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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

R3HDML Gene

protein-coding   GIFtS: 38
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)
About This Section

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, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000020.10  NC_018931.2  NT_011362.10  
Regulatory elements:
   SABiosciences 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 SABiosciences Chromatin IP Primers for R3HDML

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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 UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: CRSPL_HUMAN, Q9H3Y0 (See protein sequence)
Recommended Name: Peptidase inhibitor R3HDML precursor  
Size: 253 amino acids; 28605 Da
Subcellular location: Secreted (Potential)
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 

R3HDML Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

R3HDML Protein Expression

REFSEQ proteins: NP_848586.1  
ENSEMBL proteins: 
 ENSP00000217043  

Human Recombinant Protein Products for R3HDML: 
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Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

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

R3HDML for ontologies           About GeneDecksing



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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
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,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

Molecular Function:

     UniProtKB/Swiss-Prot Summary: CRSPL_HUMAN, Q9H3Y0
Function: Putative serine protease inhibitor (By similarity)

     Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    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:
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(Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for R3HDML

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
Browse Small Molecules at EMD Millipore
Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for R3HDML (CRSPL)

Search CenterWatch for drugs/clinical trials and news about 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,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

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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SwitchGear 3'UTR luciferase reporter plasmidR3HDML 3' UTR sequence
Inhib. RNA
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Primer
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  QIAGEN QuantiFast Probe-based Assays in human, mouse, rat R3HDML

Additional mRNA sequence: BC107048.2 

1 DOTS entry:

DT.92045296 

2 AceView cDNA sequences:

BG221330 NM_178491 

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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

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


See R3HDML Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for R3HDML

SOURCE GeneReport for Unigene cluster: Hs.580807
    SABiosciences 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)
About This Section

This gene was present in the common ancestor of chordates.

Orthologs for R3HDML gene from 4/11 species (see all 11)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia R3hdml1 , 5 R3H domain containing-like1, 5 81.61(n)1
78.17(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_003642480.1  XP_003642528.1 
lizard
(Anolis carolinensis)
Reptilia R3HDML6
Uncharacterized protein
66(a)
1 ↔ 1
4(144184323-144196140)
zebrafish
(Danio rerio)
Actinopterygii r3hdml6
R3H domain containing-like
50(a)
1 ↔ 1
23(26108394-26114709)


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)
About This Section
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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

10/467 SNPs in R3HDML are shown (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

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

(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)
About This Section

PubMed articles for R3HDML gene integrated from 9 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 ident ifies eight new loci for type 2 diabetes in east Asians. (PubMed id 22158537)1 Cho Y.S....Seielstad M. (2012)
  2. Interactions of pathological hallmark proteins: tubul in polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (2011)
  3. 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. (2004)
  4. 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. (2002)
  5. The DNA sequence and comparative analysis of human chromosome 20. (PubMed id 11780052)2 Deloukas P....Rogers J. (2001)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 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)
About This Section
Entrez Gene: 140902 HGNC: 16249 AceView: R3HDML Ensembl:ENSG00000101074 euGenes: HUgn140902
ECgene: R3HDML H-InvDB: R3HDML

(According to HUGE)
About This Section
  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
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.)
About This Section
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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
About This Section

 
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 Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat R3HDML
 inGenious Targeting Laboratory - Custom generated mouse model solutions for R3HDML
 inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for R3HDML
Customized:
 lentivirus for stable overexpression of R3HDML
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GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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(GIFtS: 73)
transforming growth factor, beta 1
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