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
  • USP6NL Intronic Transcript 1 (Non-Protein Coding) 2
  • Related To The N Terminus Of Tre 2
  • 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 Development EGFR signaling via small GTPases 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 TBC1D3K.

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

Additional gene information 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 for USP6NL Gene

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 510.4 +1.8 1794 6.4 EP300 HNRNPK ZNF217 MYC POLR2G USF1 GTF2E2 PHF8 PHB2 ZFX USP6NL LOC107984208 ECHDC3 CELF2 piR-60349 lnc-UPF2-5
GH10J011531 Promoter/Enhancer 1.3 Ensembl ENCODE dbSUPER 17.3 +78.6 78646 2.9 CTCF TEAD1 FOXA2 NR2F2 CEBPB ZBTB17 CEBPG YY1 ZBTB33 JUND USP6NL ECHDC3 LOC105376410 lnc-UPF2-5
GH10J011551 Enhancer 1.2 Ensembl ENCODE dbSUPER 17.8 +60.1 60088 7.4 JUND FOS MEF2C RCOR1 JUN ZNF341 OSR2 NCOR1 MBD2 ZNF316 USP6NL ECHDC3 UPF2 lnc-UPF2-5 LOC105376410
GH10J011586 Enhancer 1.2 Ensembl ENCODE dbSUPER 17.3 +21.1 21088 11 ZNF217 KDM6A TCF7 REST CUX1 ZBTB25 CTBP1 ZNF341 NCOR1 ZNF316 USP6NL ECHDC3 lnc-UPF2-5 LOC107984208
GH10J011578 Enhancer 1.1 Ensembl ENCODE dbSUPER 18 +32.8 32788 2.4 RELA MEF2C RCOR1 RBM25 BCL11A TCF12 FOXA2 ZNF316 CBFB ZNF384 USP6NL lnc-UPF2-5 LOC107984208
- 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 UCSC Golden Path with GeneCards custom track

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

Genomic Locations for USP6NL Gene
chr10:11,453,946-11,611,789
(GRCh38/hg38)
Size:
157,844 bases
Orientation:
Minus strand
chr10:11,495,945-11,653,753
(GRCh37/hg19)
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

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

Blocks:
  • RabGAP/TBC domain
InterPro:
ProtoNet:

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 IDA 17562788
GO:0017137 Rab 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:

Animal Model Products

CRISPR Products

miRNA for USP6NL Gene

miRTarBase miRNAs that target USP6NL

Inhibitory RNA Products

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

Clone Products

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

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

CRISPR Products

Inhibitory RNA Products

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

Clone 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

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

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

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 31 30
  • 99.33 (n)
OneToOne
dog
(Canis familiaris)
Mammalia USP6NL 31 30
  • 84.25 (n)
OneToOne
cow
(Bos Taurus)
Mammalia USP6NL 31 30
  • 82.08 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Usp6nl 30
  • 81.4 (n)
mouse
(Mus musculus)
Mammalia Usp6nl 17 31 30
  • 81.37 (n)
oppossum
(Monodelphis domestica)
Mammalia USP6NL 31
  • 75 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia USP6NL 31
  • 70 (a)
OneToOne
chicken
(Gallus gallus)
Aves USP6NL 31
  • 63 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia USP6NL 31
  • 62 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia usp6nl 30
  • 77.74 (n)
zebrafish
(Danio rerio)
Actinopterygii usp6nl 31
  • 48 (a)
OneToOne
Dr.11936 30
fruit fly
(Drosophila melanogaster)
Insecta RN-tre 31
  • 33 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea tbc-17 31
  • 20 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 56 (a)
OneToMany
Cin.3242 30
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3242 30
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)
Aminode:
Evolutionary constrained regions (ECRs) for USP6NL: view image

Paralogs for USP6NL Gene

Variants for USP6NL Gene

Additional dbSNP identifiers (rs#s) for USP6NL Gene

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

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

Additional Disease Information for USP6NL

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

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 to cells : devoted to molecular & cellular mechanisms 2009) 3 4 23 54
  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 23 54
  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 23 54
  4. 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 23 54
  5. 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 54

Products for USP6NL Gene

Sources for USP6NL Gene