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

    Gene ID: 25803, updated on 17-Jun-2024

    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
    NEW
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    Genomic context

    See SPDEF in Genome Data Viewer
    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_000006.12Genomic 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

    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

    Gene Ontology Provided by GOA

    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

    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)

    NEW Try the new Transcript table

    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
      B4DWH8, 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: 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

    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)

    mRNA and Protein(s)

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

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