U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

    PTCD2 pentatricopeptide repeat domain 2 [ Homo sapiens (human) ]

    Gene ID: 79810, updated on 6-Jun-2024

    Summary

    Official Symbol
    PTCD2provided by HGNC
    Official Full Name
    pentatricopeptide repeat domain 2provided by HGNC
    Primary source
    HGNC:HGNC:25734
    See related
    Ensembl:ENSG00000049883 MIM:615484; AllianceGenome:HGNC:25734
    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
    Enables RNA binding activity. Predicted to be involved in mitochondrion organization and regulation of mRNA processing. Predicted to act upstream of or within animal organ development; muscle cell development; and regulation of gene expression. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in thyroid (RPKM 1.9), brain (RPKM 1.5) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PTCD2 in Genome Data Viewer
    Location:
    5q13.2
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (72320373..72368395)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (72801543..72849569)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (71616200..71664222)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene mitochondrial ribosomal protein S27 Neighboring gene uncharacterized LOC107986422 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:71597159-71598114 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22646 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16079 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:71607834-71608334 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:71615118-71615659 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:71615660-71616200 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22648 Neighboring gene RNA, 7SL, cytoplasmic 153, pseudogene Neighboring gene ribosomal protein L10a pseudogene 8 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16080 Neighboring gene Y-box binding protein 1 pseudogene 5

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ12598

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in kidney development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in liver development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mitochondrion organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in multicellular organism development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in muscle cell development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of mRNA processing IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of mRNA processing ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in ventricular cardiac muscle tissue morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    pentatricopeptide repeat-containing protein 2, mitochondrial
    Names
    CTC-365E16.1

    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_001284403.2NP_001271332.1  pentatricopeptide repeat-containing protein 2, mitochondrial isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks 3 consecutive exons compared to variant 1, however, it maintains the reading frame and encodes a shorter isoform (2) missing an internal protein segment compared to isoform 1.
      Source sequence(s)
      AC026406, AC093278, AI798903, AK056761, AK298750, DC393817
      Consensus CDS
      CCDS68891.1
      UniProtKB/Swiss-Prot
      Q8WV60
      UniProtKB/TrEMBL
      B3KPU6
      Related
      ENSP00000427349.1, ENST00000503868.5
    2. NM_001284404.2NP_001271333.1  pentatricopeptide repeat-containing protein 2, mitochondrial isoform 3

      See identical proteins and their annotated locations for NP_001271333.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks 2 consecutive exons, which results in a frame-shift and translation initiation from an alternative start codon compared to variant 1. The resulting shorter isoform (3) has a distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AC026406, AC093278, AI798903, AK056761, AK303639, DC393817
      Consensus CDS
      CCDS68892.1
      UniProtKB/TrEMBL
      D6RGK0
      Related
      ENSP00000444772.1, ENST00000536805.5
    3. NM_001284405.2NP_001271334.1  pentatricopeptide repeat-containing protein 2, mitochondrial isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks an exon in the mid-coding region and initiates translation from an in-frame downstream start codon compared to variant 1. The resulting isoform (4) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AC026406, AC093278, AI798903, AK056761, AK303776
      Consensus CDS
      CCDS75258.1
      UniProtKB/TrEMBL
      D6RGK0, F6S289
      Related
      ENSP00000438810.2, ENST00000543322.5
    4. NM_024754.5NP_079030.3  pentatricopeptide repeat-containing protein 2, mitochondrial isoform 1

      See identical proteins and their annotated locations for NP_079030.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC026406, AC093278, AI798903, AK056761, DC393817
      Consensus CDS
      CCDS4014.2
      UniProtKB/Swiss-Prot
      B7Z5D0, B7Z8L7, E9PFV7, Q6IA65, Q8WV60, Q9H9R0
      Related
      ENSP00000370013.4, ENST00000380639.10
      Conserved Domains (2) summary
      sd00004
      Location:165194
      PPR; PPR repeat [structural motif]
      pfam10037
      Location:103354
      MRP-S27; Mitochondrial 28S ribosomal protein S27

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      72320373..72368395
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005248601.3XP_005248658.1  pentatricopeptide repeat-containing protein 2, mitochondrial isoform X1

      Conserved Domains (2) summary
      sd00004
      Location:165194
      PPR; PPR repeat [structural motif]
      pfam10037
      Location:103212
      MRP-S27; Mitochondrial 28S ribosomal protein S27
    2. XM_047417743.1XP_047273699.1  pentatricopeptide repeat-containing protein 2, mitochondrial isoform X2

      UniProtKB/TrEMBL
      B3KPU6, D6RGK0
    3. XM_047417745.1XP_047273701.1  pentatricopeptide repeat-containing protein 2, mitochondrial isoform X4

      UniProtKB/TrEMBL
      D6RGK0, F6S289
    4. XM_047417744.1XP_047273700.1  pentatricopeptide repeat-containing protein 2, mitochondrial isoform X3

      UniProtKB/TrEMBL
      D6RGK0
      Related
      ENSP00000426295.2, ENST00000510676.6

    RNA

    1. XR_948298.3 RNA Sequence

    2. XR_241790.6 RNA Sequence

    3. XR_007058635.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      72801543..72849569
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054353496.1XP_054209471.1  pentatricopeptide repeat-containing protein 2, mitochondrial isoform X1

    2. XM_054353497.1XP_054209472.1  pentatricopeptide repeat-containing protein 2, mitochondrial isoform X2

      UniProtKB/TrEMBL
      B3KPU6, D6RGK0
    3. XM_054353499.1XP_054209474.1  pentatricopeptide repeat-containing protein 2, mitochondrial isoform X4

      UniProtKB/TrEMBL
      D6RGK0, F6S289
    4. XM_054353498.1XP_054209473.1  pentatricopeptide repeat-containing protein 2, mitochondrial isoform X3

      UniProtKB/TrEMBL
      D6RGK0

    RNA

    1. XR_008487162.1 RNA Sequence

    2. XR_008487161.1 RNA Sequence

    3. XR_008487163.1 RNA Sequence