Aliases for USP6NL Gene

Aliases for USP6NL Gene

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

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. Diseases associated with USP6NL include Nipah Virus Encephalitis. Among its related pathways are Retrograde transport at the Trans-Golgi-Network and Vesicle-mediated transport. Gene Ontology (GO) annotations related to this gene include GTPase activator activity and Rab GTPase binding. An important paralog of this gene is TBC1D3B.

UniProtKB/Swiss-Prot Summary 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 , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for USP6NL Gene

Genomics for USP6NL Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for USP6NL Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH10J011606 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 260.4 +1.8 1759 6.4 BCLAF1 IKZF1 ZNF600 MYC NCOR1 ZNF592 ATF2 POLR2A NFIC YY1 USP6NL USP6NL-AS1 lnc-UPF2-5 ECHDC3 piR-60349 HSALNG0076166
GH10J011531 Promoter/Enhancer 1.3 Ensembl ENCODE dbSUPER 17.3 +78.6 78611 2.9 IKZF1 CEBPA ATF3 YY1 CEBPB CTCF FOXA2 RXRA TEAD3 ZBTB33 USP6NL ECHDC3 HSALNG0076166 USP6NL-AS1
GH10J011551 Enhancer 1.2 Ensembl ENCODE dbSUPER 17.8 +60.1 60053 7.4 BCLAF1 NCOR1 JUND FEZF1 MBD2 ZNF341 EP300 MAFF SAP130 ZNF316 USP6NL ECHDC3 UPF2 HSALNG0076166 USP6NL-AS1
GH10J011681 Promoter/Enhancer 1.7 Ensembl ENCODE CraniofacialAtlas dbSUPER 12.1 -74.2 -74155 9.5 BCLAF1 NCOR1 MYC ZNF600 IKZF1 JUND ZNF580 ZNF592 POLR2A CEBPA piR-31534-047 ENSG00000228302 ECHDC3 USP6NL ENSG00000271046 LOC105376413 piR-32285-009 HSALNG0076175 HSALNG0076170
GH10J011578 Enhancer 1.1 Ensembl ENCODE dbSUPER 18 +32.8 32843 2.2 BCLAF1 IKZF1 ZMYM3 CEBPA BCL11A MAFF SMAD4 SAP130 IRF4 THRB USP6NL lnc-UPF2-5 USP6NL-AS1 HSALNG0076166
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around USP6NL on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for USP6NL

Top Transcription factor binding sites by QIAGEN in the USP6NL gene promoter:
  • AML1a
  • ATF-2
  • Cart-1
  • FOXJ2
  • FOXJ2 (long isoform)
  • Gfi-1
  • IRF-1
  • p53
  • TBP

Genomic Locations for USP6NL Gene

Latest Assembly
chr10:11,453,946-11,611,754
(GRCh38/hg38)
Size:
157,809 bases
Orientation:
Minus strand

Previous Assembly
chr10:11,495,945-11,653,649
(GRCh37/hg19 by Entrez Gene)
Size:
157,705 bases
Orientation:
Minus strand

chr10:11,495,945-11,653,753
(GRCh37/hg19 by Ensembl)
Size:
157,809 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=Extended N-terminus.; 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

Antibodies for research

No data available for DME Specific Peptides for USP6NL Gene

Domains & Families for USP6NL Gene

Gene Families for USP6NL Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for USP6NL Gene

InterPro:
Blocks:
  • RabGAP/TBC domain

Suggested Antigen Peptide Sequences for USP6NL Gene

GenScript: Design optimal peptide antigens:
  • USP6NL protein (Q96FW8_HUMAN)
  • Related to the N-terminus of tre (US6NL_HUMAN)
genes like me logo Genes that share domains with USP6NL: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot 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.

Phenotypes From GWAS Catalog for USP6NL Gene

Gene Ontology (GO) - Molecular Function for USP6NL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005096 GTPase activator activity IBA,IDA 17562788
GO:0031267 small GTPase binding IPI 17562788
genes like me logo Genes that share ontologies with USP6NL: view
genes like me logo Genes that share phenotypes with USP6NL: view

Animal Models for USP6NL Gene

MGI Knock Outs for USP6NL:

miRNA for USP6NL Gene

miRTarBase miRNAs that target USP6NL

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for USP6NL

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , 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
golgi apparatus 5
cytosol 4
nucleus 3
endosome 2
extracellular 1
cytoskeleton 1
endoplasmic reticulum 1
lysosome 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:0031410 cytoplasmic vesicle IBA,IDA 17684057
GO:0032588 trans-Golgi network membrane TAS --
genes like me logo Genes that share ontologies with USP6NL: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for USP6NL Gene

Pathways & Interactions for USP6NL Gene

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

Pathways by source for USP6NL Gene

1 GeneGo (Thomson Reuters) pathway for USP6NL Gene
  • Development EGFR signaling via small GTPases

Gene Ontology (GO) - Biological Process for USP6NL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006886 intracellular protein transport IBA 21873635
GO:0007030 Golgi organization IMP 17684057
GO:0019068 virion assembly IMP 21680502
GO:0035526 retrograde transport, plasma membrane to Golgi IMP 17684057
GO:0043547 positive regulation of GTPase activity IDA 17562788
genes like me logo Genes that share ontologies with USP6NL: view

No data available for SIGNOR curated interactions for USP6NL Gene

Drugs & Compounds for USP6NL Gene

No Compound Related Data Available

Transcripts for USP6NL Gene

mRNA/cDNA for USP6NL Gene

5 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for USP6NL

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

No ASD Table

Relevant External Links for USP6NL Gene

GeneLoc Exon Structure 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, MaxQB, and MOPED for USP6NL Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for 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.

Evidence on tissue expression from TISSUES for USP6NL Gene

  • Nervous system(4.3)
  • Bone marrow(4.2)
  • Liver(4.2)
genes like me logo Genes that share expression patterns with USP6NL: view

Primer products for research

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 29 30
  • 99.33 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia USP6NL 29 30
  • 84.25 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia USP6NL 29 30
  • 82.08 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Usp6nl 29
  • 81.4 (n)
Mouse
(Mus musculus)
Mammalia Usp6nl 29 16 30
  • 81.37 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia USP6NL 30
  • 75 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia USP6NL 30
  • 70 (a)
OneToOne
Chicken
(Gallus gallus)
Aves USP6NL 30
  • 63 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia USP6NL 30
  • 62 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia usp6nl 29
  • 77.74 (n)
Zebrafish
(Danio rerio)
Actinopterygii usp6nl 30
  • 48 (a)
OneToOne
Dr.11936 29
Fruit Fly
(Drosophila melanogaster)
Insecta RN-tre 30
  • 33 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea tbc-17 30
  • 20 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 56 (a)
OneToMany
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.3242 29
Species where no ortholog for USP6NL was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
Aminode:
Evolutionary constrained regions (ECRs) for USP6NL: view image
Alliance of Genome Resources:
Additional Orthologs for USP6NL

Paralogs for USP6NL Gene

Variants for USP6NL Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for USP6NL Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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)

Additional Variant Information for USP6NL Gene

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

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for USP6NL Gene

Disorders for USP6NL Gene

MalaCards: The human disease database

(1) MalaCards diseases for USP6NL Gene - From: COP

Disorder Aliases PubMed IDs
nipah virus encephalitis
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for USP6NL

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with USP6NL: view

No data available for 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 to cells : devoted to molecular & cellular mechanisms 2009) 3 4 22
  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 MM (The Journal of biological chemistry 2002) 2 3 22
  3. The Eps8 protein coordinates EGF receptor signalling through Rac and trafficking through Rab5. (PMID: 11099046) Lanzetti L … Di Fiore PP (Nature 2000) 3 4 22
  4. RN-tre identifies a family of tre-related proteins displaying a novel potential protein binding domain. (PMID: 8700515) Matòsková B … Di Fiore PP (Oncogene 1996) 2 3 4
  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) Matòsková B … Di Fiore PP (Oncogene 1996) 2 3 22

Products for USP6NL Gene

Sources for USP6NL Gene