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MT1DP Gene

pseudogene   GIFtS: 25
GCID: GC16P056677

Metallothionein 1D, Pseudogene

  Search for MT1DP
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Metallothionein 1D, Pseudogene1 2
MTM2 3

External Ids:    HGNC: 73961   Entrez Gene: 3263432   Ensembl: ENSG000002053617   UniProtKB: A1L3X43   
ORGUL members:         

Export aliases for MT1DP gene to outside databases

Previous GC identifers: GC16U990039 GC16P055236 GC16P042547


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for MT1DP Gene:
MT1DP (metallothionein 1D, pseudogene) is a pseudogene, and is affiliated with the lncRNA class.

UniProtKB/Swiss-Prot: MT1DP_HUMAN, A1L3X4
Function: Metallothioneins have a high content of cysteine residues that bind various heavy metals (By similarity)




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Regulatory transcription factor binding sites in the MT1DP gene promoter:
         TBP   p53   Sp1   Zic1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for MT1DP

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat MT1DP


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 16q13   Ensembl cytogenetic band:  16q12.2   HGNC cytogenetic band: 16q13

MT1DP Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
MT1DP gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16P056677:  view genomic region     (about GC identifiers)

Start:
56,677,599 bp from pter      End:
56,678,853 bp from pter
Size:
1,255 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for MT1DP

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: MT1DP_HUMAN, A1L3X4 (See protein sequence)
Recommended Name: Putative metallothionein MT1DP  
Size: 49 amino acids; 4983 Da
Caution: Could be the product of a pseudogene
Secondary accessions: Q86YX1

Explore the universe of human proteins at neXtProt for MT1DP: NX_A1L3X4

Explore proteomics data for MT1DP at MOPED


See MT1DP Protein Expression from SPIRE MOPED, PaxDB, and MaxQB


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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
MT: Metallothioneins

4 InterPro protein domains:
 IPR000006 Metalthion_vert
 IPR003019 Metalthion_sfam_euk
 IPR023587 Metalthion_dom_vert
 IPR017854 Metalthion_dom

Graphical View of Domain Structure for InterPro Entry A1L3X4

ProtoNet protein and cluster: A1L3X4

UniProtKB/Swiss-Prot: MT1DP_HUMAN, A1L3X4
Similarity: Belongs to the metallothionein superfamily. Type 1 family


Find genes that share domains with MT1DP           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: MT1DP_HUMAN, A1L3X4
Function: Metallothioneins have a high content of cysteine residues that bind various heavy metals (By similarity)

     Genatlas biochemistry entry for MT1DP:
metallothionein 1DP cluster

     Gene Ontology (GO): 1 molecular function term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0046872metal ion binding IEA--
     
Find genes that share ontologies with MT1DP           About GenesLikeMe


Animal Models:
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
extracellular3
cytosol1
nucleus1

(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for MT1DP
Interactions:

    Search GeneGlobe Interaction Network for MT1DP

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Tocris compounds for MT1DP



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for MT1DP gene: 
NM_175620.1  

2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000463480(uc010cci.3 uc010vhf.2) ENST00000486551
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GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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MT1DP expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
MT1DP Expression
About this image

MT1DP Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

MT1DP Protein Expression
    Custom PCR Arrays for MT1DP
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In Situ
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(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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  --

ENSEMBL Gene Tree for MT1DP (if available)
TreeFam Gene Tree for MT1DP (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for MT1DP gene
2 SIMAP similar genes for MT1DP using alignment to 1 protein entry:     MT1DP_HUMAN:
MT1M    MTE

Find genes that share paralogs with MT1DP           About GenesLikeMe



(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for MT1DP (see all 100)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 16 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1140524371,2
C,F--56675651(+) AAATAA/GGGATC 1 -- us2k11Minor allele frequency- G:0.01WA 118
rs1864403831,2
--56675679(+) GCCACA/GAGCAA 1 -- us2k10--------
rs73594881,2
C--56675741(+) ATCGCC/TTGCGC 2 -- us2k10--------
rs15998231,2
C,F,A,H--56675817(-) GTCAAA/GGAGTT 2 -- us2k1101Minor allele frequency- G:0.49NS EA NA PA EU CA WA CSA 5241
rs1908693351,2
--56675854(+) CTTGCA/GGATAT 2 -- us2k10--------
rs16102141,2
C,F,A,H--56675888(-) AAGGGT/ATGTAT 2 -- us2k191Minor allele frequency- A:0.36NS EA NA PA EU CA WA 4812
rs620386901,2
C--56676036(+) ACCCAC/TAGTAC 2 -- us2k13Minor allele frequency- T:0.11NA EA 242
rs1824508561,2
--56676073(+) GTTCTC/TAGTAC 2 -- us2k10--------
rs1136964901,2
C,F--56676076(+) CTTAGT/AACCTT 2 -- us2k12Minor allele frequency- A:0.08CSA WA 119
rs16102131,2
C,F,A,H--56676081(-) tgttcA/Gaggta 2 -- us2k16Minor allele frequency- G:0.03NS NA 794

HapMap Linkage Disequilibrium report for MT1DP (56677599 - 56678853 bp)

Structural Variations
     Database of Genomic Variants (DGV) 1 variation for MT1DP:    About this table    
Variant IDTypeSubtypePubMed ID
nsv906720CNV Loss21882294

Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing MT1DP
DNA2.0 Custom Variant and Variant Library Synthesis for MT1DP

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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  --

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for MT1DP gene integrated from 10 sources:
(articles sorted by number of sources associating them with MT1DP)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Structure and tissue-specific expression of the human metallothionein IB gene. (PubMed id 3785191)1, 3 Heguy A.... Karin M. (Mol. Cell. Biol. 1986)
  2. Structural and functional analysis of the human metallothionein-IA gene: differential induction by metal ions and glucocorticoids. (PubMed id 6327055)1, 3 Richards R.I.... Karin M. (Cell 1984)
  3. Human metallothionein genes are clustered on chromosome 16. (PubMed id 6089206)1, 3 Karin M....Shows T.B. (Proc. Natl. Acad. Sci. U.S.A. 1984)
  4. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  6. Creation of genome-wide protein expression libraries using random activation of gene expression. (PubMed id 11329013)1 Harrington J.J.... Ducar M. (Nat. Biotechnol. 2001)
  7. Human metallothionein genes: structure of the functional locus at 16q13. (PubMed id 2286373)1 West A.K....Richards R.I. (Genomics 1990)
  8. Metallothionein gene cluster is split by chromosome 16 rearrangements in myelomonocytic leukaemia. (PubMed id 3856101)1 Le Beau M.M....Rowley J.D. (Nature 1985)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 326343 HGNC: 7396 Ensembl:ENSG00000205361 euGenes: HUgn326343 ECgene: MT1DP
H-InvDB: MT1DP

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for MT1DP Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for MT1DP gene:
Search GeneIP for patents involving MT1DP

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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