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Aliases for METAP1D Gene

Aliases for METAP1D Gene

  • Methionyl Aminopeptidase Type 1D, Mitochondrial 2 3 4 5
  • Peptidase M 1D 3 4
  • MetAP 1D 3 4
  • MAP 1D 3 4
  • MAP1D 3 4
  • Methionine Aminopeptidase 1D, Mitochondrial 3
  • CDS Of MetAP-3 Within PCR Fragment 3
  • Methionine Aminopeptidase 1D 2
  • EC 3.4.11.18 4
  • Metap1l 3

External Ids for METAP1D Gene

Previous GeneCards Identifiers for METAP1D Gene

  • GC02P164748
  • GC02P172865

Summaries for METAP1D Gene

Entrez Gene Summary for METAP1D Gene

  • 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]

GeneCards Summary for METAP1D Gene

METAP1D (Methionyl Aminopeptidase Type 1D, Mitochondrial) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include aminopeptidase activity and metalloaminopeptidase activity. An important paralog of this gene is METAP1.

UniProtKB/Swiss-Prot for METAP1D Gene

  • Removes the N-terminal methionine from nascent proteins. The N-terminal methionine is often cleaved when the second residue in the primary sequence is small and uncharged (Met-Ala-, Cys, Gly, Pro, Ser, Thr, or Val). Requires deformylation of the N(alpha)-formylated initiator methionine before it can be hydrolyzed (By similarity). May play a role in colon tumorigenesis.

Additional gene information for METAP1D Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for METAP1D Gene

Genomics for METAP1D Gene

GeneHancer (GH) Regulatory Elements for METAP1D Gene

Promoters and enhancers for METAP1D Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02I171999 Promoter/Enhancer 1.6 Ensembl ENCODE 560.9 +0.7 693 2 HDGF CLOCK SMAD1 FOXA2 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 METAP1D SLC25A12 DCAF17 DAP3P2 RPS15P4 GC02P172074
GH02I172092 Promoter/Enhancer 3.4 VISTA UCNEbase EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.2 +98.6 98598 10.5 MLX ZFP64 FEZF1 DMAP1 SLC30A9 SP3 NFYC SSRP1 GLIS1 RCOR2 DLX2 DCAF17 DAP3P2 RPS15P4 METAP1D HAT1 ITGA6 ENSG00000232788 DLX1 DYNC1I2
GH02I171158 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 10.2 -839.3 -839272 4.4 HDGF PKNOX1 CLOCK FOXA2 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 TLK1 GORASP2 DCAF17 HAT1 METAP1D DAP3P2 GC02P171119 GC02P171227
GH02I172552 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE 10.1 +555.6 555612 6.1 CLOCK MLX DMAP1 YY1 SLC30A9 SP3 NFYC MEF2D ZNF610 GLIS1 PDK1 ENSG00000225205 METAP1D ENSG00000199866 GC02M172559 GC02P172546
GH02I171893 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 10.5 -105.4 -105410 1.9 HDGF PKNOX1 ARID4B SIN3A YBX1 ZNF2 YY1 POLR2B ZNF766 ZNF207 SLC25A12 HAT1 METAP1D LOC105373739 RNU6-182P
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around METAP1D on UCSC Golden Path with GeneCards custom track

Genomic Locations for METAP1D Gene

Genomic Locations for METAP1D Gene
chr2:171,999,583-172,082,430
(GRCh38/hg38)
Size:
82,848 bases
Orientation:
Plus strand
chr2:172,864,490-172,947,158
(GRCh37/hg19)

Genomic View for METAP1D Gene

Genes around METAP1D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
METAP1D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for METAP1D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for METAP1D Gene

Proteins for METAP1D Gene

  • Protein details for METAP1D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6UB28-MAP12_HUMAN
    Recommended name:
    Methionine aminopeptidase 1D, mitochondrial
    Protein Accession:
    Q6UB28
    Secondary Accessions:
    • Q1WNX3

    Protein attributes for METAP1D Gene

    Size:
    335 amino acids
    Molecular mass:
    37088 Da
    Cofactor:
    Name=Co(2+); Xref=ChEBI:CHEBI:48828; Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAY55948.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for METAP1D Gene

Post-translational modifications for METAP1D Gene

No Post-translational modifications

Other Protein References for METAP1D Gene

Antibody Products

  • R&D Systems Antibodies for METAP1D (Methionine Aminopeptidase 1D/MAP1D)
  • Santa Cruz Biotechnology (SCBT) Antibodies for METAP1D

No data available for DME Specific Peptides for METAP1D Gene

Domains & Families for METAP1D Gene

Gene Families for METAP1D Gene

Suggested Antigen Peptide Sequences for METAP1D Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q6UB28

UniProtKB/Swiss-Prot:

MAP12_HUMAN :
  • Belongs to the peptidase M24A family. Methionine aminopeptidase type 1 subfamily.
Family:
  • Belongs to the peptidase M24A family. Methionine aminopeptidase type 1 subfamily.
genes like me logo Genes that share domains with METAP1D: view

Function for METAP1D Gene

Molecular function for METAP1D Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=573 uM for Met-pro-p-nitroanilide (at pH 8) {ECO:0000269 PubMed:17929833}; pH dependence: Optimum pH is 7.5-8.0. {ECO:0000269 PubMed:17929833};
UniProtKB/Swiss-Prot CatalyticActivity:
Release of N-terminal amino acids, preferentially methionine, from peptides and arylamides.
UniProtKB/Swiss-Prot Function:
Removes the N-terminal methionine from nascent proteins. The N-terminal methionine is often cleaved when the second residue in the primary sequence is small and uncharged (Met-Ala-, Cys, Gly, Pro, Ser, Thr, or Val). Requires deformylation of the N(alpha)-formylated initiator methionine before it can be hydrolyzed (By similarity). May play a role in colon tumorigenesis.

Enzyme Numbers (IUBMB) for METAP1D Gene

Phenotypes From GWAS Catalog for METAP1D Gene

Gene Ontology (GO) - Molecular Function for METAP1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004177 aminopeptidase activity TAS 14532271
GO:0008233 peptidase activity IEA --
GO:0008235 metalloexopeptidase activity TAS 14532271
GO:0016787 hydrolase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with METAP1D: view
genes like me logo Genes that share phenotypes with METAP1D: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for METAP1D Gene

Localization for METAP1D Gene

Subcellular locations from UniProtKB/Swiss-Prot for METAP1D Gene

Mitochondrion.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for METAP1D gene
Compartment Confidence
mitochondrion 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for METAP1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IDA 14532271
GO:0043231 intracellular membrane-bounded organelle IDA --
genes like me logo Genes that share ontologies with METAP1D: view

Pathways & Interactions for METAP1D Gene

SuperPathways for METAP1D Gene

No Data Available

Gene Ontology (GO) - Biological Process for METAP1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006508 proteolysis IEA --
GO:0018206 peptidyl-methionine modification TAS 14532271
GO:0031365 N-terminal protein amino acid modification TAS 14532271
genes like me logo Genes that share ontologies with METAP1D: view

No data available for Pathways by source and SIGNOR curated interactions for METAP1D Gene

Drugs & Compounds for METAP1D Gene

(1) Drugs for METAP1D Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Cobalt Pharma 174
genes like me logo Genes that share compounds with METAP1D: view

Transcripts for METAP1D Gene

mRNA/cDNA for METAP1D Gene

(4) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(3) Selected AceView cDNA sequences:
(7) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for METAP1D Gene

Methionyl aminopeptidase type 1D (mitochondrial):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for METAP1D Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10a · 10b · 10c
SP1: - -
SP2: - - -
SP3:
SP4:

Relevant External Links for METAP1D Gene

GeneLoc Exon Structure for
METAP1D
ECgene alternative splicing isoforms for
METAP1D

Expression for METAP1D Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for METAP1D Gene

Protein differential expression in normal tissues from HIPED for METAP1D Gene

This gene is overexpressed in Bone (65.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for METAP1D Gene



Protein tissue co-expression partners for METAP1D Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of METAP1D Gene:

METAP1D

SOURCE GeneReport for Unigene cluster for METAP1D Gene:

Hs.298250

mRNA Expression by UniProt/SwissProt for METAP1D Gene:

Q6UB28-MAP12_HUMAN
Tissue specificity: Overexpressed in colon cancer cell lines and colon tumors as compared to normal tissues (at protein level).

Evidence on tissue expression from TISSUES for METAP1D Gene

  • Nervous system(4.1)
genes like me logo Genes that share expression patterns with METAP1D: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for METAP1D Gene

Orthologs for METAP1D Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for METAP1D Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia METAP1D 33 34
  • 99.5 (n)
dog
(Canis familiaris)
Mammalia METAP1D 33 34
  • 94.43 (n)
cow
(Bos Taurus)
Mammalia METAP1D 33
  • 93.39 (n)
MAP1D 34
  • 93 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Metap1d 33 16 34
  • 90.45 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia METAP1D 34
  • 88 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Metap1d 33
  • 87.82 (n)
oppossum
(Monodelphis domestica)
Mammalia METAP1D 34
  • 83 (a)
OneToOne
chicken
(Gallus gallus)
Aves METAP1D 33 34
  • 81.24 (n)
lizard
(Anolis carolinensis)
Reptilia METAP1D 34
  • 78 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia metap1d 33
  • 80.37 (n)
zebrafish
(Danio rerio)
Actinopterygii metap1d 33 34
  • 64.87 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009013 33
  • 55.15 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG5188 33 34
  • 54.92 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes MAP1 34
  • 31 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons MAP1D 33
  • 54.95 (n)
soybean
(Glycine max)
eudicotyledons Gma.6970 33
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.5080 33
rice
(Oryza sativa)
Liliopsida Os02g0761700 33
  • 55.19 (n)
Os.10727 33
corn
(Zea mays)
Liliopsida Zm.3493 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 53 (a)
OneToOne
Species where no ortholog for METAP1D was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for METAP1D Gene

ENSEMBL:
Gene Tree for METAP1D (if available)
TreeFam:
Gene Tree for METAP1D (if available)

Paralogs for METAP1D Gene

Paralogs for METAP1D Gene

(2) SIMAP similar genes for METAP1D Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with METAP1D: view

Variants for METAP1D Gene

Sequence variations from dbSNP and Humsavar for METAP1D Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs1000002340 -- 172,081,311(+) C/T 3_prime_UTR_variant, non_coding_transcript_variant
rs1000082801 -- 172,007,222(+) T/C genic_upstream_transcript_variant, intron_variant
rs1000095234 -- 172,036,621(+) T/G genic_upstream_transcript_variant, intron_variant
rs1000131599 -- 172,014,403(+) T/C genic_upstream_transcript_variant, intron_variant
rs1000150237 -- 172,021,184(+) A/C genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for METAP1D Gene

Variant ID Type Subtype PubMed ID
dgv675n67 CNV loss 20364138
dgv7159n54 CNV gain+loss 21841781
dgv7160n54 CNV loss 21841781
dgv7161n54 CNV gain 21841781
dgv7162n54 CNV gain 21841781
dgv7163n54 CNV loss 21841781
dgv746e199 CNV deletion 23128226
dgv747e199 CNV deletion 23128226
dgv90e180 CNV loss 20482838
esv1004708 CNV deletion 20482838
esv21895 CNV gain+loss 19812545
esv2458501 CNV deletion 19546169
esv2662767 CNV deletion 23128226
esv2721131 CNV deletion 23290073
esv2721132 CNV deletion 23290073
esv2721135 CNV deletion 23290073
esv2721136 CNV deletion 23290073
esv3560544 CNV deletion 23714750
esv3584170 CNV loss 25503493
esv3593357 CNV loss 21293372
nsv1071270 CNV deletion 25765185
nsv1116808 CNV deletion 24896259
nsv1126570 CNV deletion 24896259
nsv1127782 CNV deletion 24896259
nsv1130757 CNV deletion 24896259
nsv1142290 CNV tandem duplication 24896259
nsv3031 CNV deletion 18451855
nsv583616 CNV gain+loss 21841781
nsv583617 CNV gain 21841781
nsv583629 CNV loss 21841781
nsv820002 CNV gain 19587683
nsv820939 CNV deletion 20802225
nsv953514 CNV deletion 24416366

Variation tolerance for METAP1D Gene

Residual Variation Intolerance Score: 70.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.41; 77.16% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for METAP1D Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
METAP1D

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for METAP1D Gene

Disorders for METAP1D Gene

Additional Disease Information for METAP1D

No disorders were found for METAP1D Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for METAP1D Gene

Publications for METAP1D Gene

  1. An unusual peptide deformylase features in the human mitochondrial N-terminal methionine excision pathway. (PMID: 14532271) Serero A … Meinnel T (The Journal of biological chemistry 2003) 2 3 4 22 58
  2. MAP1D, a novel methionine aminopeptidase family member is overexpressed in colon cancer. (PMID: 16568094) Leszczyniecka M … Phillips PE (Oncogene 2006) 2 3 4 58
  3. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  4. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. (PMID: 26496610) Hein MY … Mann M (Cell 2015) 3 58
  5. N-terminome analysis of the human mitochondrial proteome. (PMID: 25944712) Vaca Jacome AS … Carapito C (Proteomics 2015) 4 58

Products for METAP1D Gene

Sources for METAP1D Gene

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