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

USP6NL Gene

protein-coding   GIFtS: 54
GCID: GC10M011502

USP6 N-Terminal Like

(Previous name: USP6NL intronic transcript 1 (non-protein coding))
(Previous symbol: USP6NL-IT1)
  Search for USP6NL
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
USP6 N-Terminal Like1 2     RN-tre2 3
USP6NL-IT11 2     RNTRE2 5
USP6NL Intronic Transcript 1 (Non-Protein Coding)1 2     TRE2NL2
Related To The N Terminus Of Tre1 2     USP6 N-Terminal-Like Protein2
Related To The N-Terminus Of Tre2 3     KIAA00193

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

GeneCards Summary for USP6NL Gene: 
USP6NL (USP6 N-terminal like) is a protein-coding gene. Among its related super-pathways are Development HGF signaling pathway. GO annotations related to this gene include Rab GTPase activator activity. An important paralog of this gene is TBC1D3H.

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 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000010.10  NT_008705.16  NC_018921.2  
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 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: 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

Explore proteomics data for USP6NL at MOPED 

Post-translational modifications:

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

  • USP6NL Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    USP6NL Protein Expression
    REFSEQ proteins (2 alternative transcripts): 
    NP_001073960.1  NP_055503.1  

    ENSEMBL proteins: 
     ENSP00000368539   ENSP00000277575  

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    Cloud-Clone Corp. Proteins for USP6NL 

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

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

    USP6NL for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    1 InterPro protein domain:
     IPR000195 Rab-GTPase-TBC_dom

    Graphical View of Domain Structure for InterPro Entry Q92738

    ProtoNet protein and cluster: Q92738

    1 Blocks protein domain: IPB000195 RabGAP/TBC domain

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


    USP6NL 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: 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 Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005097Rab GTPase activator activity IDA17684057
         
    USP6NL for ontologies           About GeneDecksing


    Animal Models:
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    (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

    SuperPaths for USP6NL About                                                                                                See pathways by source

    SuperPathContained pathways About
    1Development HGF signaling pathway
    Development EGFR signaling via small GTPases0.44
    2EGFR1 Signaling Pathway
    EGFR1 Signaling Pathway
    3ErbB1 downstream signaling
    ErbB1 downstream signaling

    Pathways by source                                                                                                                                                                 See SuperPaths
    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:0032313regulation of Rab GTPase activity ----
    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, 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 USP6NL (US6NL)

    Search CenterWatch for drugs/clinical trials and news about USP6NL / US6NL

    (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,
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    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
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000379237 ENST00000443016(uc001iku.3) ENST00000606752 ENST00000277575(uc001iks.1)

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    Additional mRNA 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):

    AW418528 AA678052 BU167224 AA991739 BM728824 BM665965 BU742735 AA730063 
    W91891 BU735259 AA777333 AA902107 AL044885 AA700244 CB128906 BC042943 
    AI634722 BQ639385 BM804096 F08834 AA741061 R41359 AI247011 BM696742 

    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 <intensity>2/3
    CGAP TAG: CTAAAAGTAA
    USP6NL 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

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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 6/15 species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Usp6nl1 , 5 USP6 N-terminal like1, 5 81.37(n)1
    82.17(a)1
      2 (3.63 cM)5
    989101  NM_181399.31  NP_852064.21 
     63226675 
    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
    Uncharacterized protein
    62(a)
    1 ↔ 1
    5(5818838-5967484)
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.119362 Transcribed sequence with weak similarity to protein more 76.82(n)    BG727834.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta RN-tre6
    tre oncogene-related protein
    30(a)
    1 → many
    2R(9872320-9878215)
    worm
    (Caenorhabditis elegans)
    Secernentea tbc-176
    Protein TBC-17, isoform a
    18(a)
    1 → many
    II(12694410-12725483)


    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  TBC1D3F2  TBC1D32  TBC1D262  ENSG000002487512  TBC1D3C2  GRTP12  TBC1D10C2  
    TBC1D10A2  TBC1D3G2  TBC1D10B2  TBC1D282  TBC1D3B2  

    USP6NL 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

    10/2519 SNPs in USP6NL are shown (see all 2519)    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
    rs1380389071,2
    --11502580(+) ATAAAC/TGACAT 2 -- ut310--------
    rs1996141211,2
    --11502650(+) TATAT-/ATATAA
            
    AAATC
    2 -- cds10--------
    rs34891,2
    H--11502838(+) CTGCAT/ACAACA 2 -- ut314Minor allele frequency- A:0.00NS EA 418
    rs70835931,2
    C,F,H--11502873(+) GTTTGC/TGTTTC 2 -- ut31 ese35Minor allele frequency- T:0.01NS EA WA 516

    HapMap Linkage Disequilibrium report for USP6NL (11502509 - 11653753 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for USP6NL:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2658637CNV Deletion23128226
    esv2732995CNV Deletion23290073
    esv2732984CNV Deletion23290073
    nsv24455CNV Insertion16902084
    nsv831784CNV Gain17160897

    SABiosciences Cancer Mutation PCR Assays
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    (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

    USP6NL for disorders           About MalaCards
    OMIM gene information: 605405    OMIM disorders: --


    USP6NL for disorders           About GeneDecksing

    Genetic Association Database (GAD): USP6NL
    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 32):
    (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. Endocytosis of epidermal growth factor receptor regulated by Grb2-mediated recruitment of the Rab5 GTPase-activating protein RN-tre. (PubMed id 12399475)1, 3, 9 Martinu L....Chou M.M. (2002)
    3. 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)
    4. 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)
    5. 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)
    6. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (2010)
    7. 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)
    8. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (2006)
    9. 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)
    10. 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)

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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:
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