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

Gene ID: 25803, updated on 2-Nov-2024

Summary

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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; AllianceGenome:HGNC:17257
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
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Genomic context

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See SPDEF in Genome Data Viewer
Location:
6p21.31
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (34537802..34556329, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (34361651..34380177, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (34505579..34524106, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene RPS10-NUDT3 readthrough Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:34393285-34393989 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17077 Neighboring gene ribosomal protein S10 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17078 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24382 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:34440734-34441492 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24383 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:34457197-34457701 Neighboring gene protein kinase C and casein kinase substrate in neurons 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:34481139-34482042 Neighboring gene Sharpr-MPRA regulatory region 11676 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:34484751-34485653 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17079 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:34495675-34496656 Neighboring gene Sharpr-MPRA regulatory region 1455 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:34502315-34502814 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:34505376-34505582 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:34518352-34519346 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:34522694-34523210 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:34528110-34528841 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:34528842-34529572 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:34529573-34530303 Neighboring gene IFITM3 pseudogene 3 Neighboring gene inflammation and lipid regulator with UBA-like and NBR1-like domains Neighboring gene ribosomal protein L7 pseudogene 25

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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 Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Proteomic analysis of a PDEF Ets transcription factor-interacting protein complex. Cho JY, et al. J Proteome Res, 2009 Mar. PMID 19203193
  2. Prostate-derived Ets factor, an oncogenic driver in breast cancer. Sood AK, et al. Tumour Biol, 2017 May. PMID 28468594
  3. Targeted epigenetic editing of SPDEF reduces mucus production in lung epithelial cells. Song J, et al. Am J Physiol Lung Cell Mol Physiol, 2017 Mar 1. PMID 28011616
  4. Signatures of prostate-derived Ets factor (PDEF) in cancer. Mahajan N. Tumour Biol, 2016 Nov. PMID 27612480
  5. Prostate-derived ets factor represses tumorigenesis and modulates epithelial-to-mesenchymal transition in bladder carcinoma cells. Tsui KH, et al. Cancer Lett, 2016 May 28. PMID 26965996

See all (87) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Regulation of SPDEF expression by DNA methylation in advanced prostate cancer.
    Title: Regulation of SPDEF expression by DNA methylation in advanced prostate cancer.
  2. Lactobacillus rhamnosus 76 alleviates airway inflammation in ovalbumin-allergic mice and improves mucus secretion by down-regulating STAT6/SPDEF pathway.
    Title: Lactobacillus rhamnosus 76 alleviates airway inflammation in ovalbumin-allergic mice and improves mucus secretion by down-regulating STAT6/SPDEF pathway.
  3. SPDEF enhances cancer stem cell-like properties and tumorigenesis through directly promoting GALNT7 transcription in luminal breast cancer.
    Title: SPDEF enhances cancer stem cell-like properties and tumorigenesis through directly promoting GALNT7 transcription in luminal breast cancer.
  4. The role of SPDEF in cancer: promoter or suppressor.
    Title: The role of SPDEF in cancer: promoter or suppressor.
  5. The subtype-specific molecular function of SPDEF in breast cancer and insights into prognostic significance.
    Title: The subtype-specific molecular function of SPDEF in breast cancer and insights into prognostic significance.
  6. SPDEF suppresses head and neck squamous cell carcinoma progression by transcriptionally activating NR4A1.
    Title: SPDEF suppresses head and neck squamous cell carcinoma progression by transcriptionally activating NR4A1.
  7. Assessment of mucin-related gene alterations following treatment with rebamipide ophthalmic suspension in Sjogren's syndrome-associated dry eyes.
    Title: Assessment of mucin-related gene alterations following treatment with rebamipide ophthalmic suspension in Sjögren's syndrome-associated dry eyes.
  8. Targeting SPDEF led to proportional decreases in MUC5AC expression in human bronchial epithelial cells stimulated with IL-13. Near-complete targeting of SPDEF abolished IL-13-induced MUC5AC expression and goblet cell differentiation. Targeting of SPDEF prevented IL-13-induced impairment of mucociliary clearance.
    Title: Efficient RNP-directed Human Gene Targeting Reveals SPDEF Is Required for IL-13-induced Mucostasis.
  9. Hypermethylation of SPDEF gene locus was associated with a greater number of stressful life events in an allele-dependent way. Among individuals with the minor G-allele, SPDEF methylation moderated the association between psychosocial stress and substance abuse. SPDEF methylation interacted with lifetime stress in gray matter volume in the right cuneus, which was associated with the frequency of alcohol and tobacco use.
    Title: Allele-Specific Methylation of SPDEF: A Novel Moderator of Psychosocial Stress and Substance Abuse.
  10. SPDEF is overexpressed in gastric cancer and triggers cell proliferation by forming a positive regulation loop with FoxM1
    Title: SPDEF is overexpressed in gastric cancer and triggers cell proliferation by forming a positive regulation loop with FoxM1.
Submit: New GeneRIF Correction See all GeneRIFs (58)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See Variation Viewer (GRCh37.p13)

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 GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in epithelial cell fate commitment IEA
Inferred from Electronic Annotation
more info
  
involved_in glandular epithelial cell development IEA
Inferred from Electronic Annotation
more info
  
involved_in intestinal epithelial cell development IEA
Inferred from Electronic Annotation
more info
  
involved_in lung goblet cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of cell fate commitment IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of apoptotic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of cell fate commitment IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of transcription by RNA polymerase II 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 transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in chromatin ISA
Inferred from Sequence Alignment
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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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)

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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_001252294.2 → NP_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:134 → 212
    SAM_PNT-PDEF-like; Sterile alpha motif (SAM)/Pointed domain of prostate-derived ETS factor
    pfam00178
    Location:235 → 316
    Ets; Ets-domain

  2. NM_012391.3 → NP_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
    B4DWH8, F5H778, O95238
    Related
    ENSP00000363149.3, ENST00000374037.8
    Conserved Domains (2) summary
    cd08532
    Location:134 → 214
    SAM_PNT-PDEF-like; Sterile alpha motif (SAM)/Pointed domain of prostate-derived ETS factor
    smart00413
    Location:248 → 334
    ETS; erythroblast transformation specific domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    34537802..34556329 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005248988.6 → XP_005249045.2  SAM pointed domain-containing Ets transcription factor isoform X1

    Conserved Domains (2) summary
    cd08532
    Location:206 → 286
    SAM_PNT-PDEF-like; Sterile alpha motif (SAM)/Pointed domain of prostate-derived ETS factor
    pfam00178
    Location:323 → 404
    Ets; Ets-domain

  2. XM_011514457.4 → XP_011512759.1  SAM pointed domain-containing Ets transcription factor isoform X2

    Conserved Domains (1) summary
    cd08532
    Location:206 → 283
    SAM_PNT-PDEF-like; Sterile alpha motif (SAM)/Pointed domain of prostate-derived ETS factor

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    34361651..34380177 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054355092.1 → XP_054211067.1  SAM pointed domain-containing Ets transcription factor isoform X1

  2. XM_054355093.1 → XP_054211068.1  SAM pointed domain-containing Ets transcription factor isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O95238.1 GenPept UniProtKB/Swiss-Prot:O95238

Gene LinkOut

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