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XPNPEP3 X-prolyl aminopeptidase 3 [ Homo sapiens (human) ]

Gene ID: 63929, updated on 11-Jun-2021

Summary

Official Symbol
XPNPEP3provided by HGNC
Official Full Name
X-prolyl aminopeptidase 3provided by HGNC
Primary source
HGNC:HGNC:28052
See related
Ensembl:ENSG00000196236 MIM:613553
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
APP3; ICP55; NPHPL1
Summary
The protein encoded by this gene belongs to the family of X-pro-aminopeptidases that utilize a metal cofactor, and remove the N-terminal amino acid from peptides with a proline residue in the penultimate position. This protein has been shown to localize to the mitochondria of renal cells, and have a role in ciliary function. Mutations in this gene are associated with nephronophthisis-like nephropathy-1. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene, however, expression of some of these isoforms in vivo is not known.[provided by RefSeq, Mar 2011]
Expression
Broad expression in testis (RPKM 4.3), kidney (RPKM 2.0) and 25 other tissues See more
Orthologs
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Genomic context

See XPNPEP3 in Genome Data Viewer
Location:
22q13.2
Exon count:
12
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 22 NC_000022.11 (40857148..40932815)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (41253152..41328819)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene solute carrier family 25 member 17 Neighboring gene microRNA 4766 Neighboring gene ST13 Hsp70 interacting protein Neighboring gene DnaJ heat shock protein family (Hsp40) member B7 Neighboring gene RNA, U6 small nuclear 379, pseudogene Neighboring gene ring-box 1 Neighboring gene ribosomal protein S9 pseudogene 2

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

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Potential readthrough

Included gene: RBX1

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables aminopeptidase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables aminopeptidase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables manganese ion binding IDA
Inferred from Direct Assay
more info
PubMed 
enables metalloaminopeptidase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables peptidase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein homodimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within glomerular filtration IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within protein processing IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in proteolysis IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 
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
xaa-Pro aminopeptidase 3
Names
Intermediate Cleaving Peptidase 55
X-Pro aminopeptidase 3
X-prolyl aminopeptidase 3, mitochondrial
probable Xaa-Pro aminopeptidase 3
NP_001191756.1
NP_071381.1

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.

Genomic

  1. NG_028221.1 RefSeqGene

    Range
    5068..80735
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001204827.2NP_001191756.1  xaa-Pro aminopeptidase 3 isoform 2

    See identical proteins and their annotated locations for NP_001191756.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) shares the first exon in common with variant 1 and contains two alternate exons at the 3' end. This results in a frame-shift and a very short isoform (2) with a distinct C-terminus compared to isoform 1. This variant is supported by transcript evidence, but the encoded isoform lacks experimental support.
    Source sequence(s)
    BC053556, BM980889, BP346902
    Consensus CDS
    CCDS74869.1
    UniProtKB/TrEMBL
    A0A087X0Z2
    Related
    ENSP00000483752.1, ENST00000614001.1
    Conserved Domains (1) summary
    pfam13900
    Location:2648
    GVQW; Putative domain of unknown function
  2. NM_022098.4NP_071381.1  xaa-Pro aminopeptidase 3 isoform 1

    See identical proteins and their annotated locations for NP_071381.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1, also known as APP3m). This isoform has been shown to be localized to the mitochondria (PMID:20179356).
    Source sequence(s)
    AI446638, AL035450, AL080242, AL365514, BC004989, BP346902, BX648018
    Consensus CDS
    CCDS14007.1
    UniProtKB/Swiss-Prot
    Q9NQH7
    Related
    ENSP00000349658.4, ENST00000357137.9
    Conserved Domains (3) summary
    PRK10879
    Location:67506
    PRK10879; proline aminopeptidase P II; Provisional
    cd01087
    Location:252490
    Prolidase; Prolidase. E.C. 3.4.13.9. Also known as Xaa-Pro dipeptidase, X-Pro dipeptidase, proline dipeptidase., imidodipeptidase, peptidase D, gamma-peptidase. Catalyses hydrolysis of Xaa-Pro dipeptides; also acts on aminoacyl-hydroxyproline analogs. No action on ...
    pfam05195
    Location:72205
    AMP_N; Aminopeptidase P, N-terminal domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p13 Primary Assembly

    Range
    40857148..40932815
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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