LOCUS       NM_014688               4709 bp    mRNA    linear   PRI 08-APR-2024
DEFINITION  Homo sapiens USP6 N-terminal like (USP6NL), transcript variant 1,
            mRNA.
ACCESSION   NM_014688
VERSION     NM_014688.5
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 4709)
  AUTHORS   Ma,T., Liu,H., Liu,Y., Liu,T., Wang,H., Qiao,F., Song,L. and
            Zhang,L.
  TITLE     USP6NL mediated by LINC00689/miR-142-3p promotes the development of
            triple-negative breast cancer
  JOURNAL   BMC Cancer 20 (1), 998 (2020)
   PUBMED   33054738
  REMARK    GeneRIF: USP6NL mediated by LINC00689/miR-142-3p promotes the
            development of triple-negative breast cancer.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 4709)
  AUTHORS   Avanzato,D., Pupo,E., Ducano,N., Isella,C., Bertalot,G., Luise,C.,
            Pece,S., Bruna,A., Rueda,O.M., Caldas,C., Di Fiore,P.P., Sapino,A.
            and Lanzetti,L.
  TITLE     High USP6NL Levels in Breast Cancer Sustain Chronic AKT
            Phosphorylation and GLUT1 Stability Fueling Aerobic Glycolysis
  JOURNAL   Cancer Res 78 (13), 3432-3444 (2018)
   PUBMED   29691252
  REMARK    GeneRIF: 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.
REFERENCE   3  (bases 1 to 4709)
  AUTHORS   Jun,G.R., Chung,J., Mez,J., Barber,R., Beecham,G.W., Bennett,D.A.,
            Buxbaum,J.D., Byrd,G.S., Carrasquillo,M.M., Crane,P.K.,
            Cruchaga,C., De Jager,P., Ertekin-Taner,N., Evans,D., Fallin,M.D.,
            Foroud,T.M., Friedland,R.P., Goate,A.M., Graff-Radford,N.R.,
            Hendrie,H., Hall,K.S., Hamilton-Nelson,K.L., Inzelberg,R.,
            Kamboh,M.I., Kauwe,J.S.K., Kukull,W.A., Kunkle,B.W., Kuwano,R.,
            Larson,E.B., Logue,M.W., Manly,J.J., Martin,E.R., Montine,T.J.,
            Mukherjee,S., Naj,A., Reiman,E.M., Reitz,C., Sherva,R., St
            George-Hyslop,P.H., Thornton,T., Younkin,S.G., Vardarajan,B.N.,
            Wang,L.S., Wendlund,J.R., Winslow,A.R., Haines,J., Mayeux,R.,
            Pericak-Vance,M.A., Schellenberg,G., Lunetta,K.L. and Farrer,L.A.
  CONSRTM   Alzheimer's Disease Genetics Consortium
  TITLE     Transethnic genome-wide scan identifies novel Alzheimer's disease
            loci
  JOURNAL   Alzheimers Dement 13 (7), 727-738 (2017)
   PUBMED   28183528
  REMARK    GeneRIF: 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.
REFERENCE   4  (bases 1 to 4709)
  AUTHORS   Zenner,H.L., Yoshimura,S., Barr,F.A. and Crump,C.M.
  TITLE     Analysis of Rab GTPase-activating proteins indicates that Rab1a/b
            and Rab43 are important for herpes simplex virus 1 secondary
            envelopment
  JOURNAL   J Virol 85 (16), 8012-8021 (2011)
   PUBMED   21680502
REFERENCE   5  (bases 1 to 4709)
  AUTHORS   Ishibashi,K., Kanno,E., Itoh,T. and Fukuda,M.
  TITLE     Identification and characterization of a novel Tre-2/Bub2/Cdc16
            (TBC) protein that possesses Rab3A-GAP activity
  JOURNAL   Genes Cells 14 (1), 41-52 (2009)
   PUBMED   19077034
REFERENCE   6  (bases 1 to 4709)
  AUTHORS   Brill,L.M., Salomon,A.R., Ficarro,S.B., Mukherji,M.,
            Stettler-Gill,M. and Peters,E.C.
  TITLE     Robust phosphoproteomic profiling of tyrosine phosphorylation sites
            from human T cells using immobilized metal affinity chromatography
            and tandem mass spectrometry
  JOURNAL   Anal Chem 76 (10), 2763-2772 (2004)
   PUBMED   15144186
REFERENCE   7  (bases 1 to 4709)
  AUTHORS   Martinu,L., Santiago-Walker,A., Qi,H. and Chou,M.M.
  TITLE     Endocytosis of epidermal growth factor receptor regulated by
            Grb2-mediated recruitment of the Rab5 GTPase-activating protein
            RN-tre
  JOURNAL   J Biol Chem 277 (52), 50996-51002 (2002)
   PUBMED   12399475
REFERENCE   8  (bases 1 to 4709)
  AUTHORS   Lanzetti,L., Rybin,V., Malabarba,M.G., Christoforidis,S., Scita,G.,
            Zerial,M. and Di Fiore,P.P.
  TITLE     The Eps8 protein coordinates EGF receptor signalling through Rac
            and trafficking through Rab5
  JOURNAL   Nature 408 (6810), 374-377 (2000)
   PUBMED   11099046
REFERENCE   9  (bases 1 to 4709)
  AUTHORS   Matoskova,B., Wong,W.T., Nomura,N., Robbins,K.C. and Di Fiore,P.P.
  TITLE     RN-tre specifically binds to the SH3 domain of eps8 with high
            affinity and confers growth advantage to NIH3T3 upon
            carboxy-terminal truncation
  JOURNAL   Oncogene 12 (12), 2679-2688 (1996)
   PUBMED   8700527
REFERENCE   10 (bases 1 to 4709)
  AUTHORS   Matoskova,B., Wong,W.T., Seki,N., Nagase,T., Nomura,N.,
            Robbins,K.C. and Di Fiore,P.P.
  TITLE     RN-tre identifies a family of tre-related proteins displaying a
            novel potential protein binding domain
  JOURNAL   Oncogene 12 (12), 2563-2571 (1996)
   PUBMED   8700515
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AL512631.11 and AL590416.4.
            
            On Jan 22, 2021 this sequence version replaced NM_014688.4.
            
            Sequence Note:.
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: D13644.1, BC042943.2 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000609104.6/ ENSP00000476462.1
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-208               AL512631.11        29093-29300         c
            209-295             AL512631.11        15281-15367         c
            296-363             AL590416.4         114176-114243       c
            364-446             AL590416.4         112062-112144       c
            447-486             AL590416.4         105211-105250       c
            487-567             AL590416.4         96271-96351         c
            568-675             AL590416.4         87777-87884         c
            676-785             AL590416.4         79795-79904         c
            786-834             AL590416.4         77508-77556         c
            835-955             AL590416.4         75778-75898         c
            956-1050            AL590416.4         72493-72587         c
            1051-1116           AL590416.4         71845-71910         c
            1117-1216           AL590416.4         71647-71746         c
            1217-1369           AL590416.4         68446-68598         c
            1370-4709           AL590416.4         47186-50525         c
FEATURES             Location/Qualifiers
     source          1..4709
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="10"
                     /map="10p14"
     gene            1..4709
                     /gene="USP6NL"
                     /gene_synonym="RNTRE; TRE2NL; USP6NL-IT1"
                     /note="USP6 N-terminal like"
                     /db_xref="GeneID:9712"
                     /db_xref="HGNC:HGNC:16858"
                     /db_xref="MIM:605405"
     exon            1..208
                     /gene="USP6NL"
                     /gene_synonym="RNTRE; TRE2NL; USP6NL-IT1"
                     /inference="alignment:Splign:2.1.0"
     exon            209..295
                     /gene="USP6NL"
                     /gene_synonym="RNTRE; TRE2NL; USP6NL-IT1"
                     /inference="alignment:Splign:2.1.0"
     CDS             292..2778
                     /gene="USP6NL"
                     /gene_synonym="RNTRE; TRE2NL; USP6NL-IT1"
                     /note="isoform 1 is encoded by transcript variant 1; USP6
                     N-terminal-like protein; related to the N-terminus of tre"
                     /codon_start=1
                     /product="USP6 N-terminal-like protein isoform 1"
                     /protein_id="NP_055503.1"
                     /db_xref="CCDS:CCDS53492.1"
                     /db_xref="GeneID:9712"
                     /db_xref="HGNC:HGNC:16858"
                     /db_xref="MIM:605405"
                     /translation="MNSDQDVALKLAQERAEIVAKYDRGREGAEIEPWEDADYLVYKV
                     TDRFGFLHEEELPDHNVAVERQKHLEIERTTKWLKMLKGWEKYKNTEKFHRRIYKGIP
                     LQLRGEVWALLLEIPKMKEETRDLYSKLKHRARGCSPDIRQIDLDVNRTFRDHIMFRD
                     RYGVKQQSLFHVLAAYSIYNTEVGYCQGMSQITALLLMYMNEEDAFWALVKLFSGPKH
                     AMHGFFVQGFPKLLRFQEHHEKILNKFLSKLKQHLDSQEIYTSFYTMKWFFQCFLDRT
                     PFTLNLRIWDIYIFEGERVLTAMSYTILKLHKKHLMKLSMEELVEFFQETLAKDFFFE
                     DDFVIEQLQISMTELKRAKLDLPEPGKEDEYPKKPLGQLPPELQSWGVHHLSNGQRSV
                     GRPSPLASGRRESGAPHRRHEHSPHPQSRTGTPERAQPPRRKSVEEESKKLKDEADFQ
                     RKLPSGPQDSSRQYNHAAANQNSNATSNIRKEFVPKWNKPSDVSATERTAKYTMEGKG
                     RAAHPALAVTVPGPAEVRVSNVRPKMKALDAEDGKRGSTASQYDNVPGPELDSGASVE
                     EALERAYSQSPRHALYPPSPRKHAEPSSSPSKVSNKFTFKVQPPSHARYPSQLDGEAR
                     GLAHPPSYSNPPVYHGNSPKHFPTANSSFASPQFSPGTQLNPSRRPHGSTLSVSASPE
                     KSYSRPSPLVLPSSRIEVLPVDTGAGGYSGNSGSPKNGKLIIPPVDYLPDNRTWSEVS
                     YTYRPETQGQSWTRDASRGNLPKYSAFQLAPFQDHGLPAVSVDSPVRYKASPAAEDAS
                     PSGYPYSGPPPPAYHYRNRDGLSIQESVLL"
     exon            296..363
                     /gene="USP6NL"
                     /gene_synonym="RNTRE; TRE2NL; USP6NL-IT1"
                     /inference="alignment:Splign:2.1.0"
     exon            364..446
                     /gene="USP6NL"
                     /gene_synonym="RNTRE; TRE2NL; USP6NL-IT1"
                     /inference="alignment:Splign:2.1.0"
     exon            447..486
                     /gene="USP6NL"
                     /gene_synonym="RNTRE; TRE2NL; USP6NL-IT1"
                     /inference="alignment:Splign:2.1.0"
     exon            487..567
                     /gene="USP6NL"
                     /gene_synonym="RNTRE; TRE2NL; USP6NL-IT1"
                     /inference="alignment:Splign:2.1.0"
     exon            568..675
                     /gene="USP6NL"
                     /gene_synonym="RNTRE; TRE2NL; USP6NL-IT1"
                     /inference="alignment:Splign:2.1.0"
     exon            676..785
                     /gene="USP6NL"
                     /gene_synonym="RNTRE; TRE2NL; USP6NL-IT1"
                     /inference="alignment:Splign:2.1.0"
     exon            786..834
                     /gene="USP6NL"
                     /gene_synonym="RNTRE; TRE2NL; USP6NL-IT1"
                     /inference="alignment:Splign:2.1.0"
     exon            835..955
                     /gene="USP6NL"
                     /gene_synonym="RNTRE; TRE2NL; USP6NL-IT1"
                     /inference="alignment:Splign:2.1.0"
     exon            956..1050
                     /gene="USP6NL"
                     /gene_synonym="RNTRE; TRE2NL; USP6NL-IT1"
                     /inference="alignment:Splign:2.1.0"
     exon            1051..1116
                     /gene="USP6NL"
                     /gene_synonym="RNTRE; TRE2NL; USP6NL-IT1"
                     /inference="alignment:Splign:2.1.0"
     exon            1117..1216
                     /gene="USP6NL"
                     /gene_synonym="RNTRE; TRE2NL; USP6NL-IT1"
                     /inference="alignment:Splign:2.1.0"
     exon            1217..1369
                     /gene="USP6NL"
                     /gene_synonym="RNTRE; TRE2NL; USP6NL-IT1"
                     /inference="alignment:Splign:2.1.0"
     exon            1370..4709
                     /gene="USP6NL"
                     /gene_synonym="RNTRE; TRE2NL; USP6NL-IT1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3147..3152
                     /regulatory_class="polyA_signal_sequence"
                     /gene="USP6NL"
                     /gene_synonym="RNTRE; TRE2NL; USP6NL-IT1"
                     /note="hexamer: AATAGA"
     polyA_site      3166
                     /gene="USP6NL"
                     /gene_synonym="RNTRE; TRE2NL; USP6NL-IT1"
                     /note="major polyA site"
     polyA_site      4709
                     /gene="USP6NL"
                     /gene_synonym="RNTRE; TRE2NL; USP6NL-IT1"
                     /note="major polyA site"
ORIGIN      
        1 atagcggcgg caggaggtgt cgcgccgggg aacttcctgg ttcccgggct cggcttcgcc
       61 gggatcctct tggaagggaa acaatggggc ggagggcact gcggtagccg ccgccgccgc
      121 cgcgccgcgc cgcgccggat ctgctcggcc gcccgggacc gccagctctg tccgctgccc
      181 acagcctagc agtcgggacc gtactgagga catgtattcc tctgagaaac cttggacagc
      241 agattttggt ttaatatctg attgggacaa cattcagacc catttccagt catgaattca
      301 gaccaggatg tagcactcaa acttgcccag gagcgagctg aaatagttgc taaatatgac
      361 agaggacgag aaggtgcaga gattgaacct tgggaagatg ctgattacct tgtttacaaa
      421 gtcacagata gatttggctt tttacatgag gaggagctcc cagatcataa tgtggctgtg
      481 gaacggcaaa agcacctgga aattgaaaga actaccaaat ggctgaaaat gctgaaagga
      541 tgggaaaaat acaagaacac tgaaaagttt cataggcgaa tttacaaagg aataccactc
      601 cagctcagag gtgaagtctg ggccctcctt cttgagatcc ctaaaatgaa agaagaaaca
      661 agggacctgt atagtaaatt aaaacacaga gcacggggct gttcacctga catcagacaa
      721 atagacctgg atgtcaaccg cacatttcgg gaccacatta tgtttagaga cagatatggt
      781 gttaagcaac aatccttatt ccatgtgctt gctgcctatt ctatttataa cacggaagtc
      841 gggtattgtc aggggatgag ccagatcaca gctttactcc tcatgtatat gaacgaggaa
      901 gatgccttct gggccctggt caaactcttc tcaggcccta aacatgccat gcatggcttt
      961 tttgtccaag gttttcctaa actcttgagg tttcaagaac atcatgaaaa aatactgaac
     1021 aaatttctgt ccaagcttaa gcaacacttg gattctcaag aaatctacac aagtttttac
     1081 acaatgaaat ggttttttca gtgtttcctt gatcgtactc cctttacact aaacctcaga
     1141 atatgggata tctacatctt tgaaggagaa cgagttctta ctgctatgtc ttacaccatc
     1201 ttaaaattac acaaaaaaca tctaatgaaa ttgtccatgg aagaacttgt agaatttttt
     1261 caggagaccc tggcaaagga ttttttcttt gaagatgatt ttgtgataga gcaacttcag
     1321 atttctatga cagaactaaa gcgggcaaag ttagaccttc cagaacctgg taaagaggat
     1381 gaatatccaa agaagccctt ggggcagctt ccacctgaac ttcagtcttg gggcgtccat
     1441 cacttgagca acggacagag gagcgtgggc cggccgagcc cgctggccag cggcaggagg
     1501 gagagcgggg cgccccacag gaggcacgag cactccccgc acccccagag caggaccggg
     1561 acgcccgaga gagcacagcc gccaagacgg aaatcggtgg aggaggagag caaaaagctt
     1621 aaagatgagg cagattttca aagaaaactc ccatcgggtc cacaggacag ttccaggcaa
     1681 tataatcacg cagctgccaa ccaaaatagc aacgccactt caaatatcag gaaggagttt
     1741 gtgcccaaat ggaataaacc gtcagacgtc tcagctacag agagaactgc caaatacacc
     1801 atggaaggca aaggtcgagc agcgcacccc gcgctcgcag ttaccgtccc aggtcctgcc
     1861 gaggtgcggg tgtcaaacgt gcggccaaag atgaaggccc tggatgctga ggacgggaag
     1921 cggggctcca ctgcatcgca gtacgacaac gtgccaggcc cggagctgga cagcggcgct
     1981 tccgtggagg aggcgctgga aagggcttac tcccagagcc cccggcatgc cctttaccct
     2041 cctagcccga gaaagcacgc tgagccaagt tctagtccat caaaagtatc caacaagttt
     2101 acttttaaag tacagcctcc aagtcatgca cgatatccgt cccagctaga tggggaagcc
     2161 cgagggctag ctcatccccc ctcctacagc aatccccccg tttaccacgg aaactctccc
     2221 aaacacttcc ctactgccaa cagcagcttt gcttctccac agtttagccc tgggactcaa
     2281 ctgaatcctt ccaggagacc tcatggttct actctttccg tcagtgcttc tccggagaaa
     2341 tcttacagcc gcccaagccc ccttgtactg ccgtctagtc gaatagaagt cctccctgtt
     2401 gacactggtg ctgggggata ttcgggcaat tcagggtcac caaagaatgg aaaattgatc
     2461 attccaccag tggattactt gccagataac agaacatggt cagaagttag ttatacatac
     2521 agacctgaga cgcagggaca atcatggacc cgagatgcta gccgtggcaa tttaccaaaa
     2581 tactcagcct ttcaactcgc accctttcag gaccatggcc tccctgcagt ttctgtagat
     2641 agtcccgtga gatataaagc ttcaccggcc gcagaagatg ccagtccatc tggatatcca
     2701 tattcagggc ccccgcctcc agcctaccac tacaggaatc gggacgggct ttccatccaa
     2761 gagtcagtgt tgctgtgaga tttgacgtgt acttgctaaa gacgagagag aaaccacgtg
     2821 aaacctacat tgctatgttc ataattgcca aagcagtatt tatactattg taaacaactc
     2881 gcacatctct cctgtctgtt agtagtaaga atacagggaa atgtcttcag ccccacgtag
     2941 atgctgctta agatgagcgt ttcaattgca tcatcactga cctgttagaa tttaacccgg
     3001 aaacatcgca atagcattta gggatgcacg cacagtggta atttattact cagttccggt
     3061 tatgtttttc tccaaaacct gaacattttt actctgttgg ctcattctat tttgactaat
     3121 gttacaaagt actgaaaaaa ctgtagaata gatattttta aggctatatg tagtgtatgt
     3181 gtcttttaat agatataggc atctgttcat ccacatttga acacagagct aaagaaacgt
     3241 tttttaaaaa actactttta atccagatcc atggaataat atgtaattct tgttttcctt
     3301 gtcttttagt ccagtttttc tttttccctc tcatatattt gtaacctggg tcctaaactg
     3361 actgaagagt ttgtcctgac tttattaatt gcagtctcac agaatgctca tcattctcct
     3421 tcagctgttg ccattttctt tcaatctgaa aattaaagac attggagaga aaggctaacc
     3481 acttaatggt gcttaaaaat cggggcactt aaaataagtt tacggccaaa ggtgcagcag
     3541 tgcttatcac atccacatac taagagattg gtcttagtgc gtttgtgccc tttgttctgg
     3601 tctgactctt gcgaatctca gagcaggaga agttgcagct tactgatccc tcagtgctca
     3661 cagtactcat gtggggcagc cacactaact gcattagcag tgtggttact tctttcttct
     3721 gcctcgactc acatggcttc tccccacgaa ggtcccaggg tggccattta tacaatccat
     3781 ttctgtcctc tttatggaat gtagtcgacg gatattgctg cacctcatca ggccattaca
     3841 ttgtccatgt taaaattata aaaatgatcc tagtttttca taggagtcta ggattttgat
     3901 cttttaaaaa atacagtgtg atttcatgct tttgaacatc tttttttcat tgaaacaaat
     3961 tcaagttctt ggcttaaaaa aaaattagtg atgtctttaa aaaatattct gttacactac
     4021 agataccaaa acactgacaa agatttaggc actccaagag agtatgactt cgtgtttaat
     4081 tggggagctt gttttcaaca ttgcttatat ttgaatagta gaaaacccga cattgatgtt
     4141 tcttcctgtt gcaaggtggg gctttaaact ttcaaggtac aaaagtatgt cttttaaaat
     4201 ggaagtaacg tttgtttagc tagtgaatgt gacaatatat tttatgtata taatgagtct
     4261 aatgtaattt tgatcaactt ggtaatgatg ttattaaata gcaaaacaag tgcagtgtat
     4321 taaagctaaa cactacattg aaacgcaaac aaaattctgg tgaaataact gggctgttga
     4381 tgcaggtcag gtggaagctg agaaataaat gtatataaat atgtagctga ggatattaat
     4441 tcccattata taaccataat tctgtgactt gtaataaacc aagctgtaca atttagttta
     4501 taatagcagt atctgagctg ctccaaaata tatatatcaa cagtggtaaa tactgtagat
     4561 ttttatatat atatatatat atatatatat atatgcaaaa aatatatata tacacacaag
     4621 cactattttc ttatgtcatt tatgacattt tttatctgta tacttttttg atgtgattgt
     4681 tttttaacat gctaaaagta ataagtata
//
