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

RBM42 Gene

protein-coding   GIFtS: 47
GCID: GC19P036119

RNA Binding Motif Protein 42

  Search for RBM42
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
RNA Binding Motif Protein 421 2
RNA-Binding Motif Protein 422 3
RNA-Binding Protein 422

External Ids:    HGNC: 281171   Entrez Gene: 791712   Ensembl: ENSG000001262547   OMIM: 6132325   UniProtKB: Q9BTD83   

Export aliases for RBM42 gene to outside databases

Previous GC identifers: GC19P040812 GC19P032625


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

GeneCards Summary for RBM42 Gene: 
RBM42 (RNA binding motif protein 42) is a protein-coding gene. GO annotations related to this gene include RNA binding and nucleotide binding.

UniProtKB/Swiss-Prot: RBM42_HUMAN, Q9BTD8
Function: Binds (via the RRM domain) to the 3'-untranslated region (UTR) of CDKN1A mRNA (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_000019.9  NT_011109.16  NC_018930.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the RBM42 gene promoter:
         E2F-4   E2F-3a   E2F-5   E2F-2   Gfi-1   GATA-2   E2F   E2F-1   IRF-7A   ZID   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRBM42 promoter sequence
   Search SABiosciences Chromatin IP Primers for RBM42

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RBM42


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

Entrez Gene cytogenetic band: 19q13.12   Ensembl cytogenetic band:  19q13.12   HGNC cytogenetic band: 19q13.12

RBM42 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RBM42 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P036119:  view genomic region     (about GC identifiers)

Start:
36,119,932 bp from pter      End:
36,128,588 bp from pter
Size:
8,657 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: RBM42_HUMAN, Q9BTD8 (See protein sequence)
Recommended Name: RNA-binding protein 42  
Size: 480 amino acids; 50414 Da
Subunit: Interacts with HNRNPK (By similarity)
Subcellular location: Nucleus (By similarity). Cytoplasm (By similarity). Note=Upon stress response, localizes
with HNRNPK in cytoplasmic aggregates of stalled translational preinitiation complexes called stress granules (By
similarity)
Sequence caution: Sequence=AAB57629.1; Type=Erroneous gene model prediction;
Secondary accessions: O00320 Q8N5R7 Q9BU66
Alternative splicing: 4 isoforms:  Q9BTD8-1   Q9BTD8-2   Q9BTD8-3   Q9BTD8-4   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for RBM42: NX_Q9BTD8

Explore proteomics data for RBM42 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9BTD8

  • RBM42 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    RBM42 Protein Expression
    REFSEQ proteins: NP_077297.2  
    ENSEMBL proteins: 
     ENSP00000466044   ENSP00000262633   ENSP00000467614   ENSP00000466548   ENSP00000468060  
     ENSP00000467278   ENSP00000353663  

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    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for RBM42 

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--
    GO:0005737cytoplasm IEA--

    RBM42 for ontologies           About GeneDecksing



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    Cloud-Clone Corp. ELISAs for RBM42 
    Cloud-Clone Corp. CLIAs for RBM42


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    RBM: RNA binding motif (RRM) containing

    2 InterPro protein domains:
     IPR012677 Nucleotide-bd_a/b_plait
     IPR000504 RRM_dom

    Graphical View of Domain Structure for InterPro Entry Q9BTD8

    ProtoNet protein and cluster: Q9BTD8

    1 Blocks protein domain: IPB000504 RNA-binding region RNP-1 (RNA recognition motif)

    UniProtKB/Swiss-Prot: RBM42_HUMAN, Q9BTD8
    Similarity: Belongs to the RRM RBM42 family
    Similarity: Contains 1 RRM (RNA recognition motif) domain


    RBM42 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: RBM42_HUMAN, Q9BTD8
    Function: Binds (via the RRM domain) to the 3'-untranslated region (UTR) of CDKN1A mRNA (By similarity)

         Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000166nucleotide binding IEA--
    GO:0003676nucleic acid binding ----
    GO:0003723RNA binding IEA--
         
    RBM42 for ontologies           About GeneDecksing


    Phenotypes:
         4 GenomeRNAi human phenotypes for RBM42:
     Decreased homologous recombina  Decreased influenza A H1N1 (A/  Decreased influenza A/WSN/33 r  Increased gamma-H2AX phosphory 

    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for RBM42 
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for RBM42 
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    miRNA
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    1 QIAGEN miScript miRNA Assays for microRNA that regulate RBM42:
    hsa-miR-582-3p
    SwitchGear 3'UTR luciferase reporter plasmidRBM42 3' UTR sequence
    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RBM42


    (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 RBM42

    STRING Interaction Network Preview (showing 5 interactants - click image to see 10)

    5/11 Interacting proteins for RBM42 (Q9BTD82, 3 ENSP000002626334) via UniProtKB, MINT, STRING, and/or I2D (see all 11)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HNRNPKP619782, 3, ENSP000003654394MINT-8338707 I2D: score=4 STRING: ENSP00000365439
    PCBP1Q153653, ENSP000003055564I2D: score=3 STRING: ENSP00000305556
    PRPF4O431723, ENSP000003633134I2D: score=2 STRING: ENSP00000363313
    RBFOX2O432512, ENSP000004130354MINT-8339378 STRING: ENSP00000413035
    FHL3Q136433, ENSP000003621074I2D: score=5 STRING: ENSP00000362107
    About this table

    (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 RBM42

    Search CenterWatch for drugs/clinical trials and news about RBM42

    (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 RBM42 gene: 
    NM_024321.3  

    Unigene Cluster for RBM42:

    RNA binding motif protein 42
    Hs.5086  [show with all ESTs]
    Unigene Representative Sequence: NM_024321
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000588161 ENST00000262633(uc002oan.3) ENST00000592202 ENST00000586618
    ENST00000589559 ENST00000592526 ENST00000589871 ENST00000360475(uc010xsx.2 uc002oap.3 uc002oaq.3)

    miRNA
    Products:
         
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat RBM42
    1 QIAGEN miScript miRNA Assays for microRNA that regulate RBM42:
    hsa-miR-582-3p
    SwitchGear 3'UTR luciferase reporter plasmidRBM42 3' UTR sequence
    Inhib. RNA
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
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    Primer
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      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat RBM42

    Additional mRNA sequence: 

    AK301669.1 BC002868.2 BC004204.2 BC031682.1 

    23 DOTS entries:

    DT.446634  DT.97851850  DT.100801962  DT.100709969  DT.100813302  DT.100059822  DT.95370980  DT.92450780 
    DT.100813300  DT.100813313  DT.121473767  DT.95370981  DT.100813305  DT.100813316  DT.100838808  DT.92450786 
    DT.92450790  DT.100883281  DT.100883284  DT.91919351  DT.91964675  DT.95151426  DT.95298888 

    24/491 AceView cDNA sequences (see all 491):

    BU739518 BU608865 CR617718 CR599588 CR609008 BU168416 BC004204 BM548964 
    BM978335 AI929720 BM824965 AW087103 BM718476 AI675103 CA454317 BU552407 
    BM722690 BM999857 BQ029811 BQ015251 CR605060 BQ052068 CD107999 CR621515 

    GeneLoc Exon Structure

    5/9 Alternative Splicing Database (ASD) splice patterns (SP) for RBM42 (see all 9)    About this scheme

    ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b
    SP1:                                                  -                                                               
    SP2:                                                  -           -                                                   
    SP3:                                                  -     -     -                                                   
    SP4:                                      -     -     -     -     -     -     -     -     -     -                     
    SP5:                                                  -     -     -                                                   


    ECgene alternative splicing isoforms for RBM42

    (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

    RBM42 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TGGAAGGACC
    RBM42 Expression
    About this image


    See RBM42 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for RBM42

    SOURCE GeneReport for Unigene cluster: Hs.5086
        SABiosciences Custom PCR Arrays for RBM42
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RBM42

    (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 eukaryotes.

    Orthologs for RBM42 gene from 8/21 species (see all 21)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rbm421 , 5 RNA binding motif protein 421, 5 89.73(n)1
    98.31(a)1
      7 (18.95 cM)5
    680351  NM_133693.21  NP_598454.21 
     306409945 
    lizard
    (Anolis carolinensis)
    Reptilia RBM426
    RNA binding motif protein 42
    60(a)
    1 ↔ 1
    GL343514.1(314028-324305)
    African clawed frog
    (Xenopus laevis)
    Amphibia CD302971.12   -- 77.2(n)    CD302971.1 
    zebrafish
    (Danio rerio)
    Actinopterygii rbm421 RNA binding motif protein 42 65(n)
    67.69(a)
      445360  NM_001003850.1  NP_001003850.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG29311 CG2931 57.2(n)
    52.47(a)
      40673  NM_141295.3  NP_649552.1 
    worm
    (Caenorhabditis elegans)
    Secernentea tag-2626
    Protein TAG-262
    43(a)
    1 ↔ 1
    III(5151909-5153154)
    soybean
    (Glycine max)
    eudicotyledons Gma.20932 Transcribed sequence with moderate similarity to protein more 74(n)    BI702024.1 
    rice
    (Oryza sativa)
    Liliopsida Os.355082 Oryza sativa (japonica cultivar-group) cDNA cloneJ more 74.02(n)    AK061692.1 


    ENSEMBL Gene Tree for RBM42 (if available)
    TreeFam Gene Tree for RBM42 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for RBM42 gene
    3 SIMAP similar genes for RBM42 using alignment to 5 protein entries:     RBM42_HUMAN (see all proteins):
    CIRBP    RBMX    PABPC4

    RBM42 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

    10/249 SNPs in RBM42 are shown (see all 249)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1832620631,2
    --36118012(+) AGCAAA/CAATTT 1 -- us2k10--------
    rs1414489841,2
    C--36118044(+) AAGACA/GATCAA 1 -- us2k10--------
    rs72526661,2
    C,H--36118051(+) tcaaaT/Cgcaat 1 -- us2k14Minor allele frequency- C:0.01NS EA WA 418
    rs1449500541,2
    --36118139(+) GGTGTC/TAGATG 1 -- us2k10--------
    rs761408631,2
    F--36118207(+) TTCTTG/CACACT 1 -- us2k11Minor allele frequency- C:0.01NA 120
    rs1467897671,2
    C--36118236(+) CAGGCC/TGGAGT 1 -- us2k10--------
    rs1406093871,2
    --36118265(+) CTCACC/TGCAAC 1 -- us2k10--------
    rs1504401731,2
    --36118314(+) CTCCCA/GAGTAG 1 -- us2k10--------
    rs1863823211,2
    --36118349(+) ACGGCC/TGGCTA 1 -- us2k10--------
    rs1899506901,2
    --36118514(+) TAGTTA/CTTATC 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for RBM42 (36119932 - 36128588 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for RBM42:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv911629CNV Loss21882294

    SABiosciences Cancer Mutation PCR Assays
    SeqTarget long-range PCR primers for resequencing RBM42
    DNA2.0 Custom Variant and Variant Library Synthesis for RBM42

    (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

    RBM42 for disorders           About MalaCards
    OMIM gene information: 613232    OMIM disorders: --


    RBM42 for disorders           About GeneDecksing


    Export disorders for RBM42 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)
    About This Section

    PubMed articles for RBM42 gene, integrated from 9 sources (see all 17):
    (articles sorted by number of sources associating them with RBM42)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. hnRNP K interacts with RNA binding motif protein 42 and functions in the maintenance of cellular ATP level during stress conditions. (PubMed id 19170760)1, 2 Fukuda T.... Irie K. (2009)
    2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (2002)
    3. Dynamic protein-protein interaction wiring of the huma n spliceosome. (PubMed id 22365833)1 Hegele A....Stelzl U. (2012)
    4. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    5. Host cell interactome of HIV-1 Rev includes RNA helica ses involved in multiple facets of virus production. (PubMed id 22174317)1 Naji S....Gerace L. (2012)
    6. Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. (PubMed id 23000965)1 Povlsen L.K....Choudhary C. (2012)
    7. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)
    8. 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)
    9. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)
    10. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. (PubMed id 20068231)2 Olsen J.V....Mann M. (2010)

    (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)
    About This Section
    Entrez Gene: 79171 HGNC: 28117 AceView: MGC10433 Ensembl:ENSG00000126254 euGenes: HUgn79171
    ECgene: RBM42 H-InvDB: RBM42

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
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    About This Section
    NameDescription
    PharmGKB entry for RBM42 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
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    IP news from LifeMap Sciences, Inc.)
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    Patent Information for RBM42 gene:
    Search GeneIP for patents involving RBM42

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