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

    Gene ID: 128977, updated on 10-Dec-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
    Summary
    Predicted to be involved in negative regulation of long-term synaptic potentiation. Located in mitochondrion. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in fat (RPKM 8.1), thyroid (RPKM 7.7) and 25 other tissues See more
    Orthologs
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (19440886..19447711, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (19817716..19824539, complement)
    RS_2024_09 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. Age-dependent expression pattern in the mammalian brain of a novel, small peptide encoded in the 22q11.2 deletion syndrome region. Kragness S, et al. Gene Expr Patterns, 2018 Jun. PMID 29571919
    2. An Rtn4/Nogo-A-interacting micropeptide modulates synaptic plasticity with age. Kragness S, et al. PLoS One, 2022. PMID 35771867, Free PMC Article
    3. 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
    4. UBE2O and USP7 co-regulate RECQL4 ubiquitinylation and homologous recombination-mediated DNA repair. Huang Q, et al. FASEB J, 2022 Jan. PMID 34921745
    5. A genome annotation-driven approach to cloning the human ORFeome. Collins JE, et al. Genome Biol, 2004. PMID 15461802, Free PMC Article

    See all (17) 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)

    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 mitochondrion HTP PubMed 
    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_2024_08

    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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