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

Gene ID: 56381, updated on 2-Nov-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, Nov 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 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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