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

USP6NL Gene

protein-coding   GIFtS: 52
GCID: GC10M011502

USP6 N-terminal like

 Explore 1 disease affiliated with
USP6NL via our new
 Human Malady Compendium 
Biological research products
for USP6NL
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
USP6 N-Terminal Like1 2     KIAA00191 3
RN-Tre1     Related To The N-Terminus Of Tre2 3
RNTRE1 2 5     Related To The N Terminus Of Tre2
TRE2NL1 2     USP6 N-Terminal-Like Protein2

External Ids:    HGNC: 168581   Entrez Gene: 97122   Ensembl: ENSG000001484297   OMIM: 6054055   UniProtKB: Q927383   

Export aliases for USP6NL gene to outside databases

Previous GC identifers: GC10M011506 GC10M011542


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

UniProtKB/Swiss-Prot: US6NL_HUMAN, Q92738
Function: Acts as a GTPase-activating protein for RAB5A and RAB43. Involved in receptor trafficking. In complex with
EPS8 inhibits internalization of EGFR. Involved in retrograde transport from the endocytic pathway to the Golgi
apparatus. Involved in the transport of Shiga toxin from early and recycling endosomes to the trans-Golgi network.
Required for structural integrity of the Golgi complex

Gene Wiki entry for USP6NL


(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000010.10  NC_018921.1  NT_008705.16  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the USP6NL gene promoter:
         TBP   p53   AML1a   ATF-2   IRF-1   Gfi-1   FOXJ2 (long isoform)   Cart-1   FOXJ2   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for USP6NL

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat USP6NL


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

Entrez Gene cytogenetic band: 10p13   Ensembl cytogenetic band:  10p14   HGNC cytogenetic band: 10p13

USP6NL Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
USP6NL gene location

GeneLoc information about chromosome 10         GeneLoc Exon Structure

GeneLoc location for GC10M011502:  view genomic region     (about GC identifiers)

Start:
11,502,509 bp from pter      End:
11,653,753 bp from pter
Size:
151,245 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: US6NL_HUMAN, Q92738 (See protein sequence)
Recommended Name: USP6 N-terminal-like protein  
Size: 828 amino acids; 94104 Da
Subunit: Interacts with EPS8
Subcellular location: Golgi apparatus. Cytoplasmic vesicle
Sequence caution: Sequence=BAA02807.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Secondary accessions: A8KA79 Q15400 Q5VV10 Q7L0K9
Alternative splicing: 2 isoforms:  Q92738-1   Q92738-2   

Explore the universe of human proteins at neXtProt for USP6NL: NX_Q92738

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q92738

  • USP6NL Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_001073960.1  NP_055503.1  

    ENSEMBL proteins: 
     ENSP00000368539   ENSP00000444570   ENSP00000277575  

    Human Recombinant Protein Products: 
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    Uscn Proteins for USP6NL

    Gene Ontology (GO): 5 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005575cellular_component ----
    GO:0005622intracellular ----
    GO:0005794Golgi apparatus IEA--
    GO:0016023cytoplasmic membrane-bounded vesicle IEA--
    GO:0031410cytoplasmic vesicle IDA17684057


    USP6NL for ontologies           About GeneDecksing



    USP6NL Antibody Products: 
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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    USP6NL for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR000195 Rab-GTPase-TBC_dom

    Graphical View of Domain Structure for InterPro Entry Q92738

    ProtoNet protein and cluster: Q92738

    1 Blocks protein family: IPB000195 RabGAP/TBC domain

    UniProtKB/Swiss-Prot: US6NL_HUMAN, Q92738
    Similarity: Contains 1 Rab-GAP TBC domain


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: US6NL_HUMAN, Q92738
    Function: Acts as a GTPase-activating protein for RAB5A and RAB43. Involved in receptor trafficking. In complex with
    EPS8 inhibits internalization of EGFR. Involved in retrograde transport from the endocytic pathway to the Golgi
    apparatus. Involved in the transport of Shiga toxin from early and recycling endosomes to the trans-Golgi network.
    Required for structural integrity of the Golgi complex

    miRNA
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    OriGene 3'-UTR Clone (see all 2): USP6NL
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat USP6NL
    8/31 QIAGEN miScript miRNA Assays for microRNAs that regulate USP6NL (see all 31):
    hsa-miR-142-3p hsa-miR-181c hsa-miR-429 hsa-miR-3942-5p hsa-miR-139-5p hsa-miR-29c hsa-miR-29a hsa-miR-767-5p
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for USP6NL (see all 7)
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    Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ----
    GO:0005097Rab GTPase activator activity IDA17684057


    USP6NL for ontologies           About GeneDecksing



    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
    About This Section

    Unified GeneCards pathways  About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Development HGF signaling pathway
    Development EGFR signaling via small GTPases0.44
    Development_EGFR signaling via small GTPases0.44
    2EGFR1 Signaling Pathway
    EGFR1 Signaling Pathway1.00
    3ErbB1 downstream signaling
    ErbB1 downstream signaling1.00

    Pathway sources
    See GeneCards unified pathways
    Show all pathways

    1 EMD Millipore Pathway for USP6NL
        Development EGFR signaling via small GTPases


    1 GeneGo (Thomson Reuters) Pathway for USP6NL
        Development EGFR signaling via small GTPases

    2 BioSystems Pathways for USP6NL 
        EGFR1 Signaling Pathway
    ErbB1 downstream signaling



    USP6NL for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for USP6NL

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

    5/10 Interacting proteins for USP6NL (Q927382, 3 ENSP000002775754) via UniProtKB, MINT, STRING, and/or I2D (see all 10)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    EPS8Q129292, 3, ENSP000002811724MINT-16848 I2D: score=3 STRING: ENSP00000281172
    ACTN4O437073, ENSP000002526994I2D: score=3 STRING: ENSP00000252699
    ACTA1P681333, ENSP000003556454I2D: score=2 STRING: ENSP00000355645
    GRB2P629933, ENSP000003390074I2D: score=4 STRING: ENSP00000339007
    RAB5AP203393, ENSP000002730474I2D: score=2 STRING: ENSP00000273047
    About this table

    Gene Ontology (GO): 4 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007030Golgi organization IMP17684057
    GO:0008150biological_process ----
    GO:0032851positive regulation of Rab GTPase activity IDA17684057
    GO:0035526retrograde transport, plasma membrane to Golgi IMP17684057


    USP6NL for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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 USP6NL
    Search CenterWatch for drugs/clinical trials and news about USP6NL / US6NL 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    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, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for USP6NL gene (2 alternative transcripts): 
    NM_001080491.2  NM_014688.2  

    Unigene Cluster for USP6NL:

    USP6 N-terminal like
    Hs.498661  [show with all ESTs]
    Unigene Representative Sequence: NM_014688
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000379237 ENST00000535316(uc001ikt.3) ENST00000277575(uc001iks.1)


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    hsa-miR-142-3p hsa-miR-181c hsa-miR-429 hsa-miR-3942-5p hsa-miR-139-5p hsa-miR-29c hsa-miR-29a hsa-miR-767-5p
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat USP6NL
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    Additional cDNA sequence: 

    AB449916.1 AK292944.1 AK311094.1 AK311453.1 BC010351.1 BC042943.2 D13644.1 

    6 DOTS entries:

    DT.120772  DT.101970616  DT.97812422  DT.121268845  DT.409423  DT.206666 

    24/127 AceView cDNA sequences (see all 127):

    BM665965 BM728824 BU735259 AL044885 AA991739 BX094599 AA730063 AA902107 
    BQ073754 AW418528 R41359 BM804096 AA678052 AA741061 AI247011 BU167224 
    BM696742 BC042943 BU742735 W91891 CB128906 AI634722 AA777333 AA700244 

    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™, 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

    USP6NL expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CTAAAAGTAA

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See USP6NL Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for USP6NL

    SOURCE GeneReport for Unigene cluster: Hs.498661

    UniProtKB/Swiss-Prot: US6NL_HUMAN, Q92738
    Tissue specificity: Widely expressed

        SABiosciences Custom PCR Arrays for USP6NL
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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)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for USP6NL gene from 4/21 species (see all 21)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves USP6NL1 USP6 N-terminal like 68.17(n)
    65.37(a)
      419104  NM_001030840.2  NP_001026011.2 
    lizard
    (Anolis carolinensis)
    Reptilia USP6NL6
    --
    62(a)
    1 ↔ 1
    5(5818838-5872291)
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.119362 Transcribed sequence with weak similarity to protein more 76.82(n)    BG727834.1 
    mosquito
    (Anopheles gambiae)
    Insecta AgaP_AGAP0033411 AGAP003341-PB 54.69(n)
    50.7(a)
      1275017  XM_314237.3  XP_314237.3 


    ENSEMBL Gene Tree for USP6NL (if available)
    TreeFam Gene Tree for USP6NL (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for USP6NL gene
    TBC1D3H2  SGSM32  TBC1D2B2  TBC1D3C2  GRTP12  TBC1D10C2  TBC1D10B2  TBC1D32  
    TBC1D3F2  TBC1D262  ENSG000002487512  TBC1D10A2  TBC1D22  TBC1D3G2  TBC1D282  TBC1D3B2  

    USP6NL for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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

    10/2371 NCBI SNPs in USP6NL are shown (see all 2371    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 10 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1481815581,2
    --11502064(+) AGTTAA/CAGGGC 2 -- ds50010--------
    rs112571071,2
    C,F,H,--11502220(+) AAATTA/GCATTT 2 -- ds50017Minor allele frequency- G:0.17EA NS NA 516
    rs1873193351,2
    --11502253(+) TTTTGC/TAATGA 2 -- ds50010--------
    rs1922228731,2
    --11502285(+) TATTAC/TTATTG 2 -- ds50010--------
    rs1473700631,2
    --11502325(+) GACTAC/TGTAGT 2 -- ds50010--------
    rs789573271,2
    C,F,--11502381(+) ACTGTG/AACATA 2 -- ds50011Minor allele frequency- A:0.05NA 120
    rs1427720791,2
    C,--11502563(+) ACAGA-/TTAAAA 2 -- ut310--------
    rs340574081,2
    C--11502564(+) CAGATT/-AAAAA 2 -- ut311Minor allele frequency- -:0.50NA 2
    rs1380389071,2
    --11502580(+) ATAAAC/TGACAT 2 -- ut310--------
    rs1415647411,2
    C,--11502624(+) TTTGC-/ATAT  
      ATATAT
    ATATA
    2 -- ut310--------

    HapMap Linkage Disequilibrium report for USP6NL (11502509 - 11653753 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for USP6NL: --

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing USP6NL
    DNA2.0 Custom Variant and Variant Library Synthesis for USP6NL

    (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.)
    About This Section

    USP6NL for disorders           About GeneDecksing

    OMIM gene information: 605405    OMIM disorders: --

    1 disease for USP6NL:    About MalaCards
    malaria

    Human Genome Epidemiology (HuGE) Navigator: USP6NL (1 document)

    Export disorders for USP6NL 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 USP6NL gene, integrated from 9 sources (see all 29):
    (articles sorted by number of sources associating them with USP6NL)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. RN-tre identifies a family of tre-related proteins displaying a novel potential protein binding domain. (PubMed id 8700515)1, 2, 3 Wong W.T....Matoskova B. (1996)
    2. RN-tre specifically binds to the SH3 domain of eps8 w ith high affinity and confers growth advantage to NIH3T3 upon carboxy-terminal truncation. (PubMed id 8700527)1, 3, 9 MatA^skovA! B....Di Fiore P.P. (1996)
    3. The Eps8 protein coordinates EGF receptor signalling through Rac and trafficking through Rab5. (PubMed id 11099046)1, 2, 9 Lanzetti L.... Di Fiore P.P. (2000)
    4. Identification and characterization of a novel Tre-2/Bub2/Cdc16 (TBC) protein that possesses Rab3A-GAP activity. (PubMed id 19077034)1, 2, 9 Ishibashi K.... Fukuda M. (2009)
    5. Analysis of GTPase-activating proteins: Rab1 and Rab43 are key Rabs required to maintain a functional Golgi complex in human cells. (PubMed id 17684057)1, 2 Haas A.K....Barr F.A. (2007)
    6. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (2006)
    7. Robust phosphoproteomic profiling of tyrosine phosphorylation sites from human T cells using immobilized metal affinity chromatography and tandem mass spectrometry. (PubMed id 15144186)1, 2 Brill L.M....Peters E.C. (2004)
    8. 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. (2004)
    9. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1, 2 Bonaldo M.F.... Soares M.B. (1996)
    10. Prediction of the coding sequences of unidentified human genes. I. The coding sequences of 40 new genes (KIAA0001-KIAA0040) deduced by analysis of randomly sampled cDNA clones from human immature myeloid cell line KG-1. (PubMed id 7584026)1, 2 Nomura N.... Tabata S. (1994)

    (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: 9712 HGNC: 16858 AceView: USP6NL Ensembl:ENSG00000148429 euGenes: HUgn9712
    ECgene: USP6NL H-InvDB: USP6NL

    (According to HUGE)
    About This Section
    HUGE: KIAA0019

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for USP6NL Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for USP6NL gene:
    Search GeneIP for patents involving USP6NL

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



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