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2019-03-24 19:52:19, GGRNA : RefSeq release 60 (20130726)

LOCUS       NM_001276320            6291 bp    mRNA    linear   PRI 06-JUN-2013
DEFINITION  Homo sapiens YOD1 deubiquitinase (YOD1), transcript variant 2,
            mRNA.
ACCESSION   NM_001276320
VERSION     NM_001276320.1  GI:444299625
KEYWORDS    RefSeq.
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 6291)
  AUTHORS   Ernst,R., Mueller,B., Ploegh,H.L. and Schlieker,C.
  TITLE     The otubain YOD1 is a deubiquitinating enzyme that associates with
            p97 to facilitate protein dislocation from the ER
  JOURNAL   Mol. Cell 36 (1), 28-38 (2009)
   PUBMED   19818707
  REMARK    GeneRIF: The assignment of a p97-associated ubiquitin processing
            function to YOD1 adds to our understanding of p97's role in the
            dislocation of misfolded proteins from the endoplasmic reticulum.
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AL445493.8.
            
            Summary: Protein ubiquitination controls many intracellular
            processes, including cell cycle progression, transcriptional
            activation, and signal transduction. This dynamic process,
            involving ubiquitin conjugating enzymes and deubiquitinating
            enzymes, adds and removes ubiquitin. Deubiquitinating enzymes are
            cysteine proteases that specifically cleave ubiquitin from
            ubiquitin-conjugated protein substrates. The protein encoded by
            this gene belongs to a DUB subfamily characterized by an ovarian
            tumor (OTU) domain. Alternative splicing results in multiple
            transcript variants. [provided by RefSeq, Jan 2013].
            
            Transcript Variant: This variant (2) contains alternate exons in
            the 5' UTR, lacks a portion of the 5' coding region, and initiates
            translation at an alternate start codon, compared to variant 1. The
            encoded isoform (2) has a distinct N-terminus and is shorter than
            isoform 1.
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on alignments.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AK128014.1, DB058914.1 [ECO:0000332]
            RNAseq introns              :: mixed/partial sample support
                                           ERS025085 [ECO:0000350]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-117               AL445493.8         12334-12450         c
            118-256             AL445493.8         11655-11793         c
            257-416             AL445493.8         10158-10317         c
            417-6291            AL445493.8         3319-9193           c
FEATURES             Location/Qualifiers
     source          1..6291
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="1"
                     /map="1q32.2"
     gene            1..6291
                     /gene="YOD1"
                     /gene_synonym="DUBA8; OTUD2; PRO0907; RP11-164O23.1"
                     /note="YOD1 deubiquitinase"
                     /db_xref="GeneID:55432"
                     /db_xref="HGNC:25035"
                     /db_xref="MIM:612023"
     exon            1..117
                     /gene="YOD1"
                     /gene_synonym="DUBA8; OTUD2; PRO0907; RP11-164O23.1"
                     /inference="alignment:Splign:1.39.8"
     variation       54
                     /gene="YOD1"
                     /gene_synonym="DUBA8; OTUD2; PRO0907; RP11-164O23.1"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:2629663"
     exon            118..256
                     /gene="YOD1"
                     /gene_synonym="DUBA8; OTUD2; PRO0907; RP11-164O23.1"
                     /inference="alignment:Splign:1.39.8"
     misc_feature    143..145
                     /gene="YOD1"
                     /gene_synonym="DUBA8; OTUD2; PRO0907; RP11-164O23.1"
                     /note="upstream in-frame stop codon"
     CDS             206..1120
                     /gene="YOD1"
                     /gene_synonym="DUBA8; OTUD2; PRO0907; RP11-164O23.1"
                     /EC_number="3.4.19.12"
                     /note="isoform 2 is encoded by transcript variant 2; YOD1
                     OTU deubiquinating enzyme 1 homolog ( yeast); OTU domain
                     containing 2; ubiquitin thioesterase OTU1; HIN-7; DUBA-8;
                     hsHIN7; HIV-1-induced protease 7; OTU domain-containing
                     protein 2"
                     /codon_start=1
                     /product="ubiquitin thioesterase OTU1 isoform 2"
                     /protein_id="NP_001263249.1"
                     /db_xref="GI:444299626"
                     /db_xref="GeneID:55432"
                     /db_xref="HGNC:25035"
                     /db_xref="MIM:612023"
                     /translation="
METLHIIYSEAKSFTVEGLSSRTRVRELQGQIAAITGIAPGGQRILVGYPPECLDLSNGDTILEDLPIQSGDMLIIEEDQTRPRSSPAFTKRGASSYVRETLPVLTRTVVPADNSCLFTSVYYVVEGGVLNPACAPEMRRLIAQIVASDPDFYSEAILGKTNQEYCDWIKRDDTWGGAIEISILSKFYQCEICVVDTQTVRIDRFGEDAGYTKRVLLIYDGIHYDPLQRNFPDPDTPPLTIFSSNDDIVLVQALELADEARRRRQFTDVNRFTLRCMVCQKGLTGQAEAREHAKETGHTNFGEV
"
     misc_feature    344..1114
                     /gene="YOD1"
                     /gene_synonym="DUBA8; OTUD2; PRO0907; RP11-164O23.1"
                     /note="Predicted cysteine protease (OTU family)
                     [Posttranslational modification, protein turnover,
                     chaperones]; Region: COG5539"
                     /db_xref="CDD:35098"
     misc_feature    536..877
                     /gene="YOD1"
                     /gene_synonym="DUBA8; OTUD2; PRO0907; RP11-164O23.1"
                     /note="OTU-like cysteine protease; Region: OTU; pfam02338"
                     /db_xref="CDD:202209"
     exon            257..416
                     /gene="YOD1"
                     /gene_synonym="DUBA8; OTUD2; PRO0907; RP11-164O23.1"
                     /inference="alignment:Splign:1.39.8"
     exon            417..6291
                     /gene="YOD1"
                     /gene_synonym="DUBA8; OTUD2; PRO0907; RP11-164O23.1"
                     /inference="alignment:Splign:1.39.8"
     variation       799
                     /gene="YOD1"
                     /gene_synonym="DUBA8; OTUD2; PRO0907; RP11-164O23.1"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:2054779"
     variation       1873
                     /gene="YOD1"
                     /gene_synonym="DUBA8; OTUD2; PRO0907; RP11-164O23.1"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:2054780"
     variation       2076
                     /gene="YOD1"
                     /gene_synonym="DUBA8; OTUD2; PRO0907; RP11-164O23.1"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:1385611"
     variation       2685
                     /gene="YOD1"
                     /gene_synonym="DUBA8; OTUD2; PRO0907; RP11-164O23.1"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:2629665"
     STS             6008..6208
                     /gene="YOD1"
                     /gene_synonym="DUBA8; OTUD2; PRO0907; RP11-164O23.1"
                     /standard_name="D8S2025"
                     /db_xref="UniSTS:18135"
     variation       6126
                     /gene="YOD1"
                     /gene_synonym="DUBA8; OTUD2; PRO0907; RP11-164O23.1"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:1044145"
ORIGIN      
agactattcggtaggcgtcttgagagcgggtgtgccgggtgacgagaaaatgctgcaaagattaacgctctcattcctgaatcccagcagaacctcattagatccataaatgggaacgctgtatcatccgttgcagtcgtcttgaagaaccaaggaggaaaattgcaccagcaaaaaaaaattgagtcatgaaagatgtgaaaagatggaaacattacatataatttattcagaagcaaagtcttttacagtggaggggctgtccagccggacccgggtgcgggaactccagggccaaattgccgccatcaccgggatcgcccccggcggtcagcgaatcctcgtcggataccctcccgagtgcctggatctcagcaatggggataccattctggaagacttgcccatccaatctggtgacatgctgatcattgaagaagaccaaaccaggcccagaagttcacctgcatttactaaacgtggtgcttctagttacgtcagggaaactttgcctgtgcttaccagaaccgtggtcccagcagacaactcttgcctctttactagtgtgtactatgtcgtcgaaggaggagtcttgaatccagcttgtgcccctgagatgagacgcctcatagcacaaattgtagcaagcgatccagacttctatagtgaggcaatactgggaaaaacaaatcaagagtactgtgactggatcaaaagggatgacacttggggaggagcaatagagatatcgattttgtccaagttttaccaatgtgaaatatgtgtagtggatacacagacagtaagaattgatcgttttggggaagatgcaggatataccaaaagggttctgcttatttatgatggcatccactatgatccacttcagcgtaacttccctgatccagatacacctcctctgaccattttctcctctaatgatgatattgttcttgtacaagcactggaattagcagatgaagctagaagaaggagacagtttactgatgtcaaccgcttcaccctgagatgcatggtatgtcagaaaggattaactggacaagcagaagcaagggaacatgccaaggagacaggccataccaactttggagaagtgtgacctatgcatgaatgagggttgaagcctactacctcacacatccagaaggctctgggttttccaataagctatggtaaccctaaagaacaaaggatacaatgcttgaaccatccttttaacttaaaaccactaagacactgaaattccttgttaagattaaaattagtgtgcaagtttacagatgtgtgtctacagtggtaaactgtacatacatgcctctttctgctggagtgacagaataggtgatccttgccacctactgacactgacctgaaggttgagattgagtattataaactagcacccagcagctttaacttgtagaagaaagcatcacattttgggtaatgtggaaggcctcctgtgagtccactgggcatacgattgagattgagtattataaactagcacccagcagctttaacttgtagaagaaagcatcacattttgggtaatgtggaaggcctcctgtgagtccactggacatttaccacagtgtctccagtaactgagtctttttaaaaactctgaatgagttaagtttctaaattatgaattgattcatcaaatgaagatactcagaattgtccaaactgattttatattgcaatttggtagacattataaatgtgtgcttaaccactgataagtacatcacaagcaatttttacagggatgagtctcatccttgagaatgttatcacaaaacaggaactgattgtgccctgtttaagatctctagcatataaaacgtagaatgtatgagggaataggtgcctgagcagcttcctgaagctttaaaagaccgttggcctcgtgttttaatgcaattcatgtattggtctttgtcacattggataacattttaaagttaagcagggtacttttttaattgaaattccttgaaattcgagtcctcagttttttcttcatttgcgtaaagtttatcggggggaatttaattttctcagctttttgttaagagcacttcctccaaaaaatttttttcaagtaataatgctctgctttgggttggtttttgtaagattttttgcacacctaaagagtgtttgcttttgtgctagccttatccctccactaaagttattttaaataatttcacatttctgcaaattagcactttgcttatctgcaatcttttactttgatttttgaagttttaaagcaattggagtaatactgttgaatgaactagtttcacttccaaaatagaaaaaattgtaaatccttgccttatgcagctttctcagaattctgcttcttcctagtactagatgtgtagccatttgcttagtggactaatccgcaaggcacaccctctaaaacttagcttcactacaagatcttccagataaaagttttctacctcttttcttaattattctgatcagggatgctaaattataatttgttatgtattatctcacataatgtgaagaggcttaatgtgaagttttgttattttggtctcttttttattaagtatctcacttagaaattcagtggtatactttaaagcacttggatctttttcagcatatctgcctagcaaatgttttaaaattgacatttatttttagcactttcacttggtgaaggtggccatataaaattaaggaacatttgaacaatataagagaaaagaacttttaaggaacaattcacaaagtttgtttgaaattgtcagatgacatttcttgagtaccttttgtgtgcatagttattttagacaatataagctgttatggtcagcataacttaaaagtgtttagttttctattttactgagccttaaaaatagcactgatgagcttatgatacttaatgtttggcaatcataatgtgttcaaattaatgggattgaaaatctctccacacctgactctcatctgatctggatggttttggttttgtatcttttttacttctcccagaaaatactaaatttaaaactgtaaattaagaatataccactagataacaattatcaaattgagctttatgcatcattactcagaaagcttgccttcctttctttgctacttcaggacacagagttgacatttgcttactacagctttagatctagaagtttattcgtgcaacaaatatttattgagtaatttatactgtgccaggcatgttttgatatgtttctgtcatatgttttgatatgttccaacataagtttctgtcactttatattcagtatatattttctacagtgggtaaatttaacaaatggaaaggaatagaacactgatattttacagaattaaaccccttcattgtaagggctttgtttacatattaagtgtcaagtatttattcaggggatcttatttcattgtattttatctgttatctaggttgtccatttaccggttggacactgatactctgtcaaattcctttcaaaaatgactctttagtctgctgaaatttagcactagtactttagtgttctgatcctggaaaattcaaggtgaagctttatttgtggaccatctgatttaattattgaggattaaaaacctaaacctttgctcattctaaactcaagcttttaagcctcacagaatttacaggggtttgctttttgtttgtttgttttttcattttttactgtgcttattaaactcttggaattagttattaaagggagtaaattctcatcttgggaattttgaaaatctatggacttacaactttcaggaggattaaatgtcttaagttttgtactagagcagaatgaaatctttcctattcattgagtttttgcctgccatagaggaatttttttaaaaattaaaatgacagtttatattagtggcaaagtgaataaagacctcactttcccaccccacccttcttcctttctcttacttttctttggattaaaggtcaggtgtagtactatgaagattcactcctgaataaagtgatttcagaagctaaaatttaacatacctggaaattttgtgatgtgttagccaagtgaagacattagtgtgttccatcttttgctaatggttcatggttgatttcttcattgtttcccatgaaattagcatagtcaagtggtacccttgacgcttgactgctggtcagtttgaccctgtttttaacaactaatgtagtcatgccgcttgattattccatgaagtcccagcaaaataataatgaggaattaactaacattatgttatctatctaatttgtctgtgtccctaaatgcccatgcctaacttgcttctctagtttattccttctgtggagggattaaaacgtgggtgttgcaagttgccctaagctaaacatagttttcttacatctttttgggaaaaaaaatggaatgggaagtatgcaagattaagcaagagtgatttttttttttttttgacaaatcaggtggccttcctaaacatactaagaattatgttctttcatgtgtggagacacatttgtttgcagcactttaaaaaatatatatggaataaaagtttacatgttggccctctagggatctaattaaggacattaaagtacaattcttgagctactaaccatcagctcttcttaatcaaagattgccatcagtgtagagtgtatctattggcacaacattctggtgttttgataacagtagaactcaatttcagtaactattaggagcatggtctgtgccctagcattaaaaatgttacttattattatgtgaatatcttgtattattatacaatgcagtattcaaatttgtccttgtagtgcagagatgactgataatttctaaaagattcgatccttaaaacttgtttccaagcagacttataaggaagctgatttttgagtcagaggccttaaacgtgtcatatacaagtggcatcattttaagtccaaagtgaaacacttgatttgaataagctagtttataaactaaagctgttttcttatgttacagtatttcagcacatttcattccacataaaaagaatattaagtgtccctggttgtgggagagtgtttatttttctcaaaattatctagcattttgcttacagtgctttgaatgtttgacttaaaattattattgatgttgaattgtagggtgctgatttaggtcttgattcatacacatttaaaggaggttggtaaccccctcatggtagagtgaagggagaaaagggccaagaagacaaagtaccactgataaagaagagattgtcaaatagatgcattcctagtcatgaattacccttttccaaacatttttaaagcaatgcctttgtgtcaactcaacccttcttccccatttcttgtcatagaatgtagcatggccataggtgaaaaagcttatcattaaagtatgaaaccatgaattataagcattttgccatgatgcccttttatacatatgtttttaaaagtactaaccaacatataggagtttaggaatggtgaagatataatttgattaagttgtaggtaaacagaaaggatcatcttaggctcagaatttctaatatgattacatgagtctactttataaactggtataggctatgtaattagcccgtaagttacttaaaggaccaggggacctaatttttgtcagttttccagtcacattggtgccattcaggactccagctgtttacaggaaatatgtacttagcagaatagtatttttccttgaaaaaaatttgaattcagcctaaatacagaatgaatatgaatagtttgtgaaaagggttagagaacaacaatattcctatagtttctgtattaatgcagtagagacagaggttcctaacgcaaaaagaaaaccacaagtaaagaccgtcaaattagagctttagaatatgacttgaaaaagtagggatgggcaaaacagcataagaaaatattttttcttaatgcagatggacagtgttttcttgttttaaaaatgttttgcctatttgccagcattttttgaagtaatacactgctgctacctggaagatgtctaacttcattttctacaactcttatgtgattttgccattgtcattaagatgcattgattttatttatgaggtgtatgactttaaatatctaaatgctgtattaagtgacttgtttcaaaggaataaatgaagtgaaaacgt
//

Annotations:

ANNOTATIONS from NCBI Entrez Gene (20130726):
            GeneID:55432 -> Molecular function: GO:0004843 [ubiquitin-specific protease activity] evidence: IDA
            GeneID:55432 -> Molecular function: GO:0005515 [protein binding] evidence: IPI
            GeneID:55432 -> Molecular function: GO:0046872 [metal ion binding] evidence: IEA
            GeneID:55432 -> Biological process: GO:0006520 [cellular amino acid metabolic process] evidence: ISS
            GeneID:55432 -> Biological process: GO:0030433 [ER-associated protein catabolic process] evidence: IMP
            GeneID:55432 -> Biological process: GO:0030968 [endoplasmic reticulum unfolded protein response] evidence: IMP
            GeneID:55432 -> Biological process: GO:0070536 [protein K63-linked deubiquitination] evidence: IDA
            GeneID:55432 -> Biological process: GO:0071108 [protein K48-linked deubiquitination] evidence: IDA

by @meso_cacase at DBCLS
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