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USP6NL USP6 N-terminal like [ Homo sapiens (human) ]

Gene ID: 9712, updated on 2-Nov-2024

Summary

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Official Symbol
USP6NLprovided by HGNC
Official Full Name
USP6 N-terminal likeprovided by HGNC
Primary source
HGNC:HGNC:16858
See related
Ensembl:ENSG00000148429 MIM:605405; AllianceGenome:HGNC:16858
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
RNTRE; TRE2NL; USP6NL-IT1
Summary
Enables GTPase activator activity and small GTPase binding activity. Involved in several processes, including plasma membrane to endosome transport; positive regulation of GTPase activity; and retrograde transport, plasma membrane to Golgi. Located in cytoplasmic vesicle and plasma membrane. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Broad expression in testis (RPKM 11.0), esophagus (RPKM 10.8) and 24 other tissues See more
Orthologs
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Genomic context

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See USP6NL in Genome Data Viewer
Location:
10p14
Exon count:
24
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (11460510..11611650, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (11471921..11623090, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (11502509..11653649, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene CUGBP Elav-like family member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3010 Neighboring gene uncharacterized LOC105376409 Neighboring gene CELF2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2127 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3011 Neighboring gene NANOG hESC enhancer GRCh37_chr10:11482790-11483302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:11485575-11486237 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:11486238-11486901 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3012 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3013 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:11493719-11494219 Neighboring gene uncharacterized LOC105376411 Neighboring gene uncharacterized LOC105376410 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2128 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3014 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3015 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3016 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3017 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2129 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3018 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2130 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3019 Neighboring gene uncharacterized LOC105376413 Neighboring gene USP6NL antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3020 Neighboring gene uncharacterized LOC105376412 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3021 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3022 Neighboring gene VISTA enhancer hs1382 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3023 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3026 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:11726365-11727564 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:11733173-11733674 Neighboring gene CRISPRi-validated cis-regulatory element chr10.454 Neighboring gene Sharpr-MPRA regulatory region 10517 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:11764830-11764971 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2131 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2132 Neighboring gene enoyl-CoA hydratase domain containing 3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. High USP6NL Levels in Breast Cancer Sustain Chronic AKT Phosphorylation and GLUT1 Stability Fueling Aerobic Glycolysis. Avanzato D, et al. Cancer Res, 2018 Jul 1. PMID 29691252
  2. RN-tre identifies a family of tre-related proteins displaying a novel potential protein binding domain. Matòsková B, et al. Oncogene, 1996 Jun 20. PMID 8700515
  3. RN-tre specifically binds to the SH3 domain of eps8 with high affinity and confers growth advantage to NIH3T3 upon carboxy-terminal truncation. Matòsková B, et al. Oncogene, 1996 Jun 20. PMID 8700527
  4. USP6NL mediated by LINC00689/miR-142-3p promotes the development of triple-negative breast cancer. Ma T, et al. BMC Cancer, 2020 Oct 14. PMID 33054738, Free PMC Article
  5. Regulation of the Rab5 GTPase-activating protein RN-tre by the dual specificity phosphatase Cdc14A in human cells. Lanzetti L, et al. J Biol Chem, 2007 May 18. PMID 17371873

See all (65) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. USP6NL mediated by LINC00689/miR-142-3p promotes the development of triple-negative breast cancer.
    Title: USP6NL mediated by LINC00689/miR-142-3p promotes the development of triple-negative breast cancer.
  2. Study reports that USP6NL is overexpressed in breast cancer, mainly of the basal-like/integrative cluster 10 subtype. Increased USP6NL levels were accompanied by gene amplification and were associated with worse prognosis in the METABRIC dataset. High levels of USP6NL in breast cancer cells delayed endocytosis and degradation of the EGFR, causing chronic AKT activation.
    Title: High USP6NL Levels in Breast Cancer Sustain Chronic AKT Phosphorylation and GLUT1 Stability Fueling Aerobic Glycolysis.
  3. Genome-wide significant (GWS) associations in single-nucleotide polymorphism (SNP)-based tests (P < 5 x 10(-8)) were identified for SNPs in PFDN1/HBEGF, USP6NL/ECHDC3, and BZRAP1-AS1.
    Title: Transethnic genome-wide scan identifies novel Alzheimer's disease loci.
  4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  5. RN-tre phosphorylation is critical for efficient hCdc14A association
    Title: Regulation of the Rab5 GTPase-activating protein RN-tre by the dual specificity phosphatase Cdc14A in human cells.
  6. Rab5 signals to the actin cytoskeleton through RN-tre, a previously identified Rab5-specific GTPase-activating protein; RN-tre interacts with both F-actin and actinin-4, an F-actin bundling protein
    Title: Rab5 is a signalling GTPase involved in actin remodelling by receptor tyrosine kinases.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA0019

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables GTPase activator activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables GTPase activator activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables small GTPase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in Golgi organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in plasma membrane to endosome transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in plasma membrane to endosome transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of GTPase activity IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of Golgi organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
NOT involved_in regulation of cilium assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in retrograde transport, plasma membrane to Golgi IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in virion assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytoplasmic vesicle IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasmic vesicle IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in trans-Golgi network membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
USP6 N-terminal-like protein
Names
related to the N-terminus of tre

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001080491.5 → NP_001073960.1  USP6 N-terminal-like protein isoform 2

    See identical proteins and their annotated locations for NP_001073960.1

    Status: VALIDATED

    Source sequence(s)
    AL590416
    Consensus CDS
    CCDS44357.1
    UniProtKB/Swiss-Prot
    Q92738
    Related
    ENSP00000277575.5, ENST00000277575.5
    Conserved Domains (1) summary
    smart00164
    Location:114 → 329
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

  2. NM_001391959.1 → NP_001378888.1  USP6 N-terminal-like protein isoform 3

    Status: VALIDATED

    Source sequence(s)
    AL590416
    Consensus CDS
    CCDS91212.1
    UniProtKB/TrEMBL
    X6RAB3
    Related
    ENSP00000368539.2, ENST00000379237.6
    Conserved Domains (2) summary
    smart00164
    Location:120 → 335
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    PHA03247
    Location:417 → 746
    PHA03247; large tegument protein UL36; Provisional

  3. NM_001391960.1 → NP_001378889.1  USP6 N-terminal-like protein isoform 4

    Status: VALIDATED

    Source sequence(s)
    AL512631, AL590416
    Conserved Domains (2) summary
    smart00164
    Location:48 → 263
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    PHA03247
    Location:345 → 674
    PHA03247; large tegument protein UL36; Provisional

  4. NM_001391961.1 → NP_001378890.1  USP6 N-terminal-like protein isoform 5

    Status: VALIDATED

    Source sequence(s)
    AL512631, AL590416
    Conserved Domains (2) summary
    smart00164
    Location:97 → 310
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    PHA03247
    Location:343 → 672
    PHA03247; large tegument protein UL36; Provisional

  5. NM_014688.5 → NP_055503.1  USP6 N-terminal-like protein isoform 1

    See identical proteins and their annotated locations for NP_055503.1

    Status: VALIDATED

    Source sequence(s)
    AL512631, AL590416
    Consensus CDS
    CCDS53492.1
    UniProtKB/Swiss-Prot
    A8KA79, Q15400, Q5VV10, Q7L0K9, Q92738
    Related
    ENSP00000476462.1, ENST00000609104.6
    Conserved Domains (2) summary
    smart00164
    Location:97 → 312
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cl26464
    Location:394 → 723
    Atrophin-1; Atrophin-1 family

RNA

  1. NR_125732.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks multiple exons and contains an alternate 3' terminal exon, compared to variant 1. This variant is represented as non-coding because it lacks almost the entire coding region found in variant 1.
    Source sequence(s)
    AA741061, BC010351
    Related
    ENST00000606752.1

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    11460510..11611650 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024448263.2 → XP_024304031.1  USP6 N-terminal-like protein isoform X4

    Conserved Domains (2) summary
    smart00164
    Location:18 → 233
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cl26464
    Location:315 → 644
    Atrophin-1; Atrophin-1 family

  2. XM_006717542.4 → XP_006717605.1  USP6 N-terminal-like protein isoform X1

    See identical proteins and their annotated locations for XP_006717605.1

    Conserved Domains (1) summary
    smart00164
    Location:125 → 340
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

  3. XM_017016971.2 → XP_016872460.1  USP6 N-terminal-like protein isoform X2

  4. XM_047426036.1 → XP_047281992.1  USP6 N-terminal-like protein isoform X1

  5. XM_011519762.3 → XP_011518064.1  USP6 N-terminal-like protein isoform X1

    See identical proteins and their annotated locations for XP_011518064.1

    Conserved Domains (1) summary
    smart00164
    Location:125 → 340
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

  6. XM_047426037.1 → XP_047281993.1  USP6 N-terminal-like protein isoform X3

    UniProtKB/Swiss-Prot
    A8KA79, Q15400, Q5VV10, Q7L0K9, Q92738

  7. XM_047426038.1 → XP_047281994.1  USP6 N-terminal-like protein isoform X5

  8. XM_011519763.3 → XP_011518065.1  USP6 N-terminal-like protein isoform X5

    See identical proteins and their annotated locations for XP_011518065.1

    Conserved Domains (1) summary
    smart00164
    Location:1 → 156
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    11471921..11623090 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054367237.1 → XP_054223212.1  USP6 N-terminal-like protein isoform X4

  2. XM_054367233.1 → XP_054223208.1  USP6 N-terminal-like protein isoform X1

  3. XM_054367232.1 → XP_054223207.1  USP6 N-terminal-like protein isoform X1

  4. XM_054367235.1 → XP_054223210.1  USP6 N-terminal-like protein isoform X2

  5. XM_054367234.1 → XP_054223209.1  USP6 N-terminal-like protein isoform X1

  6. XM_054367236.1 → XP_054223211.1  USP6 N-terminal-like protein isoform X3

    UniProtKB/Swiss-Prot
    A8KA79, Q15400, Q5VV10, Q7L0K9, Q92738

  7. XM_054367239.1 → XP_054223214.1  USP6 N-terminal-like protein isoform X5

  8. XM_054367238.1 → XP_054223213.1  USP6 N-terminal-like protein isoform X5

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q92738.3 GenPept UniProtKB/Swiss-Prot:Q92738

Gene LinkOut

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