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CHM Gene

protein-coding   GIFtS: 63
GCID: GC0XM085116

Choroideremia (Rab Escort Protein 1)


(Previous symbols: TCD, DXS540)
  See related diseases
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
Choroideremia (Rab Escort Protein 1)1 2     HSD-322
TCD1 2 3 5     Rab Proteins Geranylgeranyltransferase Component A 12
DXS5401 2     REP13
Choroideremia Protein2 3     Rab Escort Protein 13
REP-12 3     TCD Protein3
GGTA2     

External Ids:    HGNC: 19401   Entrez Gene: 11212   Ensembl: ENSG000001884197   OMIM: 3003905   UniProtKB: P243863   
ORGUL members:         

Export aliases for CHM gene to outside databases

Previous GC identifers: GC0XM080499 GC0XM082196 GC0XM083152 GC0XM083889 GC0XM083891 GC0XM084923 GC0XM085002 GC0XM078692


(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 CHM Gene:
This gene encodes component A of the RAB geranylgeranyl transferase holoenzyme. In the dimeric holoenzyme, this
subunit binds unprenylated Rab GTPases and then presents them to the catalytic Rab GGTase subunit for the
geranylgeranyl transfer reaction. Rab GTPases need to be geranylgeranyled on either one or two cysteine residues
in their C-terminus to localize to the correct intracellular membrane. Mutations in this gene are a cause of
choroideremia; also known as tapetochoroidal dystrophy (TCD). This X-linked disease is characterized by
progressive dystrophy of the choroid, retinal pigment epithelium and retina. Alternative splicing results in
multiple transcript variants encoding different isoforms.(provided by RefSeq, Feb 2009)

GeneCards Summary for CHM Gene:
CHM (choroideremia (Rab escort protein 1)) is a protein-coding gene. Diseases associated with CHM include charcot-marie-tooth disease, dominant intermediate d, and choroideremia. GO annotations related to this gene include Rab geranylgeranyltransferase activity and GTPase activator activity. An important paralog of this gene is GDI1.

UniProtKB/Swiss-Prot: RAE1_HUMAN, P24386
Function: Substrate-binding subunit of the Rab geranylgeranyltransferase (GGTase) complex. Binds unprenylated Rab
proteins and presents the substrate peptide to the catalytic component B composed of RABGGTA and RABGGTB, and
remains bound to it after the geranylgeranyl transfer reaction. The component A is thought to be regenerated by
transferring its prenylated Rab back to the donor membrane. Besides, a pre-formed complex consisting of CHM and
the Rab GGTase dimer (RGGT or component B) can bind to and prenylate Rab proteins; this alternative pathway is
proposed to be the predominant pathway for Rab protein geranylgeranylation

Gene Wiki entry for CHM (Rab escort protein) 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:
NC_000023.11  NT_011651.18  NC_018934.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the CHM gene promoter:
         AML1a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCHM promoter sequence
   Search Chromatin IP Primers for CHM

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


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

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

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

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM085116:  view genomic region     (about GC identifiers)

Start:
85,116,185 bp from pter      End:
85,302,566 bp from pter
Size:
186,382 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., 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: RAE1_HUMAN, P24386 (See protein sequence)
Recommended Name: Rab proteins geranylgeranyltransferase component A 1  
Size: 653 amino acids; 73476 Da
Subunit: Monomer. Heterotrimer composed of RABGGTA, RABGGTB and CHM; within this trimer, RABGGTA and RABGGTB form
the catalytic component B, while CHM (component A) mediates Rab protein binding. Can associate with the Rab
GGTase dimer (RGGT or component B) prior to Rab protein binding; the association is stabilized by geranylgeranyl
pyrophosphate (GGpp). The CHM:RGGT:Rab complex is destabilized by GGpp. Interacts with RAB1A, RAB1B, RAB5A, RAB7A
and RAB27A and mediates their prenylation
Secondary accessions: A1L4D2 O43732
Alternative splicing: 2 isoforms:  P24386-1   P24386-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for CHM: NX_P24386

Explore proteomics data for CHM at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

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

    REFSEQ proteins (2 alternative transcripts): 
    NP_000381.1  NP_001138886.1  

    ENSEMBL proteins: 
     ENSP00000350386   ENSP00000362228   ENSP00000441728  

    CHM Human Recombinant Protein Products:

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    OriGene Protein Over-expression Lysate for CHM
    OriGene Custom MassSpec
    OriGene Custom Protein Services for CHM
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    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
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    Cloud-Clone Corp. Proteins for CHM

    CHM Antibody Products:

    EMD Millipore Mono- and Polyclonal Antibodies for the study of CHM
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    OriGene Custom Antibody Services for CHM
    Novus Biologicals CHM Antibodies
    Abcam antibodies for CHM
    Cloud-Clone Corp. Antibodies for CHM
    Search ThermoFisher Antibodies for CHM
    LSBio Antibodies in human, mouse, rat for CHM

    CHM Assay Products:

    Browse Kits and Assays available from EMD Millipore
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    Browse R&D Systems for biochemical assays
    GenScript Custom Assay Services for CHM
    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for CHM
    Cloud-Clone Corp. CLIAs for CHM


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    3 InterPro protein domains:
     IPR016664 Rab_geranylTrfase_A_euk
     IPR001738 Rab_escort
     IPR018203 GDP_dissociation_inhibitor

    Graphical View of Domain Structure for InterPro Entry P24386

    ProtoNet protein and cluster: P24386

    1 Blocks protein domain: IPB001738 Rab escort (choroideraemia) protein signature

    UniProtKB/Swiss-Prot: RAE1_HUMAN, P24386
    Similarity: Belongs to the Rab GDI family


    CHM for domains           About GeneDecksing


    (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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: RAE1_HUMAN, P24386
    Function: Substrate-binding subunit of the Rab geranylgeranyltransferase (GGTase) complex. Binds unprenylated Rab
    proteins and presents the substrate peptide to the catalytic component B composed of RABGGTA and RABGGTB, and
    remains bound to it after the geranylgeranyl transfer reaction. The component A is thought to be regenerated by
    transferring its prenylated Rab back to the donor membrane. Besides, a pre-formed complex consisting of CHM and
    the Rab GGTase dimer (RGGT or component B) can bind to and prenylate Rab proteins; this alternative pathway is
    proposed to be the predominant pathway for Rab protein geranylgeranylation

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004663Rab geranylgeranyltransferase activity IEA--
    GO:0005096GTPase activator activity IEA--
    GO:0017137Rab GTPase binding IPI7957092
         
    CHM for ontologies           About GeneDecksing


    Phenotypes:
         2 GenomeRNAi human phenotypes for CHM:
     G0/1 arrest  Increased G1 DNA content 

         9 MGI mutant phenotypes (inferred from 5 alleles(MGI details for Chm):
     cardiovascular system  embryogenesis  growth/size/body  homeostasis/metabolism  mortality/aging 
     nervous system  normal  pigmentation  vision/eye 

    CHM for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-outs for CHM: Chmtm1.3Seab Chmtm1Jvdh Chmtm1.2Seab

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for CHM
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for CHM

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for CHM
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for CHM

    miRNA
    Products:
        
    miRTarBase miRNAs that target CHM:
    hsa-mir-215-5p (MIRT024694), hsa-mir-26b-5p (MIRT029824), hsa-mir-192-5p (MIRT026666)

    Block miRNA regulation of human, mouse, rat CHM using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate CHM (see all 30):
    hsa-miR-498 hsa-miR-217 hsa-miR-4311 hsa-miR-137 hsa-miR-509-5p hsa-miR-218-1* hsa-miR-944 hsa-miR-218
    SwitchGear 3'UTR luciferase reporter plasmidCHM 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for CHM
    Predesigned siRNA for gene silencing in human, mouse, rat CHM

    Gene Editing
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    Clone
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    OriGene clones in human, mouse for CHM (see all 13)
    OriGene ORF clones in mouse, rat for CHM
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): CHM (NM_000390)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for CHM
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CHM

    Cell Line
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    Browse ESI BIO Cell Lines and PureStem Progenitors for CHM 
    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CHM


    (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
    RAE1_HUMAN, P24386: Cytoplasm, cytosol
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol1
    endoplasmic reticulum1
    extracellular1
    mitochondrion1
    nucleus1
    peroxisome1
    plasma membrane1

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005829cytosol IMP7957092
    GO:0005968Rab-protein geranylgeranyltransferase complex IDA7957092

    CHM for ontologies           About GeneDecksing


    (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 CHM
    Interactions:

        GeneGlobe Interaction Network for CHM

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for CHM (P243863 ENSP000003503864) via UniProtKB, MINT, STRING, and/or I2D (see all 88)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    MAGED4BQ96JG83, ENSP000003353854I2D: score=1 STRING: ENSP00000335385
    COPS8Q996273, ENSP000003463404I2D: score=1 STRING: ENSP00000346340
    DDX19BQ9UMR23, ENSP000002880714I2D: score=1 STRING: ENSP00000288071
    ESR2Q927313, ENSP000003439254I2D: score=1 STRING: ENSP00000343925
    FAF1Q9UNN53, ENSP000003794574I2D: score=1 STRING: ENSP00000379457
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001568blood vessel development IEA--
    GO:0006612protein targeting to membrane IMP7957092
    GO:0006886intracellular protein transport ----
    GO:0007601visual perception IEA--
    GO:0018344protein geranylgeranylation IDA7957092

    CHM for ontologies           About GeneDecksing



    (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 CHM (RAE1)

    1 DrugBank Compound for CHM    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    FARNESYL-- --target--10592235

    7 Novoseek inferred chemical compound relationships for CHM gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    geranylgeranyl pyrophosphate 62.4 8 11675392 (5), 11141079 (2)
    gibberellin 48.9 3 12787245 (1), 10394640 (1)
    gdp 34.2 4 9563513 (2), 7957092 (1), 7882424 (1)
    abscisic acid 30.4 6 9435140 (1), 12787245 (1)
    cysteine 24.6 7 9435140 (1), 12787245 (1), 17935254 (1), 10394640 (1) (see all 5)
    gtp 7.11 2 9563513 (2)
    lipid 0 1 12827496 (1)



    CHM for compounds           About GeneDecksing



    (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, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for CHM gene (3 alternative transcripts): 
    NM_000390.2  NM_001145414.1  NM_001037312.1  

    Unigene Cluster for CHM:

    Choroideremia (Rab escort protein 1)
    Hs.496449  [show with all ESTs]
    Unigene Representative Sequence: NM_000390
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000357749(uc004eet.3 uc011mqz.2) ENST00000467744 ENST00000358786(uc004eeu.4 uc004eev.4)
    ENST00000487515 ENST00000483950 ENST00000537751
    miRNA
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    Block miRNA regulation of human, mouse, rat CHM using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate CHM (see all 30):
    hsa-miR-498 hsa-miR-217 hsa-miR-4311 hsa-miR-137 hsa-miR-509-5p hsa-miR-218-1* hsa-miR-944 hsa-miR-218
    SwitchGear 3'UTR luciferase reporter plasmidCHM 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for CHM
    Predesigned siRNA for gene silencing in human, mouse, rat CHM
    Clone
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    OriGene clones in human, mouse for CHM (see all 13)
    OriGene ORF clones in mouse, rat for CHM
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): CHM (NM_000390)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for CHM
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CHM
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for CHM
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat CHM
      QuantiTect SYBR Green Assays in human, mouse, rat CHM
      QuantiFast Probe-based Assays in human, mouse, rat CHM

    Additional mRNA sequence: 

    AK095883.1 AK291160.1 AK299323.1 AK312443.1 AY255796.1 BC032237.1 BC063522.1 BC065702.1 
    BC073987.1 BC105969.1 BC130494.1 BC130496.1 M83773.1 X57637.1 X78121.1 

    11 DOTS entries:

    DT.75178644  DT.121299419  DT.70103090  DT.413508  DT.102827417  DT.121299409  DT.40126657  DT.100749495 
    DT.121299453  DT.40106218  DT.95156019 

    Selected AceView cDNA sequences (see all 104):

    AI432571 CB155362 AA878377 BM677132 NM_000390 BX484921 BM700393 X78121 
    BU738048 BQ631852 AI474660 AY255796 CD106837 AA969711 AA931465 AV709873 
    AW089657 AW613181 AL524494 BQ632151 BM721494 BU688880 AI910647 BE501743 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for CHM (see all 6)    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8 ^ 9a · 9b ^ 10a · 10b
    SP1:                                -                                                                     
    SP2:                    -           -                                                                     
    SP3:                    -           -     -                                                               
    SP4:                                                                                -                     
    SP5:                                                                                                      


    ECgene alternative splicing isoforms for CHM

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

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

    CHM Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.496449
        Custom PCR Arrays for CHM
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    QuantiFast Probe-based Assays in human, mouse, rat CHM
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CHM

    (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 and fungi.

    Orthologs for CHM gene from Selected species (see all 17)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Chm1 , 5 choroidermia1, 5 86.3(n)1
    84.39(a)1
      X (48.94 cM)5
    126621  NM_018818.21  NP_061288.21 
     1130405955 
    chicken
    (Gallus gallus)
    Aves CHM1 choroideremia (Rab escort protein 1) 69.98(n)
    66.56(a)
      422266  NM_001031119.1  NP_001026290.1 
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    64(a)
    1 → many
    GL343202.1(1225836-1282192)
    African clawed frog
    (Xenopus laevis)
    Amphibia MGC685782 choroideremia (Rab escort protein 1) 74.06(n)    BC061662.1 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.170402 Danio rerio Rab escort protein 1 (chm) mRNA, complete more 74.34(n)    AY500891.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Rep1 , 3 neurotransmitter secretion RAB escort
    protein3
    Rab escort protein1
    34(a)3
    46.41(n)1
    39.43(a)1
      56D133
    372461  NM_058072.41  NP_477420.11 
    worm
    (Caenorhabditis elegans)
    Secernentea Y67D2.13   -- 30(a)   III(1642144-1648359)   --
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes GDI16
    GDP dissociation inhibitor, regulates vesicle traf...
    24(a)
    1 → many
    V(439616-440971) YER136W


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for CHM gene
    GDI12  CHML2  GDI22  
    2 SIMAP similar genes for CHM using alignment to 3 protein entries:     RAE1_HUMAN (see all proteins):
    CHML    GDI2

    CHM for paralogs           About GeneDecksing



    (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 CHM (see all 2545)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0668474
    Choroideremia (CHM)4--see VAR_0668472 H R mis40--------
    VAR_0082734
    Choroideremia (CHM)4--see VAR_0082732 Q L mis40--------
    VAR_0668484
    Choroideremia (CHM)4--see VAR_0668482 L P mis40--------
    rs1326302671,2
    Cpathogenic185123307(-) ACATGA/CATGAA 2 * C stg10--------
    rs1500994591,2
    C--85089889(+) ACAAAC/GCAGAT 1 -- ds50010--------
    rs9818461,2
    C,F,H--85089890(-) TATCTG/CCTTTG 1 -- ds50015Minor allele frequency- C:0.01MN NS EA 598
    rs1924847721,2
    --85089992(+) CAGCCG/TCTACA 1 -- ds50010--------
    rs1856700981,2
    C--85090020(+) AGAAAA/GGTATC 1 -- ds50010--------
    rs1426720011,2
    --85090165(+) TATACA/TGCTTG 1 -- ds50010--------
    rs1159350311,2
    C--85090278(+) ATGACA/GCCATG 1 -- ds50010--------

    HapMap Linkage Disequilibrium report for CHM (85116185 - 85302566 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for CHM:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2740277CNV Deletion23290073
    esv2740276CNV Deletion23290073
    nsv438141CNV Loss16468122
    nsv510545CNV Loss20534489
    nsv519786CNV Gain19592680

    Human Gene Mutation Database (HGMD): CHM
    Locus Specific Mutation Databases (LSDB): CHM

    Site Specific Mutation Identification with PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 300390   
    OMIM disorders: 303100  
    UniProtKB/Swiss-Prot: RAE1_HUMAN, P24386
  • Choroideremia (CHM) [MIM:303100]: An X-linked recessive disease characterized by a slowly progressive
    degeneration of the choroid, photoreceptors, and retinal pigment epithelium. Affected males develop night
    blindness in their teenage years followed by loss of peripheral vision and complete blindness at middle age.
    Carrier females are generally asymptomatic but funduscopic examination often shows patchy areas of chorioretinal
    atrophy. Note=The disease is caused by mutations affecting the gene represented in this entry

  • Selected diseases for CHM (see all 27):    
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    charcot-marie-tooth disease, dominant intermediate d    choroideremia    x-linked disease    charcot-marie-tooth disease type 2i
    charcot-marie-tooth disease type 1b    charcot-marie-tooth disease type 2j    charcot-marie-tooth disease type 3    charcot-marie-tooth disease type 4e
    choroiditis    charcot-marie-tooth disease    trophoblastic neoplasm    gestational trophoblastic neoplasm
    chorioretinitis    pigmentary retinopathy    eye disease    blindness
    night blindness    retinal degeneration    retinitis    parkinson's disease

    2 diseases from the University of Copenhagen DISEASES database for CHM:
    Choroideremia     Parkinson's disease

    CHM for disorders           About GeneDecksing

    7 Novoseek inferred disease relationships for CHM gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    choroideremia 99.1 72 8749050 (3), 17698759 (3), 9349950 (3), 8294464 (2) (see all 40)
    retinal degeneration 55.2 6 12401133 (2), 8294464 (1), 12014918 (1), 15370541 (1)
    blindness 52.8 2 11886217 (1), 12576024 (1)
    retinitis pigmentosa 52.3 1 11139690 (1)
    eye diseases 44.9 5 9067750 (1), 9175730 (1), 17483097 (1)
    retinopathy 19.2 3 20027300 (1)
    parkinson disease 18.5 1 16250025 (1)

    Genatlas disease: CHM
    choroideremia

    GeneTests: CHM
    GeneReviews: CHM
    Genetic Association Database (GAD): CHM

    Export disorders for CHM 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 CHM gene, integrated from 10 sources (see all 112):
    (articles sorted by number of sources associating them with CHM)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The functional effect of pathogenic mutations in Rab escort protein 1. (PubMed id 19427510)1, 2, 9 Sergeev Y.V.... Macdonald I.M. (Mutat. Res. 2009)
    2. Rab escort protein-1 is a multifunctional protein that accompanies newly prenylated rab proteins to their target membranes. (PubMed id 7957092)1, 2, 9 Alexandrov K....Zerial M. (EMBO J. 1994)
    3. Comprehensive mutation analysis (20 families) of the choroideremia gene reveals a missense variant that prevents the binding of REP1 with rab geranylgeranyl transferase. (PubMed id 21905166)1, 2 Esposito G.... Salvatore F. (Hum. Mutat. 2011)
    4. Rab geranylgeranylation occurs preferentially via the pre-formed REP- RGGT complex and is regulated by geranylgeranyl pyrophosphate. (PubMed id 18532927)1, 2 Baron R.A. and Seabra M.C. (Biochem. J. 2008)
    5. The DNA sequence of the human X chromosome. (PubMed id 15772651)1, 2 Ross M.T.... Bentley D.R. (Nature 2005)
    6. Missense mutation in the choroideremia gene. (PubMed id 7951216)1, 2 Donnelly P.... Pascal O. (Hum. Mol. Genet. 1994)
    7. Cloning and characterization of the human choroideremia gene. (PubMed id 7981670)1, 2 van Bokhoven H.... Cremers F.P. (Hum. Mol. Genet. 1994)
    8. Detection and characterization of point mutations in the choroideremia candidate gene by PCR-SSCP analysis and direct DNA sequencing. (PubMed id 1598901)1, 2 van den Hurk J.A.J.M.... Cremers F.P.M. (Am. J. Hum. Genet. 1992)
    9. Isolation of a candidate gene for choroideremia. (PubMed id 1549574)1, 2 Merry D.E.... Nussbaum R.L. (Proc. Natl. Acad. Sci. U.S.A. 1992)
    10. Three RFLPs for pZ11 (DXS540) in the choroideremia gene at Xq21.2. (PubMed id 1373238)1, 3 Molloy C.M....Cremers F.P. (Nucleic Acids Res. 1992)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    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: 1121 HGNC: 1940 AceView: CHM Ensembl:ENSG00000188419 euGenes: HUgn1121
    ECgene: CHM H-InvDB: CHM

    (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 CHM Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for CHM Genetics and Cytogenetics in Oncology and Haematology
    Mutations of the REP1 genehttp://www.retina-international.org/files/sci-news/repmut.htm
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=CHM[genesymbol]

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

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



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