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

Gene ID: 9712, updated on 1-Jun-2020

Summary

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
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
Expression
Broad expression in testis (RPKM 11.0), esophagus (RPKM 10.8) and 24 other tissues See more
Orthologs

Genomic context

See USP6NL in Genome Data Viewer
Location:
10p14
Exon count:
23
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 10 NC_000010.11 (11453946..11611789, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (11502509..11653679, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene CUGBP Elav-like family member 2 Neighboring gene uncharacterized LOC105376409 Neighboring gene CELF2 antisense RNA 1 Neighboring gene uncharacterized LOC105376411 Neighboring gene uncharacterized LOC105376410 Neighboring gene uncharacterized LOC107984208 Neighboring gene uncharacterized LOC105376413 Neighboring gene uncharacterized LOC105376412 Neighboring gene VISTA enhancer hs1382 Neighboring gene CRISPRi-validated cis-regulatory element chr10.454

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0019

Gene Ontology Provided by GOA

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

General protein information

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

NCBI Reference Sequences (RefSeq)

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_001080491.3NP_001073960.1  USP6 N-terminal-like protein isoform 2

    See identical proteins and their annotated locations for NP_001073960.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a longer and distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AL590416, BC042943, CF121539
    Consensus CDS
    CCDS44357.1
    UniProtKB/Swiss-Prot
    Q92738
    Related
    ENSP00000277575.5, ENST00000277575.5
    Conserved Domains (1) summary
    smart00164
    Location:114329
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
  2. NM_014688.4NP_055503.1  USP6 N-terminal-like protein isoform 1

    See identical proteins and their annotated locations for NP_055503.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the shorter isoform (1).
    Source sequence(s)
    AL512631, AL590416
    Consensus CDS
    CCDS53492.1
    UniProtKB/Swiss-Prot
    Q92738
    Related
    ENSP00000476462.1, ENST00000609104.5
    Conserved Domains (2) summary
    smart00164
    Location:97312
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cl26464
    Location:394723
    Atrophin-1; Atrophin-1 family

RNA

  1. NR_125732.1 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, HY012494
    Related
    ENST00000606752.1

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p13 Primary Assembly

    Range
    11453946..11611789 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006717542.3XP_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:125340
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
  2. XM_017016973.1XP_016872462.1  USP6 N-terminal-like protein isoform X5

    UniProtKB/TrEMBL
    X6RAB3
    Related
    ENSP00000368539.2, ENST00000379237.6
  3. XM_024448263.1XP_024304031.1  USP6 N-terminal-like protein isoform X3

    Conserved Domains (2) summary
    smart00164
    Location:18233
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cl26464
    Location:315644
    Atrophin-1; Atrophin-1 family
  4. XM_011519762.2XP_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:125340
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
  5. XM_011519763.2XP_011518065.1  USP6 N-terminal-like protein isoform X4

    See identical proteins and their annotated locations for XP_011518065.1

    Conserved Domains (1) summary
    smart00164
    Location:1156
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
  6. XM_017016972.1XP_016872461.1  USP6 N-terminal-like protein isoform X4

    Conserved Domains (1) summary
    smart00164
    Location:1156
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
  7. XM_017016971.1XP_016872460.1  USP6 N-terminal-like protein isoform X2

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