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CHML Gene

protein-coding   GIFtS: 53
GCID: GC01M241792

Choroideremia-Like (Rab Escort Protein 2)

  See CHML-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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Aliases
Choroideremia-Like (Rab Escort Protein 2)1 2     Rab Proteins Geranylgeranyltransferase Component A 22
REP22 3 5     REP-23
Choroideremia-Like Protein2 3     Rab Escort Protein 23
Choroideraemia-Like Protein2     

External Ids:    HGNC: 19411   Entrez Gene: 11222   Ensembl: ENSG000002036687   OMIM: 1188255   UniProtKB: P263743   

Export aliases for CHML gene to outside databases

Previous GC identifers: GC01M239882 GC01M237250 GC01M238093 GC01M238838 GC01M238122 GC01M239858 GC01M212250


(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 CHML Gene:
The product of the CHML gene supports geranylgeranylation of most Rab proteins and may substitute for REP-1 in
tissues other than retina. CHML is localized close to the gene for Usher syndrome type II. (provided by RefSeq,
Jul 2008)

GeneCards Summary for CHML Gene:
CHML (choroideremia-like (Rab escort protein 2)) is a protein-coding gene. Diseases associated with CHML include usher syndrome type ii, 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: RAE2_HUMAN, P26374
Function: Substrate-binding subunit (component A) of the Rab geranylgeranyltransferase (GGTase) complex. Binds
unprenylated Rab proteins and presents the substrate peptide to the catalytic component B. The component A is
thought to be regenerated by transferring its prenylated Rab back to the donor membrane. Less effective than CHM
in supporting prenylation of Rab3 family

Gene Wiki entry for CHML 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_000001.10  NC_018912.2  NT_167186.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the CHML gene promoter:
         AML1a   POU3F1   CUTL1   C/EBPalpha   NF-AT   E47   NF-AT4   NF-AT2   NF-AT3   NF-AT1   
         Other transcription factors

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

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


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

Entrez Gene cytogenetic band: 1q43   Ensembl cytogenetic band:  1q43   HGNC cytogenetic band: 1q43

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

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M241792:  view genomic region     (about GC identifiers)

Start:
241,792,155 bp from pter      End:
241,799,232 bp from pter
Size:
7,078 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., 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: RAE2_HUMAN, P26374 (See protein sequence)
Recommended Name: Rab proteins geranylgeranyltransferase component A 2  
Size: 656 amino acids; 74071 Da
Subunit: Monomer. Heterotrimer composed of RABGGTA, RABGGTB and CHML; within this trimer, RABGGTA and RABGGTB form
the catalytic component B, while CHML (component A) mediates Rab protein binding. Interacts with RAB1A, RAB7A and
RAB27A, but has much lower affinity for RAB1A, RAB7A and RAB27A than CHM
Miscellaneous: Substitutes for REP-1 thereby preventing widespread tissue abnormalities in patients with
choroideremia who lack REP-1
Secondary accessions: B2RAB9 Q17RE0 Q9H1Y4

Explore the universe of human proteins at neXtProt for CHML: NX_P26374

Explore proteomics data for CHML at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

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

    REFSEQ proteins: NP_001812.2  
    ENSEMBL proteins: 
     ENSP00000355511  

    CHML Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for CHML

     
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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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    3 InterPro protein domains:
     IPR016664 Rab_geranylTrfase_A_euk
     IPR001738 Rab_escort
     IPR018203 GDP_dissociation_inhibitor

    Graphical View of Domain Structure for InterPro Entry P26374

    ProtoNet protein and cluster: P26374

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

    UniProtKB/Swiss-Prot: RAE2_HUMAN, P26374
    Similarity: Belongs to the Rab GDI family


    Find genes that share domains with CHML           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: RAE2_HUMAN, P26374
    Function: Substrate-binding subunit (component A) of the Rab geranylgeranyltransferase (GGTase) complex. Binds
    unprenylated Rab proteins and presents the substrate peptide to the catalytic component B. The component A is
    thought to be regenerated by transferring its prenylated Rab back to the donor membrane. Less effective than CHM
    in supporting prenylation of Rab3 family

         Genatlas biochemistry entry for CHML:
    Rab escort protein-2 activating geranylgeranyltransferase A (prenylating C terminus of RAB (signal transduction)

         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 IPI15186776
         
    Find genes that share ontologies with CHML           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for CHML:
     Decreased G3BP1 protein expres 

    Animal Models:
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    Block miRNA regulation of human, mouse, rat CHML using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate CHML (see all 17):
    hsa-miR-539 hsa-miR-3942-5p hsa-miR-1285 hsa-miR-3908 hsa-miR-891b hsa-miR-205* hsa-miR-3143 hsa-miR-520g
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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
    RAE2_HUMAN, P26374: Cytoplasm, cytosol
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol2
    nucleus2
    extracellular1
    lysosome1
    mitochondrion1
    peroxisome1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005829cytosol IEA--
    GO:0005968Rab-protein geranylgeranyltransferase complex IMP12356470

    Find genes that share ontologies with CHML           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 CHML
    Interactions:

        Search GeneGlobe Interaction Network for CHML

    STRING Interaction Network Preview (showing 5 interactants - click image to see 21)

    Selected Interacting proteins for CHML (P263743 ENSP000003555114) via UniProtKB, MINT, STRING, and/or I2D (see all 21)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    RABGGTBP536113, ENSP000003174734I2D: score=1 STRING: ENSP00000317473
    RAB1AP628203, ENSP000003872864I2D: score=2 STRING: ENSP00000387286
    RAB5AP203393, ENSP000002730474I2D: score=2 STRING: ENSP00000273047
    RAB3AP203363, ENSP000002222564I2D: score=2 STRING: ENSP00000222256
    RAB6AP203403, ENSP000003114494I2D: score=2 STRING: ENSP00000311449
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    Gene Ontology (GO): 3 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006886intracellular protein transport IEA--
    GO:0007601visual perception ----
    GO:0018344protein geranylgeranylation IMP12356470

    Find genes that share ontologies with CHML           About GenesLikeMe



    (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 CHML (RAE2)



    (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 CHML gene: 
    NM_001821.3  

    Unigene Cluster for CHML:

    Choroideremia-like (Rab escort protein 2)
    Hs.654545  [show with all ESTs]
    Unigene Representative Sequence: NM_001821
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000366553(uc001hzd.3)
    miRNA
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    hsa-miR-539 hsa-miR-3942-5p hsa-miR-1285 hsa-miR-3908 hsa-miR-891b hsa-miR-205* hsa-miR-3143 hsa-miR-520g
    Browse SwitchGear 3'UTR luciferase reporter plasmids
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      QuantiFast Probe-based Assays in human, mouse, rat CHML

    Additional mRNA sequence: 

    AJ293390.1 AJ293391.1 AJ293392.1 AK000933.1 AK023423.1 AK314125.1 BC117360.1 X64728.1 

    3 DOTS entries:

    DT.102994  DT.100041830  DT.100743529 

    Selected AceView cDNA sequences (see all 100):

    BI088411 AA804486 CA312626 BE348356 BU509892 BQ775652 AI004823 BQ437051 
    BE895865 BM557064 AI167858 BM763291 BF437331 AI829541 T11394 CB160778 
    BE503084 AI741219 BE468155 AI373290 BX956583 AI222022 AA805916 BG108374 

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

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

    CHML Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.654545
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CHML

    (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 eukaryotes.

    Orthologs for CHML gene from Selected species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Chml1 , 5 choroideremia-like1, 5 82.88(n)1
    79.97(a)1
      1 (81.70 cM)5
    126631  NM_021350.21  NP_067325.21 
     1756864885 
    chicken
    (Gallus gallus)
    Aves CHM6
    Gallus gallus choroideremia (Rab escort protein 1)...
    66(a)
    1 → many
    4(8537982-8597328)
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    64(a)
    1 → many
    GL343202.1(1225836-1282192)
    zebrafish
    (Danio rerio)
    Actinopterygii chm1 choroideremia (Rab escort protein 1) 58.88(n)
    57.28(a)
      402935  NM_203461.1  NP_982286.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Rep3 neurotransmitter secretion RAB escort
    protein
    33(a)   56D13   --
    worm
    (Caenorhabditis elegans)
    Secernentea Y67D2.13
    rep-11
    rep-11 33(a)3
    46.71(n)1
    38.36(a)1
      III(1642144-1648359)3
    1753111  NM_001027757.31  NP_001022928.11 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes GDI16
    GDP dissociation inhibitor, regulates vesicle traf...
    25(a)
    1 → many
    V(439616-440971) YER136W
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons REP1 REP 46.71(n)
    33.64(a)
      819832  NM_111530.3  NP_187306.2 
    rice
    (Oryza sativa)
    Liliopsida Os01g02691001 Os01g0269100 45.82(n)
    39.93(a)
      4326267  NM_001049232.1  NP_001042697.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for CHML gene
    GDI12  CHM2  GDI22  
    1 SIMAP similar gene for CHML using alignment to 1 protein entry:     RAE2_HUMAN:
    CHM

    Find genes that share paralogs with CHML           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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    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for CHML:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv873368CNV Gain21882294
    nsv873372CNV Gain21882294

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

    (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: 118825    OMIM disorders: --

    3 diseases for CHML:    
    About MalaCards
    usher syndrome type ii    choroideremia    intrahepatic cholangiocarcinoma

    1 disease from the University of Copenhagen DISEASES database for CHML:
    Choroideremia

    Find genes that share disorders with CHML           About GenesLikeMe

    1 Novoseek inferred disease relationship for CHML gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    choroideremia 93.8 1 8294464 (1)

    Genetic Association Database (GAD): CHML
    Human Genome Epidemiology (HuGE) Navigator: CHML (2 documents)

    Export disorders for CHML 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 CHML gene, integrated from 10 sources (see all 30):
    (articles sorted by number of sources associating them with CHML)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. REP-2, a Rab escort protein encoded by the choroideremia-like gene. (PubMed id 8294464)1, 2, 9 Cremers F.P.M....Goldstein J.L. (J. Biol. Chem. 1994)
    2. Cloning and characterization of the human choroideremia gene. (PubMed id 7981670)1, 3, 9 van Bokhoven H.... Cremers F.P. (Hum. Mol. Genet. 1994)
    3. Follow-up examination of linkage and association to chromosome 1q43 in multiple sclerosis. (PubMed id 19626040)1, 4 McCauley J.L....Haines J.L. (Genes Immun. 2009)
    4. Identification of a novel asthma susceptibility gene on chromosome 1qter and its functional evaluation. (PubMed id 18344558)1, 4 White J.H....Pillai S.G. (Hum. Mol. Genet. 2008)
    5. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (Nature 2006)
    6. Structure of the Rab7:REP-1 complex: insights into the mechanism of Rab prenylation and choroideremia disease. (PubMed id 15186776)1, 2 Rak A....Alexandrov K. (Cell 2004)
    7. 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)
    8. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    9. Different structural organization of the encephalopsin gene in man and mouse. (PubMed id 12242008)1, 2 Kasper G.... Rump A. (Gene 2002)
    10. Expression of mammalian Rab Escort protein-1 and -2 in yeast Saccharomyces cerevisiae. (PubMed id 12356470)1, 2 Sidorovitch V.... Alexandrov K. (Protein Expr. Purif. 2002)

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

      Query String
    PubMed
    OMIM
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      (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: 1122 HGNC: 1941 AceView: CHML Ensembl:ENSG00000203668 euGenes: HUgn1122
    ECgene: CHML H-InvDB: CHML

    (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 CHML 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 CHML gene:
    Search GeneIP for patents involving CHML

    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
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