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    Spen spen family transcription repressor [ Mus musculus (house mouse) ]

    Gene ID: 56381, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Spenprovided by MGI
    Official Full Name
    spen family transcription repressorprovided by MGI
    Primary source
    MGI:MGI:1891706
    See related
    Ensembl:ENSMUSG00000040761 AllianceGenome:MGI:1891706
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Mint; mKIAA0929
    Summary
    Enables DNA-binding transcription factor activity; single-stranded DNA binding activity; and transcription corepressor activity. Involved in random inactivation of X chromosome. Acts upstream of or within negative regulation of DNA-templated transcription and positive regulation of DNA-templated transcription. Located in nucleus. Is expressed in central nervous system; genitourinary system; hemolymphoid system; sensory organ; and tooth. 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
    Ubiquitous expression in thymus adult (RPKM 10.9), adrenal adult (RPKM 8.5) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Spen in Genome Data Viewer
    Location:
    4 D3; 4 74.26 cM
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 4 NC_000070.7 (141195199..141265955, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (141467885..141538644, complement)

    Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene steroid receptor associated and regulated protein Neighboring gene predicted gene, 42337 Neighboring gene zinc finger and BTB domain containing 17 Neighboring gene STARR-positive B cell enhancer mm9_chr4:141033664-141033965 Neighboring gene RIKEN cDNA B330016D10 gene Neighboring gene STARR-positive B cell enhancer ABC_E6250 Neighboring gene predicted gene 4123 Neighboring gene STARR-positive B cell enhancer ABC_E6251 Neighboring gene STARR-positive B cell enhancer ABC_E6252 Neighboring gene STARR-seq mESC enhancer starr_11919 Neighboring gene STARR-seq mESC enhancer starr_11920 Neighboring gene STARR-seq mESC enhancer starr_11921 Neighboring gene STARR-positive B cell enhancer ABC_E1289 Neighboring gene STARR-positive B cell enhancer ABC_E1662 Neighboring gene filamin binding LIM protein 1 Neighboring gene STARR-seq mESC enhancer starr_11923

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Disturbed tooth germ development in the absence of MINT in the cultured mouse mandibular explants. Zhu MH, et al. Mol Biol Rep, 2011 Feb. PMID 20393883
    2. Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation. Carter AC, et al. Elife, 2020 May 7. PMID 32379046, Free PMC Article
    3. The C terminus of MINT forms homodimers and abrogates MINT-mediated transcriptional repression. Li J, et al. Biochim Biophys Acta, 2005 May 25. PMID 15777657
    4. SPEN protein expression and interactions with chromatin in mouse testicular cells. Korfanty J, et al. Reproduction, 2018 Sep. PMID 29880719
    5. Identification of Spen as a Crucial Factor for Xist Function through Forward Genetic Screening in Haploid Embryonic Stem Cells. Monfort A, et al. Cell Rep, 2015 Jul 28. PMID 26190100, Free PMC Article

    See all (56) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. RNA-binding protein SPEN controls hepatocyte maturation via regulating Hnf4alpha expression during liver development.
      Title: RNA-binding protein SPEN controls hepatocyte maturation via regulating Hnf4α expression during liver development.
    2. SPEN is required for Xist upregulation during initiation of X chromosome inactivation.
      Title: SPEN is required for Xist upregulation during initiation of X chromosome inactivation.
    3. Time-resolved structured illumination microscopy reveals key principles of Xist RNA spreading.
      Title: Time-resolved structured illumination microscopy reveals key principles of Xist RNA spreading.
    4. Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation.
      Title: Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation.
    5. Elements at the 5' end of Xist harbor SPEN-independent transcriptional antiterminator activity.
      Title: Elements at the 5' end of Xist harbor SPEN-independent transcriptional antiterminator activity.
    6. SPEN is a key orchestrator of X-chromosome inactivation (XCI) in vivo and its mechanism of action is elucidated; SPEN acts as a molecular integrator for the initiation of XCI, bridging Xist RNA with the transcription machinery--as well as with nucleosome remodellers and histone deacetylases-at active enhancers and promoters
      Title: SPEN integrates transcriptional and epigenetic control of X-inactivation.
    7. Structural and Functional Studies of the RBPJ-SHARP Complex Reveal a Conserved Corepressor Binding Site.
      Title: Structural and Functional Studies of the RBPJ-SHARP Complex Reveal a Conserved Corepressor Binding Site.
    8. Spenito, a small Spen family member, counteracted Spen function in fat regulation. Finally, mouse Spen and Spenito transcript levels scaled directly with body fat in vivo, suggesting a conserved role in fat liberation and catabolism. This study demonstrates that Spen is a key regulator of energy balance and provides a molecular context to understand the metabolic defects that arise from Spen dysfunction.
      Title: An autonomous metabolic role for Spen.
    9. Spen is required for Xist-mediated silencing.
      Title: A Pooled shRNA Screen Identifies Rbm15, Spen, and Wtap as Factors Required for Xist RNA-Mediated Silencing.
    10. Spen is required for gene repression by Xist. Spen is not required for Xist RNA localization and the recruitment of chromatin modifications.
      Title: Identification of Spen as a Crucial Factor for Xist Function through Forward Genetic Screening in Haploid Embryonic Stem Cells.
    Submit: New GeneRIF Correction See all GeneRIFs (19)

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • Targeted (5)  1 citation

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    NOT enables DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA binding IEA
    Inferred from Electronic Annotation
    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 protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables single-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables transcription corepressor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables transcription corepressor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in Notch signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of neurogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in random inactivation of X chromosome IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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
    Msx2 interacting nuclear target protein
    SMART/HDAC1-associated repressor protein
    SPEN homolog, transcriptional regulator

    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_001347235.1 → NP_001334164.1  msx2-interacting protein isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AL670285, AL670446
      Consensus CDS
      CCDS84815.1
      UniProtKB/Swiss-Prot
      Q62504, Q80TN9, Q99PS4, Q9QZW2
      UniProtKB/TrEMBL
      A2ADB1
      Related
      ENSMUSP00000077925.4, ENSMUST00000078886.10

    2. NM_019763.2 → NP_062737.2  msx2-interacting protein isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AF156529, AK137647, AL670285, BY726481
      Consensus CDS
      CCDS38940.1
      UniProtKB/Swiss-Prot
      Q62504, Q80TN9, Q99PS4, Q9QZW2
      UniProtKB/TrEMBL
      A2ADB0
      Related
      ENSMUSP00000101412.3, ENSMUST00000105786.3
      Conserved Domains (9) summary
      COG0724
      Location:8 → 145
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12348
      Location:7 → 81
      RRM1_SHARP; RNA recognition motif 1 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12349
      Location:338 → 411
      RRM2_SHARP; RNA recognition motif 2 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12350
      Location:438 → 511
      RRM3_SHARP; RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12351
      Location:512 → 588
      RRM4_SHARP; RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      TIGR01642
      Location:128 → 596
      U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor
      pfam05466
      Location:1611 → 1834
      BASP1; Brain acid soluble protein 1 (BASP1 protein)
      pfam07744
      Location:3488 → 3609
      SPOC; SPOC domain
      pfam15984
      Location:2641 → 2722
      Collagen_mid; Bacterial collagen, middle region

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000070.7 Reference GRCm39 C57BL/6J

      Range
      141195199..141265955 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036164267.1 → XP_036020160.1  msx2-interacting protein isoform X4

      UniProtKB/Swiss-Prot
      Q62504, Q80TN9, Q99PS4, Q9QZW2
      Conserved Domains (8) summary
      PTZ00121
      Location:580 → 1211
      PTZ00121; MAEBL; Provisional
      PHA03247
      Location:1568 → 2002
      PHA03247; large tegument protein UL36; Provisional
      pfam07744
      Location:3420 → 3583
      SPOC; SPOC domain
      pfam15984
      Location:2580 → 2658
      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:338 → 411
      RRM2_SHARP; RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12350
      Location:438 → 511
      RRM3_SHARP; RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cl17169
      Location:512 → 571
      RRM_SF; RNA recognition motif (RRM) superfamily

    2. XM_036164266.1 → XP_036020159.1  msx2-interacting protein isoform X3

      UniProtKB/Swiss-Prot
      Q62504, Q80TN9, Q99PS4, Q9QZW2
      Conserved Domains (8) summary
      PTZ00121
      Location:597 → 1234
      PTZ00121; MAEBL; Provisional
      PHA03247
      Location:1591 → 2025
      PHA03247; large tegument protein UL36; Provisional
      pfam07744
      Location:3443 → 3606
      SPOC; SPOC domain
      pfam15984
      Location:2603 → 2681
      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:338 → 411
      RRM2_SHARP; RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12350
      Location:438 → 511
      RRM3_SHARP; RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cl17169
      Location:512 → 571
      RRM_SF; RNA recognition motif (RRM) superfamily

    3. XM_006539070.4 → XP_006539133.1  msx2-interacting protein isoform X2

      UniProtKB/Swiss-Prot
      Q62504, Q80TN9, Q99PS4, Q9QZW2
      Conserved Domains (9) summary
      PTZ00121
      Location:618 → 1249
      PTZ00121; MAEBL; Provisional
      PHA03247
      Location:1606 → 2040
      PHA03247; large tegument protein UL36; Provisional
      cd12348
      Location:7 → 81
      RRM1_SHARP; RNA recognition motif 1 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12349
      Location:338 → 411
      RRM2_SHARP; RNA recognition motif 2 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12350
      Location:438 → 511
      RRM3_SHARP; RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12351
      Location:512 → 588
      RRM4_SHARP; RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      TIGR01642
      Location:128 → 596
      U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor
      pfam07744
      Location:3460 → 3619
      SPOC; SPOC domain
      pfam15984
      Location:2618 → 2699
      Collagen_mid; Bacterial collagen, middle region

    4. XM_006539073.5 → XP_006539136.1  msx2-interacting protein isoform X5

      UniProtKB/Swiss-Prot
      Q62504, Q80TN9, Q99PS4, Q9QZW2
      Conserved Domains (8) summary
      PTZ00121
      Location:635 → 1272
      PTZ00121; MAEBL; Provisional
      PHA03247
      Location:1629 → 2063
      PHA03247; large tegument protein UL36; Provisional
      cd12348
      Location:7 → 81
      RRM1_SHARP; RNA recognition motif 1 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12349
      Location:338 → 411
      RRM2_SHARP; RNA recognition motif 2 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12350
      Location:438 → 511
      RRM3_SHARP; RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12351
      Location:512 → 588
      RRM4_SHARP; RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      TIGR01642
      Location:128 → 596
      U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor
      pfam07744
      Location:3360 → 3519
      SPOC; SPOC domain

    5. XM_006539069.4 → XP_006539132.1  msx2-interacting protein isoform X1

      UniProtKB/Swiss-Prot
      Q62504, Q80TN9, Q99PS4, Q9QZW2
      Conserved Domains (9) summary
      PTZ00121
      Location:635 → 1272
      PTZ00121; MAEBL; Provisional
      PHA03247
      Location:1629 → 2063
      PHA03247; large tegument protein UL36; Provisional
      cd12348
      Location:7 → 81
      RRM1_SHARP; RNA recognition motif 1 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12349
      Location:338 → 411
      RRM2_SHARP; RNA recognition motif 2 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12350
      Location:438 → 511
      RRM3_SHARP; RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12351
      Location:512 → 588
      RRM4_SHARP; RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      TIGR01642
      Location:128 → 596
      U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor
      pfam07744
      Location:3483 → 3642
      SPOC; SPOC domain
      pfam15984
      Location:2641 → 2722
      Collagen_mid; Bacterial collagen, middle region

    6. XM_036164268.1 → XP_036020161.1  msx2-interacting protein isoform X6

      UniProtKB/Swiss-Prot
      Q62504, Q80TN9, Q99PS4, Q9QZW2
      Conserved Domains (6) summary
      PTZ00121
      Location:213 → 844
      PTZ00121; MAEBL; Provisional
      PHA03247
      Location:1201 → 1635
      PHA03247; large tegument protein UL36; Provisional
      pfam07744
      Location:3053 → 3216
      SPOC; SPOC domain
      pfam15984
      Location:2213 → 2291
      Collagen_mid; Bacterial collagen, middle region
      cd12350
      Location:33 → 106
      RRM3_SHARP; RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
      cd12351
      Location:107 → 183
      RRM4_SHARP; RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q62504.2 GenPept UniProtKB/Swiss-Prot:Q62504

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