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PDZD9 PDZ domain containing 9 [ Homo sapiens (human) ]

Gene ID: 255762, updated on 10-Dec-2024

Summary

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Official Symbol
PDZD9provided by HGNC
Official Full Name
PDZ domain containing 9provided by HGNC
Primary source
HGNC:HGNC:28740
See related
Ensembl:ENSG00000155714 AllianceGenome:HGNC:28740
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
Also known as
C16orf65
Expression
Broad expression in testis (RPKM 11.6), heart (RPKM 5.2) and 25 other tissues See more
Orthologs
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Genomic context

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See PDZD9 in Genome Data Viewer
Location:
16p12.2
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (21957540..22001116, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (22216077..22259661)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (21995186..22012437, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA U13 Neighboring gene SMG1 pseudogene 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:21945923-21946424 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:21946425-21946924 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10562 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:21964563-21965280 Neighboring gene ABCA3 pseudogene 1 Neighboring gene ubiquinol-cytochrome c reductase core protein 2 Neighboring gene cell division cycle associated 8 pseudogene Neighboring gene islet cell autoantigen 1, 69kDa pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10565 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7258 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:22037440-22038639 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7259 Neighboring gene modulator of smoothened Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10566 Neighboring gene uncharacterized LOC124903665 Neighboring gene Sharpr-MPRA regulatory region 14412 Neighboring gene uncharacterized LOC105371129

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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Related articles in PubMed

  1. The sequence and analysis of duplication-rich human chromosome 16. Martin J, et al. Nature, 2004 Dec 23. PMID 15616553
  2. LncRNAs-directed PTEN enzymatic switch governs epithelial-mesenchymal transition. Hu Q, et al. Cell Res, 2019 Apr. PMID 30631154, Free PMC Article
  3. Elevation of hsa-miR-7-5p level mediated by CtBP1-p300-AP1 complex targets ATXN1 to trigger NF-κB-dependent inflammation response. Lou LQ, et al. J Mol Med (Berl), 2023 Mar. PMID 36629882
  4. Estrogen-regulated feedback loop limits the efficacy of estrogen receptor-targeted breast cancer therapy. Xiao T, et al. Proc Natl Acad Sci U S A, 2018 Jul 31. PMID 29987050, Free PMC Article
  5. Human-chromatin-related protein interactions identify a demethylase complex required for chromosome segregation. Marcon E, et al. Cell Rep, 2014 Jul 10. PMID 24981860

See all (9) citations in PubMed

GeneRIFs: Gene References Into Functions

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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Markers

Homology

Clone Names

  • MGC50721

General protein information

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Preferred Names
PDZ domain-containing protein 9
Names
PDZ domain-containing protein C16orf65

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_001363519.1 → NP_001350448.1  PDZ domain-containing protein 9 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC092119
    Consensus CDS
    CCDS92124.1
    UniProtKB/Swiss-Prot
    F5GWW8, Q8IXQ8
    Related
    ENSP00000400514.2, ENST00000424898.3
    Conserved Domains (1) summary
    cd00992
    Location:39 → 106
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

  2. NM_001370530.1 → NP_001357459.1  PDZ domain-containing protein 9 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC092119

  3. NM_173806.4 → NP_776167.2  PDZ domain-containing protein 9 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC092119
    Consensus CDS
    CCDS10602.2
    UniProtKB/Swiss-Prot
    Q8IXQ8
    Related
    ENSP00000441685.2, ENST00000537222.6

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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    21957540..22001116 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017023109.2 → XP_016878598.1  PDZ domain-containing protein 9 isoform X1

  2. XM_047433888.1 → XP_047289844.1  PDZ domain-containing protein 9 isoform X2

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_017852933.1 Reference GRCh38.p14 PATCHES

    Range
    1103923..1147498
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054332147.1 → XP_054188122.1  PDZ domain-containing protein 9 isoform X1

  2. XM_054332148.1 → XP_054188123.1  PDZ domain-containing protein 9 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    22216077..22259661
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054379996.1 → XP_054235971.1  PDZ domain-containing protein 9 isoform X1

  2. XM_054379997.1 → XP_054235972.1  PDZ domain-containing protein 9 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8IXQ8.2 GenPept UniProtKB/Swiss-Prot:Q8IXQ8

Gene LinkOut

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