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    METAP1D methionyl aminopeptidase type 1D, mitochondrial [ Homo sapiens (human) ]

    Gene ID: 254042, updated on 2-Nov-2024

    Summary

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    Official Symbol
    METAP1Dprovided by HGNC
    Official Full Name
    methionyl aminopeptidase type 1D, mitochondrialprovided by HGNC
    Primary source
    HGNC:HGNC:32583
    See related
    Ensembl:ENSG00000172878 MIM:610267; AllianceGenome:HGNC:32583
    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
    MAP1D; MAP 1D; Metap1l; MetAP 1D
    Summary
    The N-terminal methionine excision pathway is an essential process in which the N-terminal methionine is removed from many proteins, thus facilitating subsequent protein modification. In mitochondria, enzymes that catalyze this reaction are celled methionine aminopeptidases (MetAps, or MAPs; EC 3.4.11.18) (Serero et al., 2003 [PubMed 14532271]).[supplied by OMIM, Mar 2008]
    Expression
    Ubiquitous expression in ovary (RPKM 4.2), endometrium (RPKM 2.3) and 25 other tissues See more
    Orthologs
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    Genomic context

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    See METAP1D in Genome Data Viewer
    Location:
    2q31.1
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (171999953..172082430)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (172486172..172568673)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (172864860..172947158)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene histone acetyltransferase 1 Neighboring gene PDGFA associated protein 1 pseudogene Neighboring gene uncharacterized LOC124905590 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12106 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16761 Neighboring gene VISTA enhancer hs553 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:172945060-172945588 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:172945589-172946118 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:172948655-172949268 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:172949269-172949880 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:172949881-172950494 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:172950495-172951106 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:172951721-172952332 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:172952946-172953557 Neighboring gene VISTA enhancer hs422 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12108 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12109 Neighboring gene distal-less homeobox 1 Neighboring gene distal-less homeobox 2

    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 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. Structural insights into N-terminal methionine cleavage by the human mitochondrial methionine aminopeptidase, MetAP1D. Lee Y, et al. Sci Rep, 2023 Dec 15. PMID 38102161, Free PMC Article
    2. MAP1D, a novel methionine aminopeptidase family member is overexpressed in colon cancer. Leszczyniecka M, et al. Oncogene, 2006 Jun 8. PMID 16568094
    3. An unusual peptide deformylase features in the human mitochondrial N-terminal methionine excision pathway. Serero A, et al. J Biol Chem, 2003 Dec 26. PMID 14532271
    4. Apocrine glands are bystanders in hidradenitis suppurativa and their involvement is gender specific. Zouboulis CC, et al. J Eur Acad Dermatol Venereol, 2020 Jul. PMID 32031713
    5. Large-scale genotyping identifies 41 new loci associated with breast cancer risk. Michailidou K, et al. Nat Genet, 2013 Apr. PMID 23535729, Free PMC Article

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Structural insights into N-terminal methionine cleavage by the human mitochondrial methionine aminopeptidase, MetAP1D.
      Title: Structural insights into N-terminal methionine cleavage by the human mitochondrial methionine aminopeptidase, MetAP1D.
    2. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    3. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    5. MAP1D is a potentially oncogenic, novel member of the MAP gene family that may play an important role in colon tumorigenesis
      Title: MAP1D, a novel methionine aminopeptidase family member is overexpressed in colon cancer.
    Submit: New GeneRIF Correction

    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

    EBI GWAS Catalog

    Description
    Large-scale genotyping identifies 41 new loci associated with breast cancer risk.
    EBI GWAS Catalog

    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables aminopeptidase activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables initiator methionyl aminopeptidase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metalloaminopeptidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metalloexopeptidase activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in N-terminal protein amino acid modification TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in peptidyl-methionine modification TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in proteolysis IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in mitochondrion HTP PubMed 
    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

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    Preferred Names
    methionine aminopeptidase 1D, mitochondrial
    Names
    CDS of metAP-3 within PCR fragment
    metAP 1D
    peptidase M 1D
    NP_001309207.1
    NP_001309208.1
    NP_954697.1
    XP_047299826.1
    XP_047299827.1
    XP_047299828.1
    XP_054188845.1
    XP_054188846.1
    XP_054188847.1
    XP_054197245.1
    XP_054197246.1
    XP_054197247.1

    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_001322278.2 → NP_001309207.1  methionine aminopeptidase 1D, mitochondrial isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC015976, BC143913, BM982111
      UniProtKB/Swiss-Prot
      Q6UB28
      Conserved Domains (1) summary
      cd01086
      Location:1 → 212
      MetAP1; Methionine Aminopeptidase 1. E.C. 3.4.11.18. Also known as methionyl aminopeptidase and Peptidase M. Catalyzes release of N-terminal amino acids, preferentially methionine, from peptides and arylamides.

    2. NM_001322279.2 → NP_001309208.1  methionine aminopeptidase 1D, mitochondrial isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC015976, AC114745, AY374142, BM982111
      UniProtKB/Swiss-Prot
      Q6UB28
      Conserved Domains (1) summary
      cd01086
      Location:1 → 212
      MetAP1; Methionine Aminopeptidase 1. E.C. 3.4.11.18. Also known as methionyl aminopeptidase and Peptidase M. Catalyzes release of N-terminal amino acids, preferentially methionine, from peptides and arylamides.

    3. NM_199227.3 → NP_954697.1  methionine aminopeptidase 1D, mitochondrial isoform 1 precursor

      See identical proteins and their annotated locations for NP_954697.1

      Status: VALIDATED

      Source sequence(s)
      AC015976, AY374142, BM982111
      Consensus CDS
      CCDS2246.1
      UniProtKB/Swiss-Prot
      Q1WNX3, Q6UB28
      Related
      ENSP00000315152.4, ENST00000315796.5
      Conserved Domains (1) summary
      cd01086
      Location:94 → 330
      MetAP1; Methionine Aminopeptidase 1. E.C. 3.4.11.18. Also known as methionyl aminopeptidase and Peptidase M. Catalyzes release of N-terminal amino acids, preferentially methionine, from peptides and arylamides.

    RNA

    1. NR_136273.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC015976, AC114745, BM982111

    2. NR_136276.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC015976, AY374142, BM982111

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      171999953..172082430
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047443870.1 → XP_047299826.1  methionine aminopeptidase 1D, mitochondrial isoform X1

    2. XM_047443871.1 → XP_047299827.1  methionine aminopeptidase 1D, mitochondrial isoform X2

    3. XM_047443872.1 → XP_047299828.1  methionine aminopeptidase 1D, mitochondrial isoform X3

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_025791761.1 Reference GRCh38.p14 PATCHES

      Range
      439003..521197
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054332870.1 → XP_054188845.1  methionine aminopeptidase 1D, mitochondrial isoform X1

    2. XM_054332871.1 → XP_054188846.1  methionine aminopeptidase 1D, mitochondrial isoform X2

    3. XM_054332872.1 → XP_054188847.1  methionine aminopeptidase 1D, mitochondrial isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      172486172..172568673
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054341270.1 → XP_054197245.1  methionine aminopeptidase 1D, mitochondrial isoform X1

    2. XM_054341271.1 → XP_054197246.1  methionine aminopeptidase 1D, mitochondrial isoform X2

    3. XM_054341272.1 → XP_054197247.1  methionine aminopeptidase 1D, mitochondrial isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6UB28.1 GenPept UniProtKB/Swiss-Prot:Q6UB28

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