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Aliases for USP6NL Gene

Aliases for USP6NL Gene

  • USP6 N-Terminal Like 2 3 5
  • Related To The N-Terminus Of Tre 3 4
  • USP6NL Intronic Transcript 1 (Non-Protein Coding) 2
  • Related To The N Terminus Of Tre 2
  • USP6 N-Terminal-Like Protein 3
  • USP6NL-IT1 3
  • KIAA0019 4
  • TRE2NL 3
  • RN-Tre 4
  • RNTRE 3

External Ids for USP6NL Gene

Previous HGNC Symbols for USP6NL Gene

  • USP6NL-IT1

Previous GeneCards Identifiers for USP6NL Gene

  • GC10M011506
  • GC10M011542
  • GC10M011502

Summaries for USP6NL Gene

GeneCards Summary for USP6NL Gene

USP6NL (USP6 N-Terminal Like) is a Protein Coding gene. Among its related pathways are Vesicle-mediated transport and EGFR1 Signaling Pathway. GO annotations related to this gene include GTPase activator activity and Rab GTPase binding. An important paralog of this gene is TBC1D3.

UniProtKB/Swiss-Prot for USP6NL Gene

  • 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

No data available for Entrez Gene Summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for USP6NL Gene

Genomics for USP6NL Gene

Regulatory Elements for USP6NL Gene

Enhancers for USP6NL Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH10F011559 1.3 Ensembl ENCODE 17.6 +51.1 51136 1.7 MLX ARID4B FEZF1 ZNF2 CBX5 ZNF207 FOS SP3 SP5 JUNB USP6NL GC10P011559 ENSG00000271360
GH10F011531 1.1 Ensembl ENCODE 17.2 +78.6 78647 2.9 SOX13 CTCF ETV1 CEBPG RAD21 TEAD3 ZNF664 EED SCRT2 HNF4G USP6NL ECHDC3 GC10P011559 GC10M011466
GH10F011606 1.7 FANTOM5 Ensembl ENCODE 10.5 +1.8 1794 6.4 HDGF PKNOX1 ARNT CREB3L1 WRNIP1 ZFP64 SIN3A YBX1 FEZF1 ZNF2 ECHDC3 USP6NL CELF2 ENSG00000271360 GC10P011559
GH10F011681 1.4 Ensembl ENCODE 12.1 -74.1 -74121 9.5 HDGF PKNOX1 ARNT CREB3L1 WRNIP1 ARID4B SIN3A FEZF1 ZNF2 ZNF766 ECHDC3 USP6NL ENSG00000271046 LOC105376413
GH10F011527 0.9 Ensembl ENCODE 17 +83.2 83189 2.0 OSR2 ZNF362 IRF2 ZNF316 ATF3 CEBPB ZBTB33 IRF1 PRDM1 USP6NL ECHDC3 GC10M011466 GC10P011559
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around USP6NL on UCSC Golden Path with GeneCards custom track

Promoters for USP6NL Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000218672 489 2601 HDGF PKNOX1 ARNT CREB3L1 ZFP64 SIN3A FEZF1 ZNF2 YY1 ZNF143

Genomic Location for USP6NL Gene

Chromosome:
10
Start:
11,453,946 bp from pter
End:
11,611,789 bp from pter
Size:
157,844 bases
Orientation:
Minus strand

Genomic View for USP6NL Gene

Genes around USP6NL on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
USP6NL Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for USP6NL Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for USP6NL Gene

Proteins for USP6NL Gene

  • Protein details for USP6NL Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q92738-US6NL_HUMAN
    Recommended name:
    USP6 N-terminal-like protein
    Protein Accession:
    Q92738
    Secondary Accessions:
    • A8KA79
    • Q15400
    • Q5VV10
    • Q7L0K9

    Protein attributes for USP6NL Gene

    Size:
    828 amino acids
    Molecular mass:
    94104 Da
    Quaternary structure:
    • Interacts with EPS8.
    SequenceCaution:
    • Sequence=BAA02807.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for USP6NL Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for USP6NL Gene

Post-translational modifications for USP6NL Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • Abcam antibodies for USP6NL
  • Cloud-Clone Corp. Antibodies for USP6NL

No data available for DME Specific Peptides for USP6NL Gene

Domains & Families for USP6NL Gene

Protein Domains for USP6NL Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for USP6NL Gene

Graphical View of Domain Structure for InterPro Entry

Q92738

UniProtKB/Swiss-Prot:

US6NL_HUMAN :
  • Contains 1 Rab-GAP TBC domain.
Domain:
  • Contains 1 Rab-GAP TBC domain.
genes like me logo Genes that share domains with USP6NL: view

No data available for Gene Families for USP6NL Gene

Function for USP6NL Gene

Molecular function for USP6NL Gene

UniProtKB/Swiss-Prot 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) - Molecular Function for USP6NL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005096 GTPase activator activity IDA 17562788
GO:0017137 Rab GTPase binding IPI 17562788
genes like me logo Genes that share ontologies with USP6NL: view

Phenotypes for USP6NL Gene

genes like me logo Genes that share phenotypes with USP6NL: view

Animal Model Products

miRNA for USP6NL Gene

miRTarBase miRNAs that target USP6NL

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for USP6NL Gene

Localization for USP6NL Gene

Subcellular locations from UniProtKB/Swiss-Prot for USP6NL Gene

Golgi apparatus. Cytoplasmic vesicle.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for USP6NL gene
Compartment Confidence
plasma membrane 5
cytosol 5
golgi apparatus 5
nucleus 3
endosome 1

Gene Ontology (GO) - Cellular Components for USP6NL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005794 Golgi apparatus IEA --
GO:0005829 cytosol TAS --
GO:0005886 plasma membrane IDA 17562788
GO:0012505 endomembrane system IBA --
GO:0031410 cytoplasmic vesicle IEA,IDA 17684057
genes like me logo Genes that share ontologies with USP6NL: view

Pathways & Interactions for USP6NL Gene

genes like me logo Genes that share pathways with USP6NL: view

Pathways by source for USP6NL Gene

Gene Ontology (GO) - Biological Process for USP6NL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006886 intracellular protein transport IBA --
GO:0007030 Golgi organization IMP 17684057
GO:0019068 virion assembly IMP 21680502
GO:0031338 regulation of vesicle fusion IBA --
GO:0035526 retrograde transport, plasma membrane to Golgi IMP 17684057
genes like me logo Genes that share ontologies with USP6NL: view

No data available for SIGNOR curated interactions for USP6NL Gene

Transcripts for USP6NL Gene

Unigene Clusters for USP6NL Gene

USP6 N-terminal like:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for USP6NL Gene

No ASD Table

Relevant External Links for USP6NL Gene

GeneLoc Exon Structure for
USP6NL
ECgene alternative splicing isoforms for
USP6NL

Expression for USP6NL Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for USP6NL Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for USP6NL Gene

This gene is overexpressed in Esophagus - Mucosa (x4.2).

Protein differential expression in normal tissues from HIPED for USP6NL Gene

This gene is overexpressed in Placenta (32.9), Bone marrow stromal cell (18.3), and Blymphocyte (7.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for USP6NL Gene



NURSA nuclear receptor signaling pathways regulating expression of USP6NL Gene:

USP6NL

SOURCE GeneReport for Unigene cluster for USP6NL Gene:

Hs.498661

mRNA Expression by UniProt/SwissProt for USP6NL Gene:

Q92738-US6NL_HUMAN
Tissue specificity: Widely expressed.
genes like me logo Genes that share expression patterns with USP6NL: view

Primer Products

No data available for Protein tissue co-expression partners for USP6NL Gene

Orthologs for USP6NL Gene

This gene was present in the common ancestor of animals.

Orthologs for USP6NL Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia USP6NL 34 35
  • 99.33 (n)
dog
(Canis familiaris)
Mammalia USP6NL 34 35
  • 84.25 (n)
cow
(Bos Taurus)
Mammalia USP6NL 34 35
  • 82.08 (n)
rat
(Rattus norvegicus)
Mammalia Usp6nl 34
  • 81.4 (n)
mouse
(Mus musculus)
Mammalia Usp6nl 34 16 35
  • 81.37 (n)
oppossum
(Monodelphis domestica)
Mammalia USP6NL 35
  • 75 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia USP6NL 35
  • 70 (a)
OneToOne
chicken
(Gallus gallus)
Aves USP6NL 35
  • 63 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia USP6NL 35
  • 62 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia usp6nl 34
  • 77.74 (n)
zebrafish
(Danio rerio)
Actinopterygii usp6nl 35
  • 48 (a)
OneToOne
Dr.11936 34
fruit fly
(Drosophila melanogaster)
Insecta RN-tre 35
  • 33 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea tbc-17 35
  • 20 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 56 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3242 34
Species where no ortholog for USP6NL was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for USP6NL Gene

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

Paralogs for USP6NL Gene

Variants for USP6NL Gene

Sequence variations from dbSNP and Humsavar for USP6NL Gene

SNP ID Clin Chr 10 pos Sequence Context AA Info Type
rs10008 -- 11,564,296(+) TAATT(C/T)CAAGT intron-variant, nc-transcript-variant
rs1025900 -- 11,465,651(+) ACCGT(A/G)CTGGC intron-variant
rs10508422 -- 11,471,243(+) AGGAA(C/T)TGGAA intron-variant
rs10508423 -- 11,503,527(+) TTAAA(A/C)ATCAG intron-variant
rs10508424 -- 11,525,272(+) ATATT(A/G)TAAGA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for USP6NL Gene

Variant ID Type Subtype PubMed ID
dgv175e212 CNV loss 25503493
dgv363n106 CNV deletion 24896259
dgv364n106 CNV deletion 24896259
esv2658637 CNV deletion 23128226
esv2732984 CNV deletion 23290073
esv2732995 CNV deletion 23290073
esv3578632 CNV loss 25503493
esv3622339 CNV loss 21293372
nsv1040713 CNV loss 25217958
nsv24455 CNV insertion 16902084
nsv831784 CNV gain 17160897

Variation tolerance for USP6NL Gene

Residual Variation Intolerance Score: 20.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.25; 40.39% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for USP6NL Gene

Human Gene Mutation Database (HGMD)
USP6NL
SNPedia medical, phenotypic, and genealogical associations of SNPs for
USP6NL

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for USP6NL Gene

Disorders for USP6NL Gene

Relevant External Links for USP6NL

Genetic Association Database (GAD)
USP6NL
Human Genome Epidemiology (HuGE) Navigator
USP6NL
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
USP6NL

No disorders were found for USP6NL Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for USP6NL Gene

Publications for USP6NL Gene

  1. Identification and characterization of a novel Tre-2/Bub2/Cdc16 (TBC) protein that possesses Rab3A-GAP activity. (PMID: 19077034) Ishibashi K. … Fukuda M. (Genes Cells 2009) 3 4 22 64
  2. Endocytosis of epidermal growth factor receptor regulated by Grb2-mediated recruitment of the Rab5 GTPase-activating protein RN-tre. (PMID: 12399475) Martinu L. … Chou M.M. (J. Biol. Chem. 2002) 2 3 22 64
  3. The Eps8 protein coordinates EGF receptor signalling through Rac and trafficking through Rab5. (PMID: 11099046) Lanzetti L. … Di Fiore P.P. (Nature 2000) 3 4 22 64
  4. RN-tre identifies a family of tre-related proteins displaying a novel potential protein binding domain. (PMID: 8700515) Wong W.T. … Matoskova B. (Oncogene 1996) 2 3 4 64
  5. RN-tre specifically binds to the SH3 domain of eps8 with high affinity and confers growth advantage to NIH3T3 upon carboxy-terminal truncation. (PMID: 8700527) MatA^skovA! B. … Di Fiore P.P. (Oncogene 1996) 2 3 22 64

Products for USP6NL Gene

Sources for USP6NL Gene

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