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    Spen spen family transcriptional repressor [ Rattus norvegicus (Norway rat) ]

    Gene ID: 690911, updated on 9-Dec-2024

    Summary

    Official Symbol
    Spenprovided by RGD
    Official Full Name
    spen family transcriptional repressorprovided by RGD
    Primary source
    RGD:1589867
    See related
    EnsemblRapid:ENSRNOG00000033556 AllianceGenome:RGD:1589867
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1564662
    Summary
    Predicted to enable several functions, including RNA polymerase II-specific DNA-binding transcription factor binding activity; nucleic acid binding activity; and transcription corepressor activity. Predicted to be involved in negative regulation of macromolecule biosynthetic process and positive regulation of neurogenesis. Predicted to act upstream of or within negative regulation of DNA-templated transcription and positive regulation of DNA-templated transcription. Predicted to be located in nucleoplasm. Predicted to be part of transcription repressor complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in esophagus squamous cell carcinoma. Orthologous to human SPEN (spen family transcriptional repressor). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Kidney (RPKM 70.3), Adrenal (RPKM 68.4) and 9 other tissues See more
    Orthologs
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    Try the new Transcript table

    Genomic context

    See Spen in Genome Data Viewer
    Location:
    5q36
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (159058258..159131789, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (153775287..153848677, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (160015573..160070915, complement)

    Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene transfer RNA proline (anticodon AGG) 71 Neighboring gene steroid receptor associated and regulated protein Neighboring gene zinc finger and BTB domain containing 17 Neighboring gene filamin binding LIM protein 1 Neighboring gene uncharacterized LOC134487029 Neighboring gene transmembrane protein 82

    Genomic regions, transcripts, and products

    Expression

    • 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

    General gene information

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    NOT enables DNA binding  
    enables DNA-binding transcription factor activity  
    enables RNA polymerase II-specific DNA-binding transcription factor binding  
    enables mRNA binding  
    enables single-stranded DNA binding  
    enables transcription corepressor activity  
    Component Evidence Code Pubs
    located_in nucleoplasm  
    located_in nucleoplasm  
    is_active_in nucleus  
    located_in nucleus  
    part_of transcription repressor complex  

    General protein information

    Preferred Names
    msx2-interacting protein
    Names
    SPEN homolog, transcriptional regulator
    rCG30673-like

    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.

    mRNA and Protein(s)

    1. NM_001395101.1NP_001382030.1  msx2-interacting protein

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000005
      UniProtKB/TrEMBL
      A6ITU2, F1M816
      Related
      ENSRNOP00000102912.1, ENSRNOT00000127835.1
      Conserved Domains (11) summary
      PTZ00121
      Location:7731252
      PTZ00121; MAEBL; Provisional
      PTZ00449
      Location:15291983
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      PHA03247
      Location:30813473
      PHA03247; large tegument protein UL36; Provisional
      COG0724
      Location:512671
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      pfam05109
      Location:26693118
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      pfam07744
      Location:34683631
      SPOC; SPOC domain
      pfam15984
      Location:26302723
      Collagen_mid; Bacterial collagen, middle region
      cd12348
      Location:781
      RRM1_SHARP; RNA recognition motif 1 (RRM1) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12349
      Location:336409
      RRM2_SHARP; RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12350
      Location:436509
      RRM3_SHARP; RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12351
      Location:510586
      RRM4_SHARP; RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

    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_086023.1 Reference GRCr8

      Range
      159058258..159131789 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039110807.2XP_038966735.1  msx2-interacting protein isoform X2

      UniProtKB/TrEMBL
      A6ITU2
      Conserved Domains (11) summary
      PTZ00121
      Location:7721251
      PTZ00121; MAEBL; Provisional
      PTZ00449
      Location:15281982
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      PHA03247
      Location:30803467
      PHA03247; large tegument protein UL36; Provisional
      COG0724
      Location:511670
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      pfam05109
      Location:26683117
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      pfam07744
      Location:34683631
      SPOC; SPOC domain
      pfam15984
      Location:26292722
      Collagen_mid; Bacterial collagen, middle region
      cd12348
      Location:781
      RRM1_SHARP; RNA recognition motif 1 (RRM1) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12349
      Location:335408
      RRM2_SHARP; RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12350
      Location:435508
      RRM3_SHARP; RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12351
      Location:509585
      RRM4_SHARP; RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
    2. XM_039110804.2XP_038966732.1  msx2-interacting protein isoform X1

      UniProtKB/TrEMBL
      A6ITU2
      Conserved Domains (11) summary
      PTZ00121
      Location:7731252
      PTZ00121; MAEBL; Provisional
      PTZ00449
      Location:15291983
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      PHA03247
      Location:30813468
      PHA03247; large tegument protein UL36; Provisional
      COG0724
      Location:512671
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      pfam05109
      Location:26693118
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      pfam07744
      Location:34693632
      SPOC; SPOC domain
      pfam15984
      Location:26302723
      Collagen_mid; Bacterial collagen, middle region
      cd12348
      Location:781
      RRM1_SHARP; RNA recognition motif 1 (RRM1) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12349
      Location:336409
      RRM2_SHARP; RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12350
      Location:436509
      RRM3_SHARP; RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12351
      Location:510586
      RRM4_SHARP; RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
    3. XM_039110809.2XP_038966737.1  msx2-interacting protein isoform X3

      UniProtKB/TrEMBL
      A6ITU2
      Conserved Domains (10) summary
      PTZ00121
      Location:7051184
      PTZ00121; MAEBL; Provisional
      PTZ00449
      Location:14611915
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      PHA03247
      Location:30133400
      PHA03247; large tegument protein UL36; Provisional
      COG0724
      Location:444603
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      pfam05109
      Location:26013050
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      pfam07744
      Location:34013564
      SPOC; SPOC domain
      pfam15984
      Location:25622655
      Collagen_mid; Bacterial collagen, middle region
      cd12349
      Location:268341
      RRM2_SHARP; RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12350
      Location:368441
      RRM3_SHARP; RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12351
      Location:442518
      RRM4_SHARP; RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
    4. XM_063288446.1XP_063144516.1  msx2-interacting protein isoform X4

      UniProtKB/TrEMBL
      A6ITU2

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