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

Gene ID: 30051, updated on 8-Feb-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, Apr 2022]
Expression
Biased expression in colon adult (RPKM 65.2), stomach adult (RPKM 24.2) and 4 other tissues See more
Orthologs
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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)
  • Targeted (4)  1 citation
  • Endonuclease-mediated (2) 

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 IEA
Inferred from Electronic Annotation
more info
 
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 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 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 DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
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)

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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_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