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

    Gene ID: 93349, updated on 10-Dec-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 active in nucleus. [provided by Alliance of Genome Resources, Dec 2024]
    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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    See SP140L in Genome Data Viewer
    Location:
    2q37.1
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (230327193..230403732)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (230810305..230886812)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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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    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)

    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_2024_08

    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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