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

Gene ID: 56381, updated on 29-Jan-2023

Summary

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. Acts upstream of or within negative regulation of transcription, DNA-templated and positive regulation of transcription, DNA-templated. Located in nucleus. Is expressed in central nervous system; genitourinary system; hemolymphoid system; sensory organ; and tooth. Orthologous to human SPEN (spen family transcriptional repressor). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in thymus adult (RPKM 10.9), adrenal adult (RPKM 8.5) and 28 other tissues See more
Orthologs
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Genomic context

See Spen in Genome Data Viewer
Location:
4; 4 D3
Exon count:
16
Annotation release Status Assembly Chr Location
109 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 RIKEN cDNA B330016D10 gene Neighboring gene predicted gene 4123 Neighboring gene filamin binding LIM protein 1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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
PubMed 
enables nucleic acid binding IEA
Inferred from Electronic Annotation
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
 
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
PubMed 
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

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_001347235.1NP_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/TrEMBL
    A2ADB1
    Related
    ENSMUSP00000077925.4, ENSMUST00000078886.10
  2. NM_019763.2NP_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
    UniProtKB/TrEMBL
    A2ADB0, Q3UV27
    Related
    ENSMUSP00000101412.3, ENSMUST00000105786.3
    Conserved Domains (9) summary
    COG0724
    Location:8145
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    cd12348
    Location:781
    RRM1_SHARP; RNA recognition motif 1 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
    cd12349
    Location:338411
    RRM2_SHARP; RNA recognition motif 2 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
    cd12350
    Location:438511
    RRM3_SHARP; RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
    cd12351
    Location:512588
    RRM4_SHARP; RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
    TIGR01642
    Location:128596
    U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor
    pfam05466
    Location:16111834
    BASP1; Brain acid soluble protein 1 (BASP1 protein)
    pfam07744
    Location:34883609
    SPOC; SPOC domain
    pfam15984
    Location:26412722
    Collagen_mid; Bacterial collagen, middle region

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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_036164267.1XP_036020160.1  msx2-interacting protein isoform X4

    Conserved Domains (8) summary
    PTZ00121
    Location:5801211
    PTZ00121; MAEBL; Provisional
    PHA03247
    Location:15682002
    PHA03247; large tegument protein UL36; Provisional
    pfam07744
    Location:34203583
    SPOC; SPOC domain
    pfam15984
    Location:25802658
    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:338411
    RRM2_SHARP; RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
    cd12350
    Location:438511
    RRM3_SHARP; RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
    cl17169
    Location:512571
    RRM_SF; RNA recognition motif (RRM) superfamily
  2. XM_036164266.1XP_036020159.1  msx2-interacting protein isoform X3

    Conserved Domains (8) summary
    PTZ00121
    Location:5971234
    PTZ00121; MAEBL; Provisional
    PHA03247
    Location:15912025
    PHA03247; large tegument protein UL36; Provisional
    pfam07744
    Location:34433606
    SPOC; SPOC domain
    pfam15984
    Location:26032681
    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:338411
    RRM2_SHARP; RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
    cd12350
    Location:438511
    RRM3_SHARP; RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
    cl17169
    Location:512571
    RRM_SF; RNA recognition motif (RRM) superfamily
  3. XM_006539070.4XP_006539133.1  msx2-interacting protein isoform X2

    Conserved Domains (9) summary
    PTZ00121
    Location:6181249
    PTZ00121; MAEBL; Provisional
    PHA03247
    Location:16062040
    PHA03247; large tegument protein UL36; Provisional
    cd12348
    Location:781
    RRM1_SHARP; RNA recognition motif 1 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
    cd12349
    Location:338411
    RRM2_SHARP; RNA recognition motif 2 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
    cd12350
    Location:438511
    RRM3_SHARP; RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
    cd12351
    Location:512588
    RRM4_SHARP; RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
    TIGR01642
    Location:128596
    U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor
    pfam07744
    Location:34603619
    SPOC; SPOC domain
    pfam15984
    Location:26182699
    Collagen_mid; Bacterial collagen, middle region
  4. XM_006539073.5XP_006539136.1  msx2-interacting protein isoform X5

    Conserved Domains (8) summary
    PTZ00121
    Location:6351272
    PTZ00121; MAEBL; Provisional
    PHA03247
    Location:16292063
    PHA03247; large tegument protein UL36; Provisional
    cd12348
    Location:781
    RRM1_SHARP; RNA recognition motif 1 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
    cd12349
    Location:338411
    RRM2_SHARP; RNA recognition motif 2 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
    cd12350
    Location:438511
    RRM3_SHARP; RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
    cd12351
    Location:512588
    RRM4_SHARP; RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
    TIGR01642
    Location:128596
    U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor
    pfam07744
    Location:33603519
    SPOC; SPOC domain
  5. XM_006539069.4XP_006539132.1  msx2-interacting protein isoform X1

    Conserved Domains (9) summary
    PTZ00121
    Location:6351272
    PTZ00121; MAEBL; Provisional
    PHA03247
    Location:16292063
    PHA03247; large tegument protein UL36; Provisional
    cd12348
    Location:781
    RRM1_SHARP; RNA recognition motif 1 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
    cd12349
    Location:338411
    RRM2_SHARP; RNA recognition motif 2 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
    cd12350
    Location:438511
    RRM3_SHARP; RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
    cd12351
    Location:512588
    RRM4_SHARP; RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
    TIGR01642
    Location:128596
    U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor
    pfam07744
    Location:34833642
    SPOC; SPOC domain
    pfam15984
    Location:26412722
    Collagen_mid; Bacterial collagen, middle region
  6. XM_036164268.1XP_036020161.1  msx2-interacting protein isoform X6

    Conserved Domains (6) summary
    PTZ00121
    Location:213844
    PTZ00121; MAEBL; Provisional
    PHA03247
    Location:12011635
    PHA03247; large tegument protein UL36; Provisional
    pfam07744
    Location:30533216
    SPOC; SPOC domain
    pfam15984
    Location:22132291
    Collagen_mid; Bacterial collagen, middle region
    cd12350
    Location:33106
    RRM3_SHARP; RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins
    cd12351
    Location:107183
    RRM4_SHARP; RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins