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MRPL40 Gene

protein-coding   GIFtS: 54
GCID: GC22P019419

Mitochondrial Ribosomal Protein L40

(Previous name: nuclear localization signal deleted in velocardiofacial...)
(Previous symbol: NLVCF)
  See MRPL40-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
Mitochondrial Ribosomal Protein L401 2     MRP-L402 3
NLVCF1 2 3 5     URIM2 3
Nuclear Localization Signal Deleted In Velocardiofacial Syndrome1 2     MRPL222 5
Nuclear Localization Signal-Containing Protein Deleted In Velocardiofacial
Syndrome2 3
     39S Ribosomal Protein L40, Mitochondrial2
Up-Regulated In Metastasis2 3     MRP-L222
L40mt2 3     Nuclear Localization Signal Containing Protein Deleted In Velocardiofacial
Syndrome2

External Ids:    HGNC: 144911   Entrez Gene: 649762   Ensembl: ENSG000001856087   OMIM: 6050895   UniProtKB: Q9NQ503   

Export aliases for MRPL40 gene to outside databases

Previous GC identifers: GC22U990205 GC22P016361 GC22P017794 GC22P017793 GC22P003040


(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 MRPL40 Gene:
Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the
mitochondrion. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S subunit.
They have an estimated 75% protein to rRNA composition compared to prokaryotic ribosomes, where this ratio is
reversed. Another difference between mammalian mitoribosomes and prokaryotic ribosomes is that the latter contain
a 5S rRNA. Among different species, the proteins comprising the mitoribosome differ greatly in sequence, and
sometimes in biochemical properties, which prevents easy recognition by sequence homology. This gene encodes a
39S subunit protein. Deletions in this gene may contribute to the etiology of velo-cardio-facial syndrome and
DiGeorge syndrome. (provided by RefSeq, Jul 2008)

GeneCards Summary for MRPL40 Gene:
MRPL40 (mitochondrial ribosomal protein L40) is a protein-coding gene. Diseases associated with MRPL40 include velocardiofacial syndrome, and digeorge syndrome.

Gene Wiki entry for MRPL40 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_000022.10  NT_011520.13  NC_018933.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the MRPL40 gene promoter:
         TBP   USF1   MAZR   AML1a   USF2   USF-1:USF-2   E47   AREB6   Ik-2   USF-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): MRPL40 promoter sequence
   Search Chromatin IP Primers for MRPL40

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat MRPL40


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

Entrez Gene cytogenetic band: 22q11.2   Ensembl cytogenetic band:  22q11.21   HGNC cytogenetic band: 22q11.2

MRPL40 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
MRPL40 gene location

GeneLoc information about chromosome 22         GeneLoc Exon Structure

GeneLoc location for GC22P019419:  view genomic region     (about GC identifiers)

Start:
19,419,425 bp from pter      End:
19,423,598 bp from pter
Size:
4,174 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, 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: RM40_HUMAN, Q9NQ50 (See protein sequence)
Recommended Name: 39S ribosomal protein L40, mitochondrial precursor  
Size: 206 amino acids; 24490 Da
Secondary accessions: B3KVZ7 O95134

Explore the universe of human proteins at neXtProt for MRPL40: NX_Q9NQ50

Explore proteomics data for MRPL40 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys77
  • Modification sites at PhosphoSitePlus

  • See MRPL40 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_003767.2  
    ENSEMBL proteins: 
     ENSP00000333401  

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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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    HGNC Gene Families:
    MRPL: Mitochondrial ribosomal proteins / large subunits

    1 InterPro protein domain:
     IPR019192 Ribosomal_L28/L40_mit

    Graphical View of Domain Structure for InterPro Entry Q9NQ50

    ProtoNet protein and cluster: Q9NQ50


    Find genes that share domains with MRPL40           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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         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
    GO:0044822poly(A) RNA binding IDA--
         
    Find genes that share ontologies with MRPL40           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for MRPL40:
     Increased G1 DNA content 

    Animal Models:
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    hsa-mir-17-5p (MIRT050804), hsa-mir-24-3p (MIRT030492)

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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
    RM40_HUMAN, Q9NQ50: Mitochondrion (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    mitochondrion4
    nucleus4
    cytosol1

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus TAS9790763
    GO:0005730nucleolus IDA--
    GO:0005739mitochondrion IDA--
    GO:0005761mitochondrial ribosome ISS--

    Find genes that share ontologies with MRPL40           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 MRPL40
    Interactions:

        Search GeneGlobe Interaction Network for MRPL40

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

    Selected Interacting proteins for MRPL40 (Q9NQ502, 3 ENSP000003334014) via UniProtKB, MINT, STRING, and/or I2D (see all 261)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ICT1Q141972, 3, ENSP000003015854MINT-8079030 I2D: score=1 STRING: ENSP00000301585
    HLA-BP304803, ENSP000003991684I2D: score=1 STRING: ENSP00000399168
    MRPL3P090012, ENSP000002649954MINT-8079030 STRING: ENSP00000264995
    MRPL46Q9H2W62, ENSP000003123114MINT-8079030 STRING: ENSP00000312311
    MRPL19P494062, ENSP000003774864MINT-8079030 STRING: ENSP00000377486
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0009653anatomical structure morphogenesis TAS9790763

    Find genes that share ontologies with MRPL40           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 MRPL40 (RM40)



    (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 MRPL40 gene: 
    NM_003776.2  

    Unigene Cluster for MRPL40:

    Mitochondrial ribosomal protein L40
    Hs.431307  [show with all ESTs]
    Unigene Representative Sequence: AK123768
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000333130(uc002zpg.3) ENST00000443660 ENST00000471259
    miRNA
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    Additional mRNA sequence: 

    AF034091.1 AJ295637.1 AK123768.1 BC009707.1 CR456532.1 

    10 DOTS entries:

    DT.97825739  DT.453360  DT.100000717  DT.92426221  DT.100786543  DT.120652532  DT.100786542  DT.95169494 
    DT.120652450  DT.95169495 

    Selected AceView cDNA sequences (see all 208):

    BQ049913 BM975024 AI349343 NM_003776 AA719827 BQ631141 AA829634 AI050842 
    BF914383 AA461057 AA309003 CA430729 AA039808 BU180526 BX382915 AA829722 
    BU073327 AI185989 BQ271247 AA307896 BG491617 BQ636884 BQ676854 F36974 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for MRPL40    About this scheme

    ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b · 4c · 4d
    SP1:              -                       -     -                     
    SP2:                                      -     -                     
    SP3:                                                                  
    SP4:                                      -                           


    ECgene alternative splicing isoforms for MRPL40

    (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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    MRPL40 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CTGTTAATAA
    MRPL40 Expression
    About this image

    MRPL40 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    MRPL40 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.431307

    UniProtKB/Swiss-Prot: RM40_HUMAN, Q9NQ50
    Tissue specificity: Ubiquitous

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    In Situ
    Assay Products:
     

     
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    (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 MRPL40 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Mrpl401 , 5 mitochondrial ribosomal protein L401, 5 80.26(n)1
    75.24(a)1
      16 (11.69 cM)5
    181001  NM_010922.21  NP_035052.21 
     188720185 
    chicken
    (Gallus gallus)
    Aves MRPL401 mitochondrial ribosomal protein L40 66.9(n)
    64.29(a)
      100858795  XM_003642199.2  XP_003642247.2 
    lizard
    (Anolis carolinensis)
    Reptilia aca-mir-5408a6
    aca-mir-5408a
    52(a)
    1 ↔ 1
    GL343282.1(1463449-1472949)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia mrpl401 mitochondrial ribosomal protein L40 60.31(n)
    57.23(a)
      549003  NM_001016249.2  NP_001016249.1 
    zebrafish
    (Danio rerio)
    Actinopterygii wufj54c062 Transcribed sequence with weak similarity to protein more 73.96(n)    AL909815.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta mRpL401 mitochondrial ribosomal protein L40 53.12(n)
    40.62(a)
      41364  NM_079594.5  NP_524318.1 
    worm
    (Caenorhabditis elegans)
    Secernentea mrpl-401 mrpl-40 48.77(n)
    30.88(a)
      175174  NM_064737.3  NP_497138.1 


    ENSEMBL Gene Tree for MRPL40 (if available)
    TreeFam Gene Tree for MRPL40 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for MRPL40 gene

    Find genes that share paralogs with MRPL40           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for MRPL40
    PGOHUM00000239837


    (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 MRPL40 (see all 84)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 22 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs96060171,2
    C,F,A,H--19421229(+) CATCTG/AGCACT 1 -- int118Minor allele frequency- A:0.30NS EA NA 2120
    rs1468332911,2
    --19421237(+) ACTCTC/TGACTC 1 -- int10--------
    rs611420541,2
    C,F--19421242(+) CGACTC/TTTTGT 1 -- int16Minor allele frequency- T:0.07NA WA CSA EA 364
    rs2002678161,2
    C--19421293(+) TTTTT-/TTTTTT 1 -- int10--------
    rs1856717161,2
    --19421431(+) CAGGCA/GCCCAC 1 -- int10--------
    rs1904878301,2
    --19421617(+) AATAAA/GCTTCT 1 -- int10--------
    rs2016896391,2
    --19421620(+) AAGCT-/TCTAA 
            
    TCTAA
    1 -- int10--------
    rs784104161,2
    C--19421629(+) ATCTA-/ACAGTTT 1 -- int10--------
    rs1814762991,2
    --19421807(+) GTGGCA/GCGATC 1 -- int10--------
    rs1842144731,2
    --19421892(+) AGGTGC/TGCACC 1 -- int10--------

    HapMap Linkage Disequilibrium report for MRPL40 (19419425 - 19423598 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 7 variations for MRPL40:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv435744CNV Deletion17901297
    nsv834124CNV Loss17160897
    dgv4839n71CNV Loss21882294
    nsv834127CNV Loss17160897
    dgv4840n71CNV Loss21882294
    nsv914263CNV Gain21882294
    esv2751940CNV Gain17911159

    Site Specific Mutation Identification with PCR Assays
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    DNA2.0 Custom Variant and Variant Library Synthesis for MRPL40

    (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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    OMIM gene information: 605089    OMIM disorders: --

    2 diseases for MRPL40:    
    About MalaCards
    velocardiofacial syndrome    digeorge syndrome

    1 disease from the University of Copenhagen DISEASES database for MRPL40:
    DiGeorge syndrome

    Find genes that share disorders with MRPL40           About GenesLikeMe

    Genetic Association Database (GAD): MRPL40
    Human Genome Epidemiology (HuGE) Navigator: MRPL40 (1 document)

    Export disorders for MRPL40 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 MRPL40 gene, integrated from 10 sources (see all 18):
    (articles sorted by number of sources associating them with MRPL40)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Isolation and characterization of a human gene containing a nuclear localization signal from the critical region for velo-cardio-facial syndrome on 22q11. (PubMed id 9790763)1, 2, 3 Funke B....Morrow B. (Genomics 1998)
    2. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PubMed id 20877624)1, 4 Hendrickson S.L....O'Brien S.J. (PLoS ONE 2010)
    3. 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)
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    5. A genome annotation-driven approach to cloning the human ORFeome. (PubMed id 15461802)1, 2 Collins J.E.... Dunham I. (Genome Biol. 2004)
    6. The human mitochondrial ribosomal protein genes: mapping of 54 genes to the chromosomes and implications for human disorders. (PubMed id 11543634)1, 3 Kenmochi N.... Tanaka T. (Genomics 2001)
    7. Identification of URIM, a novel gene up-regulated in metastasis. (PubMed id 10226592)1, 2 Hildebrandt T.... Zendman A.J.W. (Anticancer Res. 1999)
    8. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (Cell 2012)
    9. MMS19 assembles iron-sulfur proteins required for DNA metabolism and genomic integrity. (PubMed id 22678362)1 Stehling O.... Lill R. (Science 2012)
    10. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 64976 HGNC: 14491 AceView: MRPL40 Ensembl:ENSG00000185608 euGenes: HUgn64976
    ECgene: MRPL40 H-InvDB: MRPL40

    (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 MRPL40 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for MRPL40 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for MRPL40 gene:
    Search GeneIP for patents involving MRPL40

    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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