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RIMKLA Gene

protein-coding   GIFtS: 44
GCID: GC01P042846

Ribosomal Modification Protein RimK-Like Family Member A

(Previous names: family with sequence similarity 80, member A)
(Previous symbol: FAM80A)
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(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
Ribosomal Modification Protein RimK-Like Family Member A1 2     NAAG Synthetase A2 3
FAM80A1 2 3     NAAGS-II2
Family With Sequence Similarity 80, Member A1 2     RP11-157D18.12
N-Acetylaspartylglutamate Synthetase II1 2     N-Acetylaspartyl-Glutamate Synthetase A2
Ribosomal Protein S6 Modification-Like Protein A2 3     EC 6.3.2.n63
NAAGS2 3     

External Ids:    HGNC: 287251   Entrez Gene: 2847162   Ensembl: ENSG000001771817   UniProtKB: Q8IXN73   

Export aliases for RIMKLA gene to outside databases

Previous GC identifers: GC01P042620 GC01P040966


(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 RIMKLA Gene:
RIMKLA (ribosomal modification protein rimK-like family member A) is a protein-coding gene. GO annotations related to this gene include acid-amino acid ligase activity and N-acetyl-L-aspartate-L-glutamate ligase activity. An important paralog of this gene is RIMKLB.

UniProtKB/Swiss-Prot: RIMKA_HUMAN, Q8IXN7
Function: Catalyzes the synthesis of N-acetylaspartyl-glutamate (NAAG)




(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_000001.10  NT_032977.10  NC_018912.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the RIMKLA gene promoter:
         Brachyury   NRSF form 1   XBP-1   NRSF form 2   c-Ets-1   E47   AREB6   SRY   Sox9   IRF-7A   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRIMKLA promoter sequence
   Search Chromatin IP Primers for RIMKLA

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


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

Entrez Gene cytogenetic band: 1p34.2   Ensembl cytogenetic band:  1p34.2   HGNC cytogenetic band: 1p34.2

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

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P042846:  view genomic region     (about GC identifiers)

Start:
42,846,466 bp from pter      End:
42,889,900 bp from pter
Size:
43,435 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: RIMKA_HUMAN, Q8IXN7 (See protein sequence)
Recommended Name: N-acetylaspartyl-glutamate synthetase A  
Size: 391 amino acids; 42864 Da
Cofactor: Binds 2 magnesium or manganese ions per subunit (By similarity)
Miscellaneous: N-acetylaspartyl-glutamate (NAAG) is the most abundant dipeptide present in vertebrate central
nervous system (CNS) (By similarity)
Sequence caution: Sequence=AAH39737.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=CAH70661.1; Type=Erroneous gene model prediction;
Secondary accessions: Q5VUS5

Explore the universe of human proteins at neXtProt for RIMKLA: NX_Q8IXN7

Explore proteomics data for RIMKLA at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

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

    REFSEQ proteins: NP_775913.2  
    ENSEMBL proteins: 
     ENSP00000387064   ENSP00000414330  

    RIMKLA Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for RIMKLA

     
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    Search eBioscience for ELISAs for RIMKLA 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    Selected InterPro protein domains (see all 6):
     IPR013651 ATP-grasp_RimK-type
     IPR016185 PreATP-grasp_dom
     IPR004666 RpS6_RimK/Lys_biosynth_LsyX
     IPR011761 ATP-grasp
     IPR013815 ATP_grasp_subdomain_1

    Graphical View of Domain Structure for InterPro Entry Q8IXN7

    ProtoNet protein and cluster: Q8IXN7

    UniProtKB/Swiss-Prot: RIMKA_HUMAN, Q8IXN7
    Similarity: Belongs to the RimK family
    Similarity: Contains 1 ATP-grasp domain


    Find genes that share domains with RIMKLA           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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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: RIMKA_HUMAN, Q8IXN7
    Function: Catalyzes the synthesis of N-acetylaspartyl-glutamate (NAAG)
    Catalytic activity: ATP + N-acetyl-L-aspartate + L-glutamate = ADP + phosphate + N-acetyl-L-aspartyl-L-glutamate

         Enzyme Number (IUBMB): EC 6.3.2.n61

         Gene Ontology (GO): 5 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004363glutathione synthase activity ----
    GO:0005524ATP binding IEA--
    GO:0016881acid-amino acid ligase activity ----
    GO:0046872metal ion binding IEA--
    GO:0072590N-acetyl-L-aspartate-L-glutamate ligase activity ISS--
         
    Find genes that share ontologies with RIMKLA           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for RIMKLA:
     Increased cell number in G2M,  

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for RIMKLA
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    miRNA
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    miRTarBase miRNAs that target RIMKLA:
    hsa-mir-215-5p (MIRT024902), hsa-mir-192-5p (MIRT026388)

    Block miRNA regulation of human, mouse, rat RIMKLA using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate RIMKLA (see all 189):
    hsa-miR-520f hsa-miR-106a hsa-miR-134 hsa-miR-519a hsa-miR-3921 hsa-miR-502-3p hsa-miR-298 hsa-miR-3649
    SwitchGear 3'UTR luciferase reporter plasmidRIMKLA 3' UTR sequence
    Inhib. RNA
    Products:
        
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    Predesigned siRNA for gene silencing in human, mouse, rat RIMKLA

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    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for RIMKLA
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat RIMKLA

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RIMKLA


    (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
    RIMKA_HUMAN, Q8IXN7: Cytoplasm (Probable)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol3
    nucleus2

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

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

    Find genes that share ontologies with RIMKLA           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 RIMKLA
    Interactions:

        Search GeneGlobe Interaction Network for RIMKLA

    STRING Interaction Network Preview (showing 5 interactants - click image to see 9)

    Selected Interacting proteins for RIMKLA (ENSP000004143304) via UniProtKB, MINT, STRING, and/or I2D (see all 9)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ARTNENSP000003919984STRING: ENSP00000391998
    ENSG00000228605ENSP000004012724STRING: ENSP00000401272
    IPO13ENSP000003614184STRING: ENSP00000361418
    LRRC7ENSP000000353834STRING: ENSP00000035383
    PRPF38BENSP000003590424STRING: ENSP00000359042
    About this table

    Gene Ontology (GO): 2 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006464cellular protein modification process IEA--
    GO:0006750glutathione biosynthetic process ----

    Find genes that share ontologies with RIMKLA           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 RIMKLA (RIMKA)

    1 HMDB Compound for RIMKLA    About this table
    CompoundSynonyms CAS #PubMed Ids
    Manganesemanganese 7439-96-5--



    (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 RIMKLA gene: 
    NM_173642.3  

    Unigene Cluster for RIMKLA:

    Ribosomal modification protein rimK-like family member A
    Hs.420244  [show with all ESTs]
    Unigene Representative Sequence: NM_173642
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000410070 ENST00000431473(uc001chi.2)
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate RIMKLA (see all 189):
    hsa-miR-520f hsa-miR-106a hsa-miR-134 hsa-miR-519a hsa-miR-3921 hsa-miR-502-3p hsa-miR-298 hsa-miR-3649
    SwitchGear 3'UTR luciferase reporter plasmidRIMKLA 3' UTR sequence
    Inhib. RNA
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat RIMKLA
    Primer
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    OriGene qPCR primer pairs and template standards for RIMKLA
    OriGene qSTAR qPCR primer pairs in human, mouse for RIMKLA
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat RIMKLA
      QuantiTect SYBR Green Assays in human, mouse, rat RIMKLA
      QuantiFast Probe-based Assays in human, mouse, rat RIMKLA

    Additional mRNA sequence: BC039737.1 

    9 DOTS entries:

    DT.410720  DT.97837726  DT.310105  DT.99982330  DT.404882  DT.108385  DT.92065637  DT.121458333 
    DT.91927766 

    Selected AceView cDNA sequences (see all 47):

    CB154467 BQ220020 AA176636 AA626689 BX108269 AA932847 Z40686 BF971367 
    BE220489 BU178521 BE669885 AI279434 BE669736 AI681638 AW001564 BX114557 
    AI796946 CB147602 BQ638856 AA595285 NM_173642 CB146074 AA179690 BM796010 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for RIMKLA    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6
    SP1:              -                           
    SP2:                                          


    ECgene alternative splicing isoforms for RIMKLA

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

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

    RIMKLA Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.420244
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    In Situ
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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 chordates.

    Orthologs for RIMKLA gene from Selected species (see all 8)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rimkla1 , 5 ribosomal modification protein rimK-like family member more1, 5 87.02(n)1
    90.93(a)1
      4 (55.40 cM)5
    1942371  NM_177572.41  NP_808240.21 
     1194652835 
    zebrafish
    (Danio rerio)
    Actinopterygii rimkla6
    ribosomal modification protein rimK-like family me...
    65(a)
    1 ↔ 1
    8(27721048-27740251) ENSDARG00000016830


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for RIMKLA gene
    RIMKLB2  
    1 SIMAP similar gene for RIMKLA using alignment to 1 protein entry:     RIMKA_HUMAN:
    RIMKLB

    Find genes that share paralogs with RIMKLA           About GenesLikeMe



    (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 RIMKLA (see all 1004)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1854226021,2
    --42844549(+) AATCAA/GACTTG 1 -- us2k10--------
    rs762698921,2
    C,F--42844896(+) GGGCAC/TTATTG 1 -- us2k11Minor allele frequency- T:0.07WA 118
    rs1505450521,2
    --42844930(+) AGAACA/GGGGGA 1 -- us2k10--------
    rs1909095201,2
    --42845158(+) TACTCC/TGGAGG 1 -- us2k10--------
    rs1395036161,2
    C--42845190(+) AACCCA/GGCAGG 1 -- us2k10--------
    rs127441531,2
    C,F--42845237(+) TCCAGC/TCTGGG 1 -- us2k14Minor allele frequency- T:0.50NA 8
    rs1473435941,2
    --42845300(+) CATTGC/TTTGAA 1 -- us2k10--------
    rs1148921361,2
    F--42845424(+) TTACCC/TCATTT 1 -- us2k11Minor allele frequency- T:0.01WA 118
    rs1402021351,2
    --42845466(+) CTACTC/GTTGCT 1 -- us2k10--------
    rs1416241271,2
    C--42845491(+) AGAAA-/TTTAAA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for RIMKLA (42846466 - 42889900 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for RIMKLA:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv28389CNV Loss19812545
    nsv870704CNV Gain21882294

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

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

    1. N-acetylaspartylglutamate synthetase II synthesizes N-acetylaspartylglutamylglutamate. (PubMed id 21454531)1, 3 Lodder-Gadaczek J....Eckhardt M. (J. Biol. Chem. 2011)
    2. Molecular identification of N-acetylaspartylglutamate synthase and beta-citrylglutamate synthase. (PubMed id 20657015)1, 3 Collard F....Van Schaftingen E. (J. Biol. Chem. 2010)
    3. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (Nature 2006)
    4. 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)
    5. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
    6. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (Genomics 2007)
    7. 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)

    (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: 284716 HGNC: 28725 AceView: MGC47816 Ensembl:ENSG00000177181 euGenes: HUgn284716
    ECgene: RIMKLA H-InvDB: RIMKLA

    (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 RIMKLA 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 RIMKLA gene:
    Search GeneIP for patents involving RIMKLA

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



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