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ITM2A Gene

protein-coding   GIFtS: 56
GCID: GC0XM078615

Integral Membrane Protein 2A

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(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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Aliases
Integral Membrane Protein 2A1 2
BRICHOS Domain Containing 2A1 2
E25A2 5
BRICD2A2
Protein E253

External Ids:    HGNC: 61731   Entrez Gene: 94522   Ensembl: ENSG000000785967   OMIM: 3002225   UniProtKB: O437363   

Export aliases for ITM2A gene to outside databases

Previous GC identifers: GC0XM074161 GC0XM075577 GC0XM076657 GC0XM077371 GC0XM078422 GC0XM072195


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for ITM2A Gene:
This gene encodes a type II membrane protein that belongs to the ITM2 family. Studies in mouse suggest that it may
be involved in osteo- and chondrogenic differentiation. Alternatively spliced transcript variants encoding
different isoforms have been found for this gene. (provided by RefSeq, Jan 2010)

GeneCards Summary for ITM2A Gene:
ITM2A (integral membrane protein 2A) is a protein-coding gene. An important paralog of this gene is ITM2B.

Gene Wiki entry for ITM2A Gene


(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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RefSeq DNA sequence at NCBI GenBank:
NC_000023.10  NC_018934.2  NT_011651.18  
Regulatory elements:
   Regulatory transcription factor binding sites in the ITM2A gene promoter:
         GATA-3   FOXO4   FOXJ2 (long isoform)   FOXJ2   Zic3   GATA-1   GATA-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidITM2A promoter sequence
   Search Chromatin IP Primers for ITM2A

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ITM2A


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

Entrez Gene cytogenetic band: Xq13.3-Xq21.2   Ensembl cytogenetic band:  Xq21.1   HGNC cytogenetic band: Xq13.3-q21.2

ITM2A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ITM2A gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM078615:  view genomic region     (about GC identifiers)

Start:
78,615,881 bp from pter      End:
78,623,164 bp from pter
Size:
7,284 bases      Orientation:
minus strand

(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., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: ITM2A_HUMAN, O43736 (See protein sequence)
Recommended Name: Integral membrane protein 2A  
Size: 263 amino acids; 29741 Da
Secondary accessions: B2R7X5 B4E062
Alternative splicing: 2 isoforms:  O43736-1   O43736-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for ITM2A: NX_O43736

Explore proteomics data for ITM2A at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys3, Lys14, Lys37
  • Glycosylation2 at Asn166
  • Modification sites at PhosphoSitePlus

  • See ITM2A Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001165052.1  NP_004858.1  

    ENSEMBL proteins: 
     ENSP00000362395   ENSP00000415533  

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    antibodies-online proteins for ITM2A (3 products) 

     
    antibodies-online peptides for ITM2A

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    antibodies-online antibodies for ITM2A (24 products) 

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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:
    BRICD: BRICHOS domain containing

    1 InterPro protein domain:
     IPR007084 BRICHOS_dom

    Graphical View of Domain Structure for InterPro Entry O43736

    ProtoNet protein and cluster: O43736

    1 Blocks protein domain: IPB007084 BRICHOS domain

    UniProtKB/Swiss-Prot: ITM2A_HUMAN, O43736
    Similarity: Belongs to the ITM2 family
    Similarity: Contains 1 BRICHOS domain


    Find genes that share domains with ITM2A           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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:
         Genatlas biochemistry entry for ITM2A:
    integral membrane protein,type 2,involved in osteo and chondrogenic differentiation,involved in transcriptional
    regulation of cartilage or bone specific gene

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI15983050
         
    Find genes that share ontologies with ITM2A           About GenesLikeMe


    Phenotypes:
         4 GenomeRNAi human phenotypes for ITM2A:
     Decreased Hepatitis C virus re  Decreased number of cells in m  Decreased viability of wild-ty  Synthetic lethal with Ras 

         3 MGI mutant phenotypes (inferred from 3 alleles(MGI details for Itm2a):
     embryogenesis  nervous system  normal 

    Find genes that share phenotypes with ITM2A           About GenesLikeMe

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for ITM2A

    miRNA
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    miRTarBase miRNAs that target ITM2A:
    hsa-mir-26b-5p (MIRT029091)

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    5 qRT-PCR Assays for microRNAs that regulate ITM2A:
    hsa-miR-3065-3p hsa-miR-205* hsa-miR-485-3p hsa-miR-296-3p hsa-miR-556-3p
    SwitchGear 3'UTR luciferase reporter plasmidITM2A 3' UTR sequence
    Inhib. RNA
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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 UniProtKB/Swiss-Prot
    ITM2A_HUMAN, O43736: Membrane; Single-pass type II membrane protein (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol3
    plasma membrane2
    nucleus1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016021integral component of membrane IEA--

    Find genes that share ontologies with ITM2A           About GenesLikeMe


    (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 ITM2A
    Interactions:

        Search GeneGlobe Interaction Network for ITM2A

    STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

    3 Interacting proteins for ITM2A (O437361 ENSP000003623954) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ATP6V0A4ENSP000002538564STRING: ENSP00000253856
    UBCENSP000003448184STRING: ENSP00000344818
    APPP05067-41EBI-2431769,EBI-302641
    About this table

    (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 Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for ITM2A



    (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 ITM2A gene (2 alternative transcripts): 
    NM_001171581.1  NM_004867.4  

    Unigene Cluster for ITM2A:

    Integral membrane protein 2A
    Hs.17109  [show with all ESTs]
    Unigene Representative Sequence: NM_004867
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000373298 ENST00000469541 ENST00000482194 ENST00000462038 ENST00000461357
    ENST00000434584(uc004edh.3 uc011mqr.2)
    miRNA
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    5 qRT-PCR Assays for microRNAs that regulate ITM2A:
    hsa-miR-3065-3p hsa-miR-205* hsa-miR-485-3p hsa-miR-296-3p hsa-miR-556-3p
    SwitchGear 3'UTR luciferase reporter plasmidITM2A 3' UTR sequence
    Inhib. RNA
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    OriGene qPCR primer pairs and template standards for ITM2A
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      QuantiTect SYBR Green Assays in human, mouse, rat ITM2A
      QuantiFast Probe-based Assays in human, mouse, rat ITM2A

    Additional mRNA sequence: 

    AF038953.1 AK223327.1 AK303238.1 AK313154.1 AY359051.1 BC010511.1 BC034485.1 BC040437.1 
    CR456875.1 

    16 DOTS entries:

    DT.452204  DT.100659216  DT.40132888  DT.100659213  DT.100848076  DT.100642587  DT.121279660  DT.86854196 
    DT.121279650  DT.121279664  DT.91753146  DT.91753149  DT.95216279  DT.95216285  DT.95185495  DT.95216283 

    Selected AceView cDNA sequences (see all 314):

    BG777472 CR594227 BF432227 BM129604 CR611328 BF439698 BP368516 CR591355 
    CD105751 AI801343 CD519438 CR604015 BI835099 BP368412 BF511262 CA866028 
    CD246047 BM924258 BM674086 BP431979 BU581262 BP341130 BX108970 CA414304 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for ITM2A (see all 7)    About this scheme

    ExUns: 1 ^ 2a · 2b · 2c · 2d · 2e · 2f ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9a · 9b
    SP1:                                            -     -     -                                                         
    SP2:                                                        -                                                         
    SP3:                                            -     -     -     -                                                   
    SP4:                                            -     -     -     -     -                                             
    SP5:                                -     -     -     -     -     -     -     -                                       


    ECgene alternative splicing isoforms for ITM2A

    (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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    ITM2A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AGACAGTCAT
    ITM2A Expression
    About this image


    ITM2A expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 16) fully expand
     
     Eye (Sensory Organs)    fully expand to see all 2 entries
             Limbal Basal Epithelial Cells Limbus Epithelium
     
     Epithelial Cells
             Limbal Basal Epithelial Cells Limbus Epithelium
     
     Brain (Nervous System)    fully expand to see all 3 entries
             Adult Endothelial Cells Blood Brain Barrier
             Cerebral Cortex
     
     Ovary (Reproductive System)    fully expand to see all 2 entries
             Pre-Granulosa Cells Primordial Follicle
     
     Testis (Reproductive System)    fully expand to see all 2 entries
             Testicular Interstitial Cells Testis Interstitium
    ITM2A Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    ITM2A Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.17109
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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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    This gene was present in the common ancestor of animals.

    Orthologs for ITM2A gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Itm2a1 , 5 integral membrane protein 2A1, 5 89.61(n)1
    95.06(a)1
      X (47.52 cM)5
    164311  NM_008409.21  NP_032435.21 
     1073970995 
    chicken
    (Gallus gallus)
    Aves ITM2A1 integral membrane protein 2A 69.72(n)
    66.14(a)
      422145  NM_001012571.1  NP_001012589.1 
    lizard
    (Anolis carolinensis)
    Reptilia ITM2A6
    integral membrane protein 2A
    54(a)
    1 ↔ 1
    GL343528.1(171825-191098)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.247782 Xenopus laevis transcribed sequence with weak similarity more 73.44(n)    BJ057493.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG36626
    --
    17(a)
    1 → many
    2L(821422-824337)
    worm
    (Caenorhabditis elegans)
    Secernentea C25F6.76
    Protein C25F6.7, isoform a (C25F6.7) mRNA, complet...
    16(a)
    1 → many
    X(5445161-5448030) WBGene00016106


    ENSEMBL Gene Tree for ITM2A (if available)
    TreeFam Gene Tree for ITM2A (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for ITM2A gene
    ITM2B2  ITM2C2  
    2 SIMAP similar genes for ITM2A using alignment to 2 protein entries:     ITM2A_HUMAN (see all proteins):
    ITM2B    ITM2C

    Find genes that share paralogs with ITM2A           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 ITM2A (see all 192)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1819779771,2
    --78587020(+) AGCAGA/GTAATA 2 -- ds50010--------
    rs1842932011,2
    --78587051(+) TTCACC/TTAATA 2 -- ds50010--------
    rs17366721,2
    C,F,O,A,H--78587167(-) CTTGGT/ATAAGA 2 -- ds500118Minor allele frequency- A:0.22NA EA NS WA CSA 863
    rs1895785121,2
    --78587171(+) ATCCAA/CGGTTA 2 -- ds50010--------
    rs1470327491,2
    --78587306(+) GCCAAA/TTATGG 2 -- ds50010--------
    rs2008208261,2
    C--78587344(+) ACTGT-/AAAAGG 2 -- ds50010--------
    rs1812702471,2
    --78587363(+) TATGAA/CAATAT 2 -- ds50010--------
    rs17510951,2
    C,H--78587365(-) TTATAG/TTTTCA 2 -- ds50019Minor allele frequency- T:0.00MN WA NA CSA 196
    rs17366701,2
    C,H--78587410(-) ATGAGC/GCCAAC 2 -- ds50019Minor allele frequency- G:0.00WA NA CSA 14
    rs59593181,2
    C,F,A,H--78587423(+) TTTTAA/GATCTG 2 -- ds50019Minor allele frequency- G:0.81NS EA NA 422

    HapMap Linkage Disequilibrium report for ITM2A (78615881 - 78623164 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for ITM2A:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv519126CNV Gain19592680

    Locus Specific Mutation Databases (LSDB): ITM2A

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing ITM2A
    DNA2.0 Custom Variant and Variant Library Synthesis for ITM2A

    (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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    OMIM gene information: 300222    OMIM disorders: --


    Find genes that share disorders with ITM2A           About GenesLikeMe

    Genetic Association Database (GAD): ITM2A

    Export disorders for ITM2A gene to outside databases

    (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 ITM2A gene, integrated from 10 sources (see all 27):
    (articles sorted by number of sources associating them with ITM2A)
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    1. Many sequence variants affecting diversity of adult human height. (PubMed id 18391951)1, 4 Gudbjartsson D.F....Stefansson K. (Nat. Genet. 2008)
    2. The DNA sequence of the human X chromosome. (PubMed id 15772651)1, 2 Ross M.T.... Bentley D.R. (Nature 2005)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    4. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)1, 2 Clark H.F.... Gray A.M. (Genome Res. 2003)
    5. Genomic organization and chromosomal localization of the Itm2a gene. (PubMed id 9892734)1, 3 Pittois K....Merregaert J. (Mamm. Genome 1999)
    6. Identification of genes expressed in human CD34(+) hematopoietic stem/progenitor cells by expressed sequence tags and efficient full- length cDNA cloning. (PubMed id 9653160)1, 2 Mao M.... Chen Z. (Proc. Natl. Acad. Sci. U.S.A. 1998)
    7. Isolation of markers for chondro-osteogenic differentiation using cDNA library subtraction. Molecular cloning and characterization of a gene belonging to a novel multigene family of integral membrane proteins. (PubMed id 8702637)1, 3 Deleersnijder W....Merregaert J. (J. Biol. Chem. 1996)
    8. Robust evidence for five new Graves' disease risk loci from a staged genome-wide association analysis. (PubMed id 23612905)1 Zhao S.X....Song H.D. (Hum. Mol. Genet. 2013)
    9. Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (amp 2012)
    10. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 9452 HGNC: 6173 AceView: ITM2A Ensembl:ENSG00000078596 euGenes: HUgn9452
    ECgene: ITM2A H-InvDB: ITM2A

    (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 ITM2A 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 ITM2A gene:
    Search GeneIP for patents involving ITM2A

    GeneCards and IP:
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