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ARL13A Gene

protein-coding   GIFtS: 41
GCID: GC0XP100224

ADP-Ribosylation Factor-Like 13A

(Previous name: ADP-ribosylation factor-like 13)
(Previous symbol: ARL13)
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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
ADP-Ribosylation Factor-Like 13A1 2
ARL131 2
ADP-Ribosylation Factor-Like 131 2
ADP-Ribosylation Factor-Like Protein 13A2
dJ341D10.22

External Ids:    HGNC: 317091   Entrez Gene: 3925092   Ensembl: ENSG000001742257   UniProtKB: Q5H9133   

Export aliases for ARL13A gene to outside databases

Previous GC identifers: GC0XP100035 GC0XP100111 GC0XP090022


(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 ARL13A Gene:
ARL13A (ADP-ribosylation factor-like 13A) is a protein-coding gene. GO annotations related to this gene include GTP binding. An important paralog of this gene is ARFRP1.


(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_000023.10  NT_011651.18  NC_018934.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the ARL13A gene promoter:
         HFH-3   GATA-3   GATA-1   GATA-2   MEF-2A   RORalpha1   FOXI1   POU2F1   POU2F1a   aMEF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidARL13A promoter sequence
   Search Chromatin IP Primers for ARL13A

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ARL13A


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

Entrez Gene cytogenetic band: Xq22.1   Ensembl cytogenetic band:  Xq22.1   HGNC cytogenetic band: Xq22.1

ARL13A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ARL13A gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XP100224:  view genomic region     (about GC identifiers)

Start:
100,224,697 bp from pter      End:
100,245,820 bp from pter
Size:
21,124 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: AR13A_HUMAN, Q5H913 (See protein sequence)
Recommended Name: ADP-ribosylation factor-like protein 13A  
Size: 290 amino acids; 33003 Da
Sequence caution: Sequence=CAI42661.1; Type=Erroneous gene model prediction;
Secondary accessions: B2RTT6 B4DX50
Alternative splicing: 2 isoforms:  Q5H913-1   Q5H913-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for ARL13A: NX_Q5H913

Explore proteomics data for ARL13A at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See ARL13A Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001155963.1  
    ENSEMBL proteins: 
     ENSP00000414757   ENSP00000398637   ENSP00000362044   ENSP00000445825  

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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:
    ARL: ADP-ribosylation factors-like
    ARF: ADP-ribosylation factors

    3 InterPro protein domains:
     IPR027417 P-loop_NTPase
     IPR006689 Small_GTPase_ARF/SAR
     IPR024156 Small_GTPase_ARF

    Graphical View of Domain Structure for InterPro Entry Q5H913

    ProtoNet protein and cluster: Q5H913

    UniProtKB/Swiss-Prot: AR13A_HUMAN, Q5H913
    Similarity: Belongs to the small GTPase superfamily. Arf family


    Find genes that share domains with ARL13A           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): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005525GTP binding IEA--
         
    Find genes that share ontologies with ARL13A           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for ARL13A:
     Synthetic lethal with Ras 

    Animal Models:
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    hsa-miR-1266 hsa-miR-526b hsa-miR-26b* hsa-miR-4294
    SwitchGear 3'UTR luciferase reporter plasmidARL13A 3' UTR sequence
    Inhib. RNA
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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 COMPARTMENTS: 

    CompartmentConfidence
    extracellular2
    mitochondrion2
    cytoskeleton1
    cytosol1
    endosome1
    golgi apparatus1
    nucleus1
    peroxisome1
    plasma membrane1
    vacuole1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622intracellular IEA--

    Find genes that share ontologies with ARL13A           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 ARL13A
    Interactions:

        Search GeneGlobe Interaction Network for ARL13A

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

    Selected Interacting proteins for ARL13A (ENSP000004147574) via UniProtKB, MINT, STRING, and/or I2D (see all 49)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ARPC2ENSP000002956854STRING: ENSP00000295685
    KYENSP000003975984STRING: ENSP00000397598
    PFDN4ENSP000003604734STRING: ENSP00000360473
    PRDX5ENSP000002654624STRING: ENSP00000265462
    ALYREFENSP000003318174STRING: ENSP00000331817
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006886intracellular protein transport ----
    GO:0007264small GTPase mediated signal transduction IEA--

    Find genes that share ontologies with ARL13A           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 ARL13A (AR13A)



    (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 ARL13A gene: 
    NM_001162491.1  

    Unigene Cluster for ARL13A:

    ADP-ribosylation factor-like 13A
    Hs.147237  [show with all ESTs]
    Unigene Representative Sequence: NM_001162490
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000450457(uc004ego.3 uc011mrf.2 uc010nng.3) ENST00000450049
    ENST00000372953 ENST00000494863
    miRNA
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    4 qRT-PCR Assays for microRNAs that regulate ARL13A:
    hsa-miR-1266 hsa-miR-526b hsa-miR-26b* hsa-miR-4294
    SwitchGear 3'UTR luciferase reporter plasmidARL13A 3' UTR sequence
    Inhib. RNA
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      QuantiTect SYBR Green Assays in human, mouse, rat ARL13A
      QuantiFast Probe-based Assays in human, mouse, rat ARL13A

    Additional mRNA sequence: 

    AK301813.1 BC140808.1 BC144603.1 

    2 DOTS entries:

    DT.65284394  DT.92053102 

    6 AceView cDNA sequences:

    AI205921 AW118931 AA401549 CD300373 BX119507 BG188455 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for ARL13A    About this scheme

    ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6
    SP1:                                          
    SP2:              -     -     -               
    SP3:                                          


    ECgene alternative splicing isoforms for ARL13A

    (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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    ARL13A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AAAGAAGGTG
    ARL13A Expression
    About this image


    ARL13A expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 2) fully expand
     
     Testis (Reproductive System)
             Spermatid Seminiferous Tubules
     
     Gonad
             Spermatid Seminiferous Tubules
    ARL13A Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    ARL13A Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.147237
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ARL13A

    (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 and fungi.

    Orthologs for ARL13A gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Arl13a1 , 5 ADP-ribosylation factor-like 13A1, 5 75.4(n)1
    64.92(a)1
      X (55.90 cM)5
    744481  NM_028947.11  NP_083223.11 
     1341875015 
    chicken
    (Gallus gallus)
    Aves ARL13A6
    ADP-ribosylation factor-like 13A
    42(a)
    1 ↔ 1
    4(5111873-5115556)
    lizard
    (Anolis carolinensis)
    Reptilia ARL13A6
    ADP-ribosylation factor-like 13A
    34(a)
    1 ↔ 1
    GL343451.1(50809-52940)
    zebrafish
    (Danio rerio)
    Actinopterygii arl13a6
    ADP-ribosylation factor-like 13A
    20(a)
    1 ↔ 1
    14(42768751-42784202) ENSDARG00000052575
    fruit fly
    (Drosophila melanogaster)
    Insecta CG178196
    --
    25(a)
    1 → many
    3R(17710450-17711272)
    worm
    (Caenorhabditis elegans)
    Secernentea Y54E10BR.26
    Protein Y54E10BR.2 (Y54E10BR.2) mRNA, complete cds...
    21(a)
    1 → many
    I(3032967-3034761) WBGene00021841
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes ARL36
    GTPase of the Ras superfamily required to recruit ...
    26(a)
    1 → many
    XVI(459963-460559) YPL051W


    ENSEMBL Gene Tree for ARL13A (if available)
    TreeFam Gene Tree for ARL13A (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for ARL13A gene
    ARFRP12  ARL13B2  
    4 SIMAP similar genes for ARL13A using alignment to 3 protein entries:     AR13A_HUMAN (see all proteins):
    ARL3    ARL2    ARF6    DKFZp434B2017

    Find genes that share paralogs with ARL13A           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 ARL13A (see all 278)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1378788581,2
    --100222842(+) AGTTCA/CAAACC 3 -- us2k10--------
    rs1913564901,2
    --100222999(+) AGATCA/GTGCCA 3 -- us2k10--------
    rs1494622661,2
    --100223118(+) AAAGAA/GCTCCC 3 -- us2k10--------
    rs1814066381,2
    --100223134(+) CAAAGC/TTGGAA 3 -- us2k10--------
    rs344707311,2
    C--100223256(+) ACAGA-/CCCCCC 3 -- us2k10--------
    rs599306141,2
    C--100223266(+) CCCCC-/C/CC  
            
    ATACA
    3 -- us2k10--------
    rs1443701911,2
    C--100223406(+) TCTTTA/GCAGTG 3 -- us2k10--------
    rs1848940311,2
    --100223436(+) GCCTCA/GGCCAG 3 -- us2k10--------
    rs97854411,2
    C,F,H--100223663(+) tggctG/Agatgt 3 -- us2k110Minor allele frequency- A:0.08NS EA NA 1190
    rs1433621961,2
    --100223751(+) CCTGGA/GCAATA 3 -- us2k10--------

    HapMap Linkage Disequilibrium report for ARL13A (100224697 - 100245820 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for ARL13A:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv7012CNV Insertion18451855
    nsv515758CNV Gain19592680
    nsv517937CNV Gain19592680

    Site Specific Mutation Identification with PCR Assays
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    (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 ARL13A gene integrated from 10 sources:
    (articles sorted by number of sources associating them with ARL13A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. SUMOylation of the small GTPase ARL-13 promotes ciliary targeting of sensory receptors. (PubMed id 23128241)1 Li Y....Hu J. (J. Cell Biol. 2012)
    2. The DNA sequence of the human X chromosome. (PubMed id 15772651)2 Ross M.T.... Bentley D.R. (Nature 2005)
    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. (Genome Res. 2004)
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)
    5. 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: 392509 HGNC: 31709 AceView: ARL13 Ensembl:ENSG00000174225 euGenes: HUgn392509
    ECgene: ARL13A H-InvDB: ARL13A

    (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 ARL13A 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 ARL13A gene:
    Search GeneIP for patents involving ARL13A

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    (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
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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