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

Gene ID: 79810, updated on 12-Aug-2022

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
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Genomic context

See PTCD2 in Genome Data Viewer
Location:
5q13.2
Exon count:
11
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (72320373..72368395)
110 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 RNA, 7SL, cytoplasmic 153, pseudogene Neighboring gene ribosomal protein L10a pseudogene 8 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

Homology

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
PubMed 
involved_in multicellular organism development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
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
PubMed 
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)

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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_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/Swiss-Prot
    Q8WV60
    UniProtKB/TrEMBL
    B3KPU6
    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
    B3KPU6, B7Z8R2, 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
    Q8WV60, Q9H9R0
    UniProtKB/TrEMBL
    A0A024RAM6, B3KPU6
    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: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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
  3. XM_047417745.1XP_047273701.1  pentatricopeptide repeat-containing protein 2, mitochondrial isoform X4

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

    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)