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    Sp140 SP140 nuclear body protein [ Rattus norvegicus (Norway rat) ]

    Gene ID: 316580, updated on 9-Dec-2024

    Summary

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    Symbol
    Sp140provided by RGD
    Full Name
    SP140 nuclear body proteinprovided by RGD
    Primary source
    RGD:1306355
    See related
    EnsemblRapid:ENSRNOG00000022800 AllianceGenome:RGD:1306355
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    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 fibrillar center and mitochondrion. Predicted to be active in nucleus. Orthologous to several human genes including SP140 (SP140 nuclear body protein). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Spleen (RPKM 324.9), Thymus (RPKM 160.9) and 8 other tissues See more
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    Genomic context

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    See Sp140 in Genome Data Viewer
    Location:
    9q35
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 9 NC_086027.1 (93672536..93722596)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 9 NC_051344.1 (86224472..86274724)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (92618088..92665431)

    Chromosome 9 - NC_086027.1Genomic Context describing neighboring genes Neighboring gene solute carrier family 16, member 14 Neighboring gene uncharacterized LOC120094727 Neighboring gene uncharacterized LOC134480599 Neighboring gene component of Sp100-rs Neighboring gene SP110 nuclear body protein Neighboring gene SP100 nuclear antigen Neighboring gene RIKEN cDNA A630001G21 gene like

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    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 fibrillar center ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in mitochondrion ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    nuclear body protein SP140
    Names
    nuclear body protein SP140-like

    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_001012133.1 → NP_001012133.1  nuclear body protein SP140

      See identical proteins and their annotated locations for NP_001012133.1

      Status: PROVISIONAL

      Source sequence(s)
      BC081971
      UniProtKB/TrEMBL
      A0A0G2JZU7, F7EWA3, Q66H87
      Related
      ENSRNOP00000031057.7, ENSRNOT00000034603.8
      Conserved Domains (4) summary
      cd15626
      Location:547 → 588
      PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
      pfam01342
      Location:442 → 517
      SAND; SAND domain
      pfam03172
      Location:28 → 119
      Sp100; Sp100 domain
      cl02556
      Location:611 → 714
      Bromodomain; Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086027.1 Reference GRCr8

      Range
      93672536..93722596
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039083714.2 → XP_038939642.1  nuclear body protein SP140 isoform X1

      UniProtKB/TrEMBL
      A0A0G2JZU7
      Conserved Domains (4) summary
      cd15626
      Location:547 → 588
      PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
      pfam01342
      Location:442 → 517
      SAND; SAND domain
      pfam03172
      Location:25 → 122
      HSR; HSR domain
      cl02556
      Location:611 → 747
      Bromodomain; Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.

    2. XM_039083716.2 → XP_038939644.1  nuclear body protein SP140 isoform X3

      UniProtKB/TrEMBL
      A0A0G2JZU7
      Conserved Domains (4) summary
      cd15626
      Location:533 → 574
      PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
      pfam01342
      Location:442 → 517
      SAND; SAND domain
      pfam03172
      Location:25 → 122
      HSR; HSR domain
      cl02556
      Location:597 → 733
      Bromodomain; Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.

    3. XM_063267283.1 → XP_063123353.1  nuclear body protein SP140 isoform X7

      UniProtKB/TrEMBL
      A0A0G2JZU7, A0A8I5ZPF5

    4. XM_039083717.2 → XP_038939645.1  nuclear body protein SP140 isoform X4

      UniProtKB/TrEMBL
      A0A0G2JZU7
      Conserved Domains (4) summary
      cd15626
      Location:530 → 571
      PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
      pfam01342
      Location:425 → 500
      SAND; SAND domain
      pfam03172
      Location:25 → 122
      HSR; HSR domain
      cl02556
      Location:594 → 730
      Bromodomain; Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.

    5. XM_063267284.1 → XP_063123354.1  nuclear body protein SP140 isoform X8

      UniProtKB/TrEMBL
      A0A0G2JZU7, A0A8I6APK4
      Related
      ENSRNOP00000071192.3, ENSRNOT00000078987.3

    6. XM_063267282.1 → XP_063123352.1  nuclear body protein SP140 isoform X6

      UniProtKB/TrEMBL
      A0A0G2JZU7

    7. XM_063267286.1 → XP_063123356.1  nuclear body protein SP140 isoform X11

      UniProtKB/TrEMBL
      A0A0G2JZU7

    8. XM_039083719.2 → XP_038939647.1  nuclear body protein SP140 isoform X9

      UniProtKB/TrEMBL
      A0A0G2JZU7
      Conserved Domains (4) summary
      cd15626
      Location:496 → 537
      PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
      pfam01342
      Location:391 → 466
      SAND; SAND domain
      pfam03172
      Location:25 → 122
      HSR; HSR domain
      cl02556
      Location:560 → 696
      Bromodomain; Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.

    9. XM_063267287.1 → XP_063123357.1  nuclear body protein SP140 isoform X13

      UniProtKB/TrEMBL
      A0A0G2JZU7
      Related
      ENSRNOP00000096593.2, ENSRNOT00000110179.2

    10. XM_039083722.2 → XP_038939650.1  nuclear body protein SP140 isoform X12

      UniProtKB/TrEMBL
      A0A0G2JZU7
      Conserved Domains (4) summary
      cd15626
      Location:474 → 515
      PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
      pfam01342
      Location:369 → 444
      SAND; SAND domain
      pfam03172
      Location:25 → 122
      HSR; HSR domain
      cl02556
      Location:538 → 674
      Bromodomain; Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.

    11. XM_063267289.1 → XP_063123359.1  nuclear body protein SP140 isoform X15

      UniProtKB/TrEMBL
      A0A0G2JZU7

    12. XM_063267288.1 → XP_063123358.1  nuclear body protein SP140 isoform X14

      UniProtKB/TrEMBL
      A0A0G2JZU7

    13. XM_063267291.1 → XP_063123361.1  nuclear body protein SP140 isoform X17

      UniProtKB/TrEMBL
      A0A0G2JZU7

    14. XM_039083718.2 → XP_038939646.1  nuclear body protein SP140 isoform X5

      UniProtKB/TrEMBL
      A0A0G2JZU7
      Conserved Domains (4) summary
      cd15626
      Location:519 → 560
      PHD_SP110_140; PHD finger found in the Sp100/Sp140 family of nuclear body components
      pfam01342
      Location:414 → 489
      SAND; SAND domain
      pfam03172
      Location:25 → 119
      HSR; HSR domain
      cl02556
      Location:583 → 719
      Bromodomain; Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.

    15. XM_063267285.1 → XP_063123355.1  nuclear body protein SP140 isoform X10

      UniProtKB/TrEMBL
      A0A0G2JZU7

    16. XM_063267290.1 → XP_063123360.1  nuclear body protein SP140 isoform X16

      UniProtKB/TrEMBL
      A0A0G2JZU7

    17. XM_039083724.2 → XP_038939652.1  nuclear body protein SP140 isoform X18

      Conserved Domains (2) summary
      pfam01342
      Location:442 → 517
      SAND; SAND domain
      pfam03172
      Location:25 → 122
      HSR; HSR domain

    18. XM_063267292.1 → XP_063123362.1  nuclear body protein SP140 isoform X19

    19. XM_039083715.2 → XP_038939643.1  nuclear body protein SP140 isoform X2

      UniProtKB/TrEMBL
      A0A0G2JZU7
      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:431 → 506
      SAND; SAND domain
      pfam03172
      Location:14 → 111
      HSR; HSR domain
      cl02556
      Location:600 → 736
      Bromodomain; Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.

    RNA

    1. XR_010054606.1 RNA Sequence

    2. XR_010054607.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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