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

Gene ID: 316580, updated on 2-Nov-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, Nov 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 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
    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
    A0A8I6APK4
    Related
    ENSRNOP00000071192.3, ENSRNOT00000078987.3

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

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

  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

    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

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

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

  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

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

  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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