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

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

    Summary

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    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
    human mouse all
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    Genomic context

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    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

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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. Mutational Characterization and Potential Prognostic Biomarkers of Chinese Patients with Esophageal Squamous Cell Carcinoma. Zhang N, et al. Onco Targets Ther, 2020. PMID 33363385, Free PMC Article
    2. SPEN induces miR-4652-3p to target HIPK2 in nasopharyngeal carcinoma. Li Y, et al. Cell Death Dis, 2020 Jul 2. PMID 32641685, Free PMC Article
    3. The RRM domain of MINT, a novel Msx2 binding protein, recognizes and regulates the rat osteocalcin promoter. Newberry EP, et al. Biochemistry, 1999 Aug 17. PMID 10451362
    4. Interaction of the Epstein-Barr virus mRNA export factor EB2 with human Spen proteins SHARP, OTT1, and a novel member of the family, OTT3, links Spen proteins with splicing regulation and mRNA export. Hiriart E, et al. J Biol Chem, 2005 Nov 4. PMID 16129689
    5. Mint represses transactivation of the type II collagen gene enhancer through interaction with alpha A-crystallin-binding protein 1. Yang X, et al. J Biol Chem, 2005 May 13. PMID 15778499

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    NOT enables DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-binding transcription factor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA polymerase II-specific DNA-binding transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables single-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables transcription corepressor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of neurogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in random inactivation of X chromosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulatory ncRNA-mediated heterochromatin formation ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm 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
    		  
    part_of transcription repressor complex ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    msx2-interacting protein
    Names
    SPEN homolog, transcriptional regulator
    rCG30673-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_001395101.1 → NP_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:773 → 1252
      PTZ00121; MAEBL; Provisional
      PTZ00449
      Location:1529 → 1983
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      PHA03247
      Location:3081 → 3473
      PHA03247; large tegument protein UL36; Provisional
      COG0724
      Location:512 → 671
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      pfam05109
      Location:2669 → 3118
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      pfam07744
      Location:3468 → 3631
      SPOC; SPOC domain
      pfam15984
      Location:2630 → 2723
      Collagen_mid; Bacterial collagen, middle region
      cd12348
      Location:7 → 81
      RRM1_SHARP; RNA recognition motif 1 (RRM1) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12349
      Location:336 → 409
      RRM2_SHARP; RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12350
      Location:436 → 509
      RRM3_SHARP; RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12351
      Location:510 → 586
      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_039110807.2 → XP_038966735.1  msx2-interacting protein isoform X2

      UniProtKB/TrEMBL
      A6ITU2
      Conserved Domains (11) summary
      PTZ00121
      Location:772 → 1251
      PTZ00121; MAEBL; Provisional
      PTZ00449
      Location:1528 → 1982
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      PHA03247
      Location:3080 → 3467
      PHA03247; large tegument protein UL36; Provisional
      COG0724
      Location:511 → 670
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      pfam05109
      Location:2668 → 3117
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      pfam07744
      Location:3468 → 3631
      SPOC; SPOC domain
      pfam15984
      Location:2629 → 2722
      Collagen_mid; Bacterial collagen, middle region
      cd12348
      Location:7 → 81
      RRM1_SHARP; RNA recognition motif 1 (RRM1) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12349
      Location:335 → 408
      RRM2_SHARP; RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12350
      Location:435 → 508
      RRM3_SHARP; RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12351
      Location:509 → 585
      RRM4_SHARP; RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

    2. XM_039110804.2 → XP_038966732.1  msx2-interacting protein isoform X1

      UniProtKB/TrEMBL
      A6ITU2
      Conserved Domains (11) summary
      PTZ00121
      Location:773 → 1252
      PTZ00121; MAEBL; Provisional
      PTZ00449
      Location:1529 → 1983
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      PHA03247
      Location:3081 → 3468
      PHA03247; large tegument protein UL36; Provisional
      COG0724
      Location:512 → 671
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      pfam05109
      Location:2669 → 3118
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      pfam07744
      Location:3469 → 3632
      SPOC; SPOC domain
      pfam15984
      Location:2630 → 2723
      Collagen_mid; Bacterial collagen, middle region
      cd12348
      Location:7 → 81
      RRM1_SHARP; RNA recognition motif 1 (RRM1) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12349
      Location:336 → 409
      RRM2_SHARP; RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12350
      Location:436 → 509
      RRM3_SHARP; RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12351
      Location:510 → 586
      RRM4_SHARP; RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

    3. XM_039110809.2 → XP_038966737.1  msx2-interacting protein isoform X3

      UniProtKB/TrEMBL
      A6ITU2
      Conserved Domains (10) summary
      PTZ00121
      Location:705 → 1184
      PTZ00121; MAEBL; Provisional
      PTZ00449
      Location:1461 → 1915
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      PHA03247
      Location:3013 → 3400
      PHA03247; large tegument protein UL36; Provisional
      COG0724
      Location:444 → 603
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      pfam05109
      Location:2601 → 3050
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      pfam07744
      Location:3401 → 3564
      SPOC; SPOC domain
      pfam15984
      Location:2562 → 2655
      Collagen_mid; Bacterial collagen, middle region
      cd12349
      Location:268 → 341
      RRM2_SHARP; RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12350
      Location:368 → 441
      RRM3_SHARP; RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12351
      Location:442 → 518
      RRM4_SHARP; RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

    4. XM_063288446.1 → XP_063144516.1  msx2-interacting protein isoform X4

      UniProtKB/TrEMBL
      A6ITU2

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001271495.1: Suppressed sequence

      Description
      NM_001271495.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version

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