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

Gene ID: 690911, updated on 10-Oct-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 DNA-binding transcription factor activity; nucleic acid binding activity; and transcription corepressor activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II and positive regulation of neurogenesis. Predicted to act upstream of or within negative regulation of transcription, DNA-templated and positive regulation of transcription, DNA-templated. Predicted to be located in nucleoplasm. Predicted to be part of transcription repressor complex. Predicted to be active in nucleus. Orthologous to human SPEN (spen family transcriptional repressor). [provided by Alliance of Genome Resources, Apr 2022]
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 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 IEA
Inferred from Electronic Annotation
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 IEA
Inferred from Electronic Annotation
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

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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