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    SETDB2-PHF11 SETDB2-PHF11 readthrough [ Homo sapiens (human) ]

    Gene ID: 107303344, updated on 17-Sep-2024

    Summary

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    Gene symbol
    SETDB2-PHF11
    Gene description
    SETDB2-PHF11 readthrough
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    This gene represents naturally-occurring readthrough transcription between the upstream SETDB2 (SET domain bifurcated 2) gene to the downstream PHF11 (PHD finger protein 11) gene. Readthrough transcripts may encode fusion proteins with similarity to proteins encoded by each of the individual genes or may encode candidates for nonsense-mediated decay (NMD). [provided by RefSeq, Mar 2016]
    Expression
    Ubiquitous expression in lymph node (RPKM 11.8), spleen (RPKM 10.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SETDB2-PHF11 in Genome Data Viewer
    Location:
    13q14.2
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (49444274..49528976)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (48662906..48747507)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (50018410..50103112)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:49821922-49822484 Neighboring gene cytidine and dCMP deaminase domain containing 1 Neighboring gene Sharpr-MPRA regulatory region 13963 Neighboring gene Sharpr-MPRA regulatory region 6847 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:49880333-49880832 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr13:49888093-49889292 Neighboring gene calcium binding protein 39 like Neighboring gene NANOG hESC enhancer GRCh37_chr13:49961302-49961803 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7746 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:50018017-50018789 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:50018790-50019563 Neighboring gene SET domain bifurcated histone lysine methyltransferase 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:50068895-50069580 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7748 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5342 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7749 Neighboring gene small nuclear ribonucleoprotein polypeptide G pseudogene 14 Neighboring gene PHD finger protein 11 Neighboring gene RCC1 and BTB domain containing protein 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:50139673-50140480 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5343 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7750 Neighboring gene uncharacterized LOC105370204 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:50194124-50194624

    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. Positional cloning of a quantitative trait locus on chromosome 13q14 that influences immunoglobulin E levels and asthma. Zhang Y, et al. Nat Genet, 2003 Jun. PMID 12754510

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. detects readthrough transcripts by PCR
      Title: Positional cloning of a quantitative trait locus on chromosome 13q14 that influences immunoglobulin E levels and asthma.
    Submit: New GeneRIF Correction

    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)

    Genotypes

    General gene information

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    Homology

    General protein information

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    Preferred Names
    SETDB2-PHF11 protein

    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_001320727.2 → NP_001307656.1  SETDB2-PHF11 protein

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes a putative protein.
      Source sequence(s)
      AL136218, AL139321
      Conserved Domains (4) summary
      smart00317
      Location:355 → 416
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      cd01395
      Location:152 → 212
      HMT_MBD; Methyl-CpG binding domains (MBD) present in putative histone methyltransferases (HMT) such as CLLD8 and SETDB1 proteins; CLLD8 contains a MBD, a PreSET and a bifurcated SET domain, suggesting that CLLD8 might be associated with methylation-mediated ...
      cd15712
      Location:539 → 653
      ePHD_PHF11; Extended PHD finger found in PHD finger protein 11 (PHF11)
      pfam05033
      Location:234 → 347
      Pre-SET; Pre-SET motif

    RNA

    1. NR_135324.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks two exons and contains three alternate exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL136218, AL139321

    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_000013.11 Reference GRCh38.p14 Primary Assembly

      Range
      49444274..49528976
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      48662906..48747507
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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    Research Materials