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

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; 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: mouse all
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Genomic context

Location:: 6p21.31

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (34537802..34556329, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (34361651..34380177, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (34505579..34524106, complement)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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 Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Regulation of SPDEF expression by DNA methylation in advanced prostate cancer.
Title: Regulation of SPDEF expression by DNA methylation in advanced prostate cancer.
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.
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.
The role of SPDEF in cancer: promoter or suppressor.
Title: The role of SPDEF in cancer: promoter or suppressor.
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.
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.
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.
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.
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.
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 variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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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
part_of 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)

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
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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000006.12 Reference GRCh38.p14 Primary Assembly

Range

34537802..34556329 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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

NC_060930.1 Alternate T2T-CHM13v2.0

Range

34361651..34380177 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054355092.1 → XP_054211067.1 SAM pointed domain-containing Ets transcription factor isoform X1
XM_054355093.1 → XP_054211068.1 SAM pointed domain-containing Ets transcription factor isoform X2