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C22orf39 chromosome 22 open reading frame 39 [ Homo sapiens (human) ]

Gene ID: 128977, updated on 5-Mar-2024

Summary

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Official Symbol
C22orf39provided by HGNC
Official Full Name
chromosome 22 open reading frame 39provided by HGNC
Primary source
HGNC:HGNC:27012
See related
Ensembl:ENSG00000242259 AllianceGenome:HGNC:27012
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
Pants
Expression
Ubiquitous expression in fat (RPKM 8.1), thyroid (RPKM 7.7) and 25 other tissues See more
Orthologs
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Genomic context

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See C22orf39 in Genome Data Viewer
Location:
22q11.21
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (19440886..19447711, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (19817716..19824539, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (19428409..19435234, complement)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene histone cell cycle regulator Neighboring gene RNA, 7SL, cytoplasmic 168, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18658 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:19418111-19418858 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13459 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13460 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr22:19434430-19435332 Neighboring gene mitochondrial ribosomal protein L40 Neighboring gene UFD1 antisense RNA 1 Neighboring gene ubiquitin recognition factor in ER associated degradation 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13462 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18660 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13463 Neighboring gene cell division cycle 45 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:19486137-19486353 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19493394-19493894 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19493895-19494395 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19502006-19502506 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19502507-19503007

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
  • 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. Effects of chronic ascariasis and trichuriasis on cytokine production and gene expression in human blood: a cross-sectional study. Reina Ortiz M, et al. PLoS Negl Trop Dis, 2011 Jun. PMID 21666788, Free PMC Article
  2. UBE2O and USP7 co-regulate RECQL4 ubiquitinylation and homologous recombination-mediated DNA repair. Huang Q, et al. FASEB J, 2022 Jan. PMID 34921745
  3. A genome annotation-driven approach to cloning the human ORFeome. Collins JE, et al. Genome Biol, 2004. PMID 15461802, Free PMC Article
  4. Phospho-tyrosine dependent protein-protein interaction network. Grossmann A, et al. Mol Syst Biol, 2015 Mar 26. PMID 25814554, Free PMC Article
  5. A directed protein interaction network for investigating intracellular signal transduction. Vinayagam A, et al. Sci Signal, 2011 Sep 6. PMID 21900206

See all (14) 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)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC74441, DKFZp686I08210

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in negative regulation of long-term synaptic potentiation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of synaptic plasticity ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in synapse ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in synaptic cleft ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
synaptic plasticity regulator PANTS
Names
Plasticity Associated Neural Transcript
UPF0545 protein C22orf39

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_001166242.2 → NP_001159714.2  synaptic plasticity regulator PANTS isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AC000068
    Consensus CDS
    CCDS54498.2
    Related
    ENSP00000382478.1, ENST00000399568.5
    Conserved Domains (1) summary
    pfam11326
    Location:13 → 64
    DUF3128; Protein of unknown function (DUF3128)

  2. NM_173793.5 → NP_776154.4  synaptic plasticity regulator PANTS isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC000068
    Consensus CDS
    CCDS33599.3
    UniProtKB/Swiss-Prot
    A0A075B6P1, A8MTW6, D3DX18, F5H3A8, J3KNP9, Q6P5X5
    Related
    ENSP00000382474.5, ENST00000399562.9
    Conserved Domains (1) summary
    pfam11326
    Location:13 → 88
    DUF3128; Protein of unknown function (DUF3128)

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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    19440886..19447711 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    19817716..19824539 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6P5X5.3 GenPept UniProtKB/Swiss-Prot:Q6P5X5

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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