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RMRP Gene

RNA gene   GIFtS: 22
GCID: GC09M035655

RNA Component Of Mitochondrial RNA Processing Endoribonuclease

(Previous name: cartilage-hair hypoplasia)
(Previous symbol: CHH)
  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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Subcategory (RNA class): lncRNA

Quality score for this RNA gene is 6

Aliases
RNA Component Of Mitochondrial RNA Processing Endoribonuclease1 2
CHH1 2 5
RMRPR2 5
Cartilage-Hair Hypoplasia1
NME12
RRP22

External Ids:    HGNC: 100311   Entrez Gene: 60232   Ensembl: ENSG000002699007   OMIM: 1576605   
ORGUL members:    fRNAdb10:FR380380 FR355912 FR215892 FR355912 FR260307      
NCBI13:AF458227 AF458225 AF458223 AF458226 AF458224 see all 20    
NONCODE14:u1860 u1344 u4113 u1859 n5543    
Rfam:RF00030    
RNAdb15:LIT1753 LIT1758 LIT1757    

Export aliases for RMRP gene to outside databases

Previous GC identifer: GC09U990067


(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 RMRP Gene:
This gene encodes the RNA component of mitochondrial RNA processing endoribonuclease, which cleaves mitochondrial
RNA at a priming site of mitochondrial DNA replication. This RNA also interacts with the telomerase reverse
transcriptase catalytic subunit to form a distinct ribonucleoprotein complex that has RNA-dependent RNA
polymerase activity and produces double-stranded RNAs that can be processed into small interfering RNA. Mutations
in this gene are associated with cartilage-hair hypoplasia.(provided by RefSeq, Mar 2010)

GeneCards Summary for RMRP Gene:
RMRP (RNA component of mitochondrial RNA processing endoribonuclease) is an RNA gene, and is affiliated with the lncRNA class. Diseases associated with RMRP include cartilage-hair hypoplasia, and anauxetic dysplasia.

Gene Wiki entry for RMRP Gene

fRNAdb sequence ontologies for RMRP - the ORGUL cluster for this gene includes several descriptions:
RNase MRP - RNase MRP is an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs. Despite distinct functions, RNase MRP has been shown to be evolutionarily related to RNase P. Like eukaryotic RNase P, RNase MRP is not catalytically active without associated protein subunits.
RNase_MRP_RNA - The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs.

View fRNAdb secondary structures for RMRP

(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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Regulatory elements:
   Regulatory transcription factor binding sites in the RMRP gene promoter:
         IRF-2   Sp1   p300   Nkx2-5   Tal-1beta   ITF-2   
         Other transcription factors

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

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


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

Entrez Gene cytogenetic band: 9p21-p12   Ensembl cytogenetic band:  9p13.3   HGNC cytogenetic band: 9p21-p12

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

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09M035655:  view genomic region     (about GC identifiers)

Start:
35,657,748 bp from pter      End:
35,658,015 bp from pter
Size:
268 bases      Orientation:
minus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for RMRP

(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: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
MISCRNA: ncRNAs / Small misc ncRNAs

  --

(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:
     Genatlas biochemistry entry for RMRP:
endoribonuclease,mitochondrial RNA-processing

Phenotypes:
     2 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Rmrp):
 mortality/aging  normal 

RMRP for phenotypes           About GeneDecksing

Animal Models:
     MGI mouse knock-outs for RMRP: Rmrptm1.1Whah Rmrptm1Whah

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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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(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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3 Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for RMRP
    Granzyme-A Pathway
Remodeling of Adherens Junctions
Granzyme Pathway


    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for RMRP
Interactions:

    GeneGlobe Interaction Network for RMRP

(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 RMRP



(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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5/9 fRNAdb Secondary structures (see all 9):


2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000602361(lincRNA) ENST00000363046(lincRNA)(uc003zxh.2)
miRNA
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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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Expression evidence for RMRP:RNAdb

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

RMRP Protein expression data from MOPED1, PaxDb2 and MaxQB3 --
    Custom PCR Arrays for RMRP
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RMRP

(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 chordates.

Orthologs for RMRP gene from Selected species (see all 10)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Rmrp5 RNA component of mitochondrial RNAase P   --   4 (23.04 cM) 43492788 
chicken
(Gallus gallus)
Aves RNase_MRP6
RNase MRP
59(a)
1 → many
4(39276202-39276488) ENSGALG00000025557
lizard
(Anolis carolinensis)
Reptilia RNase_MRP6
RNase MRP
57(a)
1 → many
5(113820494-113820799)
zebrafish
(Danio rerio)
Actinopterygii RNase_MRP6
RNase MRP
53(a)
many ↔ many
1(40379299-40379554)


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

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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(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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2 SNPs for RMRP    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 9 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1994761031,2
--pathogenic135625895(-) AGGGGA/GAAGTC 1 -- nc-transcript-variant0--------
rs3122628961,2
--untested135625895(-) AGGGG-/GAAAGT 1 -- nc-transcript-variant0--------

HapMap Linkage Disequilibrium report for RMRP (35657748 - 35658015 bp)

Structural Variations
     Database of Genomic Variants (DGV) 1 variation for RMRP:    About this table    
Variant IDTypeSubtypePubMed ID
dgv8168n71CNV Gain21882294

Human Gene Mutation Database (HGMD): RMRP
Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing RMRP
DNA2.0 Custom Variant and Variant Library Synthesis for RMRP

(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: 157660OMIM information:   
OMIM disorders: 250250  250460  607095  
18 diseases for RMRP:    
About MalaCards
cartilage-hair hypoplasia    anauxetic dysplasia    cartilage-hair hypoplasia - anauxetic dysplasia spectrum disorders    autoimmune hypoparathyroidism
developmental disabilities    metaphyseal dysplasia without hypotrichosis    metaphyseal dysplasia    omenn syndrome
hypoparathyroidism    non-hodgkin lymphoma    hypotrichosis    short stature
hodgkin's lymphoma    skeletal dysplasias    basal cell carcinoma    severe combined immunodeficiency
multiple myeloma    myeloma


RMRP for disorders           About GeneDecksing

8 Novoseek inferred disease relationships for RMRP gene    About this table

Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
cartilage-hair hypoplasia 97.8 12 11940090 (2), 14608646 (2), 16244706 (1), 19626344 (1) (see all 9)
metaphyseal dysplasia 93.7 4 16244706 (2), 16252239 (1), 17701897 (1)
short stature 74.9 2 16244706 (1), 16252239 (1)
skeletal dysplasia 61.4 2 17189938 (1), 17701897 (1)
hypoplasia 56.1 4 19626344 (1), 16252239 (1), 17701897 (1), 17937437 (1)
developmental disabilities 44.8 1 17189938 (1)
cancer 21.2 2 16244706 (1), 16252239 (1)
anemia 14 2 16244706 (2)


Export disorders for RMRP 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 RMRP gene, integrated from 10 sources (see all 42):
(articles sorted by number of sources associating them with RMRP)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Mutations in the RNA component of RNase MRP cause a pleiotropic human disease, cartilage-hair hypoplasia. (PubMed id 11207361)1, 3, 9 RidanpAoAo M....de la Chapelle A. (Cell 2001)
  2. A role for RNAase MRP in mitochondrial RNA processing. (PubMed id 1623519)1, 3 Topper J.N....Clayton D.A. (Cell 1992)
  3. Evolutionary comparison provides evidence for pathogenicity of RMRP mutations. (PubMed id 16244706)1, 9 BonafAc L....Reymond A. (PLoS Genet. 2005)
  4. Cartilage hair hypoplasia mutations that lead to RMRP promoter inefficiency or RNA transcript instability. (PubMed id 17937437)1, 9 Nakashima E....Schlessinger D. (Am. J. Med. Genet. A 2007)
  5. An RNA-dependent RNA polymerase formed by TERT and the RMRP RNA. (PubMed id 19701182)1, 9 Maida Y....Masutomi K. (Nature 2009)
  6. Type and level of RMRP functional impairment predicts phenotype in the cartilage hair hypoplasia-anauxetic dysplasia spectrum. (PubMed id 17701897)1, 9 Thiel C.T....Rauch A. (Am. J. Hum. Genet. 2007)
  7. Identification of novel RMRP mutations and specific founder haplotypes in Japanese patients with cartilage-hair hypoplasia. (PubMed id 16832578)1, 9 Hirose Y....Ikegawa S. (J. Hum. Genet. 2006)
  8. RMRP gene sequence analysis confirms a cartilage-hair hypoplasia variant with only skeletal manifestations and reveals a high density of single-nucleotide polymorphisms. (PubMed id 11940090)1, 9 BonafAc L....Superti-Furga A. (Clin. Genet. 2002)
  9. Severely incapacitating mutations in patients with extreme short stature identify RNA-processing endoribonuclease RMRP as an essential cell growth regulator. (PubMed id 16252239)1, 9 Thiel C.T....Rauch A. (Am. J. Hum. Genet. 2005)
  10. Multiple myeloma-associated chromosomal translocation activates orphan snoRNA ACA11 to suppress oxidative stress. (PubMed id 22751105)1 Chu L....Tomasson M.H. (J. Clin. Invest. 2012)

(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: 6023 HGNC: 10031 Ensembl:ENSG00000269900 euGenes: HUgn6023 ECgene: RMRP
H-InvDB: RMRP

(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 RMRP 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 RMRP gene:
Search GeneIP for patents involving RMRP

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



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