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

Gene ID: 25803, updated on 22-Jan-2023

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
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Genomic context

See SPDEF in Genome Data Viewer
Location:
6p21.31
Exon count:
8
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (34537802..34556329, complement)
110 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_000006.12Genomic Context describing neighboring genes Neighboring gene protein kinase C and casein kinase substrate in neurons 1 Neighboring gene Sharpr-MPRA regulatory region 11676 Neighboring gene Sharpr-MPRA regulatory region 1455 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

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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

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
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)

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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_001252294.2NP_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_012391.3NP_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
    F5H778, O95238
    Related
    ENSP00000363149.3, ENST00000374037.8
    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 110 details...Open this link in a new tab

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_005248988.6XP_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_011514457.4XP_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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

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