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SPDEF SAM pointed domain containing ETS transcription factor [ Homo sapiens (human) ]

Gene ID: 25803, updated on 2-Oct-2018

Summary

Official Symbol
SPDEFprovided by HGNC
Official Full Name
SAM pointed domain containing ETS transcription factorprovided by HGNC
Primary source
HGNC:HGNC:17257
See related
Ensembl:ENSG00000124664 MIM:608144; Vega:OTTHUMG00000014548
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PDEF; bA375E1.3
Summary
The protein encoded by this gene belongs to the ETS family of transcription factors. It is highly expressed in the prostate epithelial cells, and functions as an androgen-independent transactivator of prostate-specific antigen (PSA) promoter. Higher expression of this protein has also been reported in brain, breast, lung and ovarian tumors, compared to the corresponding normal tissues, and it shows better tumor-association than other cancer-associated molecules, making it a more suitable target for developing specific cancer therapies. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]
Expression
Biased expression in prostate (RPKM 50.1), salivary gland (RPKM 10.8) and 5 other tissues See more
Orthologs

Genomic context

See SPDEF in Genome Data Viewer
Location:
6p21.31
Exon count:
8
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 6 NC_000006.12 (34537800..34556333, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (34505579..34524110, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene RPS10-NUDT3 readthrough Neighboring gene ribosomal protein S10 Neighboring gene protein kinase C and casein kinase substrate in neurons 1 Neighboring gene interferon induced transmembrane protein pseudogene Neighboring gene chromosome 6 open reading frame 106 Neighboring gene ribosomal protein L7 pseudogene 25

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
intestinal epithelial cell development IEA
Inferred from Electronic Annotation
more info
 
lung goblet cell differentiation IEA
Inferred from Electronic Annotation
more info
 
multicellular organism development TAS
Traceable Author Statement
more info
PubMed 
negative regulation of cell fate commitment IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of apoptotic process IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of cell fate commitment IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

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

NCBI Reference Sequences (RefSeq)

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_001252294.1NP_001239223.1  SAM pointed domain-containing Ets transcription factor isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame coding exon compared to variant 1. This results in a shorter isoform (2) missing an internal protein segment compared to isoform 1.
    Source sequence(s)
    AK301543, BC021299
    Consensus CDS
    CCDS59013.1
    UniProtKB/Swiss-Prot
    O95238
    Related
    ENSP00000442715.1, ENST00000544425.2
    Conserved Domains (2) summary
    cd08532
    Location:134212
    SAM_PNT-PDEF-like; Sterile alpha motif (SAM)/Pointed domain of prostate-derived ETS factor
    pfam00178
    Location:235316
    Ets; Ets-domain
  2. NM_012391.2NP_036523.1  SAM pointed domain-containing Ets transcription factor isoform 1

    See identical proteins and their annotated locations for NP_036523.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AK301543, BC021299
    Consensus CDS
    CCDS4794.1
    UniProtKB/Swiss-Prot
    O95238
    Related
    ENSP00000363149.3, OTTHUMP00000016234, ENST00000374037.7, OTTHUMT00000040246
    Conserved Domains (2) summary
    cd08532
    Location:134214
    SAM_PNT-PDEF-like; Sterile alpha motif (SAM)/Pointed domain of prostate-derived ETS factor
    smart00413
    Location:248334
    ETS; erythroblast transformation specific domain

RefSeqs of Annotated Genomes: Homo sapiens 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 GRCh38.p12 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p12 Primary Assembly

    Range
    34537800..34556333 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005248988.5XP_005249045.2  SAM pointed domain-containing Ets transcription factor isoform X1

    Conserved Domains (2) summary
    cd08532
    Location:206286
    SAM_PNT-PDEF-like; Sterile alpha motif (SAM)/Pointed domain of prostate-derived ETS factor
    pfam00178
    Location:323404
    Ets; Ets-domain
  2. XM_011514457.3XP_011512759.1  SAM pointed domain-containing Ets transcription factor isoform X2

    Conserved Domains (1) summary
    cd08532
    Location:206283
    SAM_PNT-PDEF-like; Sterile alpha motif (SAM)/Pointed domain of prostate-derived ETS factor
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