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    Spdef SAM pointed domain containing ets transcription factor [ Mus musculus (house mouse) ]

    Gene ID: 30051, updated on 3-Dec-2024

    Summary

    Official Symbol
    Spdefprovided by MGI
    Official Full Name
    SAM pointed domain containing ets transcription factorprovided by MGI
    Primary source
    MGI:MGI:1353422
    See related
    Ensembl:ENSMUSG00000024215 AllianceGenome:MGI:1353422
    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
    Pse; PDEF
    Summary
    Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and sequence-specific double-stranded DNA binding activity. Acts upstream of or within several processes, including columnar/cuboidal epithelial cell differentiation; positive regulation of cell fate commitment; and regulation of transcription by RNA polymerase II. Located in nucleus. Is expressed in several structures, including alimentary system; brain; genitourinary system; integumental system; and sensory organ. Orthologous to human SPDEF (SAM pointed domain containing ETS transcription factor). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in colon adult (RPKM 65.2), stomach adult (RPKM 24.2) and 4 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Spdef in Genome Data Viewer
    Location:
    17 A3.3; 17 14.59 cM
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 17 NC_000083.7 (27933416..27949977, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 17 NC_000083.6 (27714446..27731003, complement)

    Chromosome 17 - NC_000083.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_42169 Neighboring gene predicted gene 15420 Neighboring gene ribosomal protein S10 Neighboring gene protein kinase C and casein kinase substrate in neurons 1 Neighboring gene STARR-seq mESC enhancer starr_42171 Neighboring gene inflammation and lipid regulator with UBA-like and NBR1-like domains Neighboring gene ribosomal protein S2, pseudogene 9 Neighboring gene STARR-seq mESC enhancer starr_42174 Neighboring gene STARR-positive B cell enhancer ABC_E2475 Neighboring gene STARR-positive B cell enhancer ABC_E4198 Neighboring gene CapStarr-seq enhancer MGSCv37_chr17:27976840-27977098 Neighboring gene U1 small nuclear ribonucleoprotein C

    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)
    • Endonuclease-mediated (2) 
    • Targeted (4)  1 citation

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables sequence-specific double-stranded DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables sequence-specific double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    involved_in cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of cell fate commitment IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of epithelial cell fate commitment IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within glandular epithelial cell development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within intestinal epithelial cell development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within lung goblet cell differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of cell fate commitment IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of apoptotic process ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within positive regulation of cell fate commitment IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II 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
     
    acts_upstream_of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of transcription by RNA polymerase II IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    SAM pointed domain-containing Ets transcription factor
    Names
    prostate epithelium-specific Ets transcription factor
    prostate specific ets transcription factor
    prostate-derived Ets factor
    prostate-specific Ets

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001357728.1NP_001344657.1  SAM pointed domain-containing Ets transcription factor

      Status: VALIDATED

      Source sequence(s)
      AC131800, BY446800
      Consensus CDS
      CCDS28568.1
      UniProtKB/Swiss-Prot
      Q9WTP3
      UniProtKB/TrEMBL
      A0A3F2YNL9
      Conserved Domains (2) summary
      cd08532
      Location:124204
      SAM_PNT-PDEF-like; Sterile alpha motif (SAM)/Pointed domain of prostate-derived ETS factor
      smart00413
      Location:238324
      ETS; erythroblast transformation specific domain
    2. NM_001414277.1NP_001401206.1  SAM pointed domain-containing Ets transcription factor

      Status: VALIDATED

      Source sequence(s)
      AC131800
      UniProtKB/Swiss-Prot
      Q9WTP3
      UniProtKB/TrEMBL
      A0A3F2YNL9
    3. NM_001414278.1NP_001401207.1  SAM pointed domain-containing Ets transcription factor

      Status: VALIDATED

      Source sequence(s)
      AC131800
      UniProtKB/Swiss-Prot
      Q9WTP3
      UniProtKB/TrEMBL
      A0A3F2YNL9
    4. NM_013891.4NP_038919.1  SAM pointed domain-containing Ets transcription factor

      See identical proteins and their annotated locations for NP_038919.1

      Status: VALIDATED

      Source sequence(s)
      AK078863, AV370101, AV370994
      Consensus CDS
      CCDS28568.1
      UniProtKB/Swiss-Prot
      Q9WTP3
      UniProtKB/TrEMBL
      A0A3F2YNL9
      Related
      ENSMUSP00000025054.3, ENSMUST00000025054.10
      Conserved Domains (2) summary
      cd08532
      Location:124204
      SAM_PNT-PDEF-like; Sterile alpha motif (SAM)/Pointed domain of prostate-derived ETS factor
      smart00413
      Location:238324
      ETS; erythroblast transformation specific domain

    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_000083.7 Reference GRCm39 C57BL/6J

      Range
      27933416..27949977 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006524380.5XP_006524443.1  SAM pointed domain-containing Ets transcription factor isoform X1

      See identical proteins and their annotated locations for XP_006524443.1

      UniProtKB/Swiss-Prot
      Q9WTP3
      UniProtKB/TrEMBL
      A0A3F2YNL9
      Conserved Domains (2) summary
      cd08532
      Location:124204
      SAM_PNT-PDEF-like; Sterile alpha motif (SAM)/Pointed domain of prostate-derived ETS factor
      smart00413
      Location:238324
      ETS; erythroblast transformation specific domain
    2. XM_006524379.5XP_006524442.1  SAM pointed domain-containing Ets transcription factor isoform X1

      See identical proteins and their annotated locations for XP_006524442.1

      UniProtKB/Swiss-Prot
      Q9WTP3
      UniProtKB/TrEMBL
      A0A3F2YNL9
      Conserved Domains (2) summary
      cd08532
      Location:124204
      SAM_PNT-PDEF-like; Sterile alpha motif (SAM)/Pointed domain of prostate-derived ETS factor
      smart00413
      Location:238324
      ETS; erythroblast transformation specific domain
    3. XM_006524381.5XP_006524444.1  SAM pointed domain-containing Ets transcription factor isoform X1

      See identical proteins and their annotated locations for XP_006524444.1

      UniProtKB/Swiss-Prot
      Q9WTP3
      UniProtKB/TrEMBL
      A0A3F2YNL9
      Conserved Domains (2) summary
      cd08532
      Location:124204
      SAM_PNT-PDEF-like; Sterile alpha motif (SAM)/Pointed domain of prostate-derived ETS factor
      smart00413
      Location:238324
      ETS; erythroblast transformation specific domain