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R3HDML Gene

protein-coding   GIFtS: 40
GCID: GC20P042965

R3H Domain Containing-Like

(Previous name: R3H domain (binds single-stranded nucleic acids) containing-like)
  Search for R3HDML
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
R3H Domain Containing-Like1 2
Cysteine-Rich Secretory Protein R3HDML2 3
R3H Domain (Binds Single-Stranded Nucleic Acids) Containing-Like1
dJ881L22.32
Peptidase Inhibitor R3HDML2

External Ids:    HGNC: 162491   Entrez Gene: 1409022   Ensembl: ENSG000001010747   UniProtKB: Q9H3Y03   

Export aliases for R3HDML gene to outside databases

Previous GC identifers: GC20U990180 GC20M042654 GC20P043605 GC20P043651 GC20P042399 GC20P039703


(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 R3HDML Gene:
R3HDML (R3H domain containing-like) is a protein-coding gene. GO annotations related to this gene include peptidase inhibitor activity. An important paralog of this gene is CLEC18B.

UniProtKB/Swiss-Prot: CRSPL_HUMAN, Q9H3Y0
Function: Putative serine protease inhibitor (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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RefSeq DNA sequence:
NC_000020.11  NC_018931.2  NT_011362.11  
Regulatory elements:
   Regulatory transcription factor binding sites in the R3HDML gene promoter:
         NF-1   Spz1   RP58   AML1a   Lmo2   C/EBPalpha   Nkx6-1   ATF   ATF6   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidR3HDML promoter sequence
   Search Chromatin IP Primers for R3HDML

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat R3HDML


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

Entrez Gene cytogenetic band: 20q13.12   Ensembl cytogenetic band:  20q13.12   HGNC cytogenetic band: 20q13.12

R3HDML Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
R3HDML gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20P042965:  view genomic region     (about GC identifiers)

Start:
42,965,626 bp from pter      End:
42,979,875 bp from pter
Size:
14,250 bases      Orientation:
plus 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: CRSPL_HUMAN, Q9H3Y0 (See protein sequence)
Recommended Name: Peptidase inhibitor R3HDML precursor  
Size: 253 amino acids; 28605 Da
Caution: Despite its name, it does not contain a R3H domain

Explore the universe of human proteins at neXtProt for R3HDML: NX_Q9H3Y0

Explore proteomics data for R3HDML at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn120

  • See R3HDML Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_848586.1  
    ENSEMBL proteins: 
     ENSP00000217043  

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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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    2 InterPro protein domains:
     IPR014044 CAP_domain
     IPR001283 Allrgn_V5/Tpx1

    Graphical View of Domain Structure for InterPro Entry Q9H3Y0

    ProtoNet protein and cluster: Q9H3Y0

    1 Blocks protein domain: IPB001283 Allergen V5/Tpx-1 related

    UniProtKB/Swiss-Prot: CRSPL_HUMAN, Q9H3Y0
    Similarity: Belongs to the CRISP family
    Similarity: Contains 1 SCP domain


    R3HDML 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: CRSPL_HUMAN, Q9H3Y0
    Function: Putative serine protease inhibitor (By similarity)

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0030414peptidase inhibitor activity IEA--
         
    R3HDML for ontologies           About GeneDecksing


    Phenotypes:
         1 MGI phenotypic allele for R3hdml (no phenotypes)

    R3HDML for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for R3HDML
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    hsa-mir-335-5p (MIRT017398)

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    2 qRT-PCR Assays for microRNAs that regulate R3HDML:
    hsa-miR-1252 hsa-miR-3921
    SwitchGear 3'UTR luciferase reporter plasmidR3HDML 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
    CRSPL_HUMAN, Q9H3Y0: Secreted (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular3
    nucleus2
    cytosol1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region IEA--

    R3HDML 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 R3HDML
    Interactions:

        Search GeneGlobe Interaction Network for R3HDML

    (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 R3HDML (CRSPL)



    (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 R3HDML gene: 
    NM_178491.3  

    Unigene Cluster for R3HDML:

    R3H domain containing-like
    Hs.580807  [show with all ESTs]
    Unigene Representative Sequence: NM_178491
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000217043(uc002xls.1)
    miRNA
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    2 qRT-PCR Assays for microRNAs that regulate R3HDML:
    hsa-miR-1252 hsa-miR-3921
    SwitchGear 3'UTR luciferase reporter plasmidR3HDML 3' UTR sequence
    Inhib. RNA
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      QuantiTect SYBR Green Assays in human, mouse, rat R3HDML
      QuantiFast Probe-based Assays in human, mouse, rat R3HDML

    Additional mRNA sequence: BC107048.2 

    1 DOTS entry:

    DT.92045296 

    2 AceView cDNA sequences:

    NM_178491 BG221330 

    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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    R3HDML expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GGTCAAAAGA
    R3HDML Expression
    About this image

    R3HDML Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    R3HDML Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.580807
        Custom PCR Arrays for R3HDML
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for R3HDML

    (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 R3HDML gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia R3hdml1 , 5 R3H domain containing-like1, 5 81.55(n)1
    77.87(a)1
      2 (84.31 cM)5
    1000438991  NM_001099331.21  NP_001092801.11 
     1634923185 
    chicken
    (Gallus gallus)
    Aves LOC1008580891 peptidase inhibitor R3HDML-like 67.72(n)
    64.43(a)
      100858089  XM_004947041.1  XP_004947098.1 
    lizard
    (Anolis carolinensis)
    Reptilia R3HDML6
    R3H domain containing-like
    66(a)
    1 ↔ 1
    4(144184323-144196140)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia r3hdml1 R3H domain containing-like 65.22(n)
    60.08(a)
      100492715  XM_002933184.2  XP_002933230.1 
    zebrafish
    (Danio rerio)
    Actinopterygii r3hdml6
    R3H domain containing-like
    50(a)
    1 ↔ 1
    23(26108394-26114709) ENSDARG00000030650
    fruit fly
    (Drosophila melanogaster)
    Insecta CG84836
    --
    17(a)
    1 → many
    3R(9034470-9040187)
    worm
    (Caenorhabditis elegans)
    Secernentea scl-236
    scl-226
    (see all 3)
    Protein SCL-22 (scl-22) mRNA, complete cds
    (see all 3)
    18(a)
    12(a)
    (see all 3)
    many ↔ many
    many ↔ many
    (see all 3)
    IV(86875-90082) WBGene00015246
    X(10789678-10792018) WBGene00011462


    ENSEMBL Gene Tree for R3HDML (if available)
    TreeFam Gene Tree for R3HDML (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for R3HDML gene
    CLEC18B2  CRISPLD22  CLEC18C2  PI162  GLIPR12  CRISP22  PI152  CRISP12  
    CRISPLD12  CRISP32  GLIPR1L12  CLEC18A2  GLIPR1L22  
    5 SIMAP similar genes for R3HDML using alignment to 1 protein entry:     CRSPL_HUMAN:
    PI15    CRISPLD2    CRISPLD1    PI16    GLIPR1L1

    R3HDML 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 R3HDML (see all 467)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 20 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1902465461,2
    --42963631(+) ACACAC/TGTACA 1 -- us2k10--------
    rs72744251,2
    C--42963632(+) cacacA/Gtacac 1 -- us2k10--------
    rs768558201,2
    C,F--42963692(+) ACTGTA/GCTAAG 1 -- us2k12Minor allele frequency- G:0.16CSA NA 122
    rs1395447421,2
    --42963721(+) CATTTA/CATCTT 1 -- us2k10--------
    rs1497218441,2
    --42963753(+) GCACCA/GCTATT 1 -- us2k10--------
    rs28680931,2
    C,F,H--42963798(+) AGTAAC/TGTGCC 1 -- us2k125Minor allele frequency- T:0.09NS EA NA WA 2986
    rs1446005331,2
    --42963918(+) TCACCA/CTAGGC 1 -- us2k10--------
    rs1398167281,2
    C--42963940(+) TGCATA/CTATAT 1 -- us2k10--------
    rs557253221,2
    C--42963945(+) CTATAT/CTTGGT 1 -- us2k12Minor allele frequency- C:0.03WA 120
    rs1445958171,2
    --42963970(+) GCATCC/TTTGGC 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for R3HDML (42965626 - 42979875 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for R3HDML:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv3389CNV Insertion18451855

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing R3HDML
    DNA2.0 Custom Variant and Variant Library Synthesis for R3HDML

    (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 R3HDML gene integrated from 10 sources:
    (articles sorted by number of sources associating them with R3HDML)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Meta-analysis of genome-wide association studies identifies eight new loci for type 2 diabetes in east Asians. (PubMed id 22158537)1 Cho Y.S....Seielstad M. (Nat. Genet. 2012)
    2. A whole genome screen for HIV restriction factors. (PubMed id 22082156)1 Liu L....McKnight A. (Retrovirology 2011)
    3. Interactions of pathological hallmark proteins: tubulin polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (J. Biol. Chem. 2011)
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    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. The DNA sequence and comparative analysis of human chromosome 20. (PubMed id 11780052)2 Deloukas P....Rogers J. (Nature 2001)

    (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: 140902 HGNC: 16249 AceView: R3HDML Ensembl:ENSG00000101074 euGenes: HUgn140902
    ECgene: R3HDML H-InvDB: R3HDML

    (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 R3HDML 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 R3HDML gene:
    Search GeneIP for patents involving R3HDML

    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, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, 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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