protein SP140-like protein isoform X3

  7. XM_047446417.1 → XP_047302373.1  nuclear body protein SP140-like protein isoform X7

  8. XM_011512190.4 → XP_011510492.1  nuclear body protein SP140-like protein isoform X8

    Conserved Domains (3) summary
    cd15626
    Location:422 → 455
    PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
    pfam01342
    Location:315 → 390
    SAND; SAND domain
    pfam03172
    Location:52 → 146
    Sp100; Sp100 domain

  9. XM_047446418.1 → XP_047302374.1  nuclear body protein SP140-like protein isoform X8

  10. XM_047446419.1 → XP_047302375.1  nuclear body protein SP140-like protein isoform X9

  11. XM_047446420.1 → XP_047302376.1  nuclear body protein SP140-like protein isoform X10

    Related
    ENSP00000395195.1, ENST00000444636.5

  12. XM_017005301.3 → XP_016860790.1  nuclear body protein SP140-like protein isoform X11

  13. XM_011512191.2 → XP_011510493.1  nuclear body protein SP140-like protein isoform X12

    Conserved Domains (2) summary
    pfam03172
    Location:52 → 146
    Sp100; Sp100 domain
    cl02536
    Location:315 → 344
    SAND; SAND domain

  14. XM_047446421.1 → XP_047302377.1  nuclear body protein SP140-like protein isoform X13

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    230810305..230886812
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054344615.1 → XP_054200590.1  nuclear body protein SP140-like protein isoform X1

  2. XM_054344616.1 → XP_054200591.1  nuclear body protein SP140-like protein isoform X2

  3. XM_054344619.1 → XP_054200594.1  nuclear body protein SP140-like protein isoform X5

  4. XM_054344618.1 → XP_054200593.1  nuclear body protein SP140-like protein isoform X4

  5. XM_054344620.1 → XP_054200595.1  nuclear body protein SP140-like protein isoform X6

  6. XM_054344617.1 → XP_054200592.1  nuclear body protein SP140-like protein isoform X3

  7. XM_054344621.1 → XP_054200596.1  nuclear body protein SP140-like protein isoform X7

  8. XM_054344622.1 → XP_054200597.1  nuclear body protein SP140-like protein isoform X8

  9. XM_054344623.1 → XP_054200598.1  nuclear body protein SP140-like protein isoform X8

  10. XM_054344624.1 → XP_054200599.1  nuclear body protein SP140-like protein isoform X9

  11. XM_054344625.1 → XP_054200600.1  nuclear body protein SP140-like protein isoform X10

  12. XM_054344626.1 → XP_054200601.1  nuclear body protein SP140-like protein isoform X11

  13. XM_054344627.1 → XP_054200602.1  nuclear body protein SP140-like protein isoform X12

  14. XM_054344628.1 → XP_054200603.1  nuclear body protein SP140-like protein isoform X13

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H930.3 GenPept UniProtKB/Swiss-Prot:Q9H930

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