LOCUS       NM_172230               3038 bp    mRNA    linear   PRI 12-NOV-2024
DEFINITION  Homo sapiens synoviolin 1 (SYVN1), transcript variant 2, mRNA.
ACCESSION   NM_172230
VERSION     NM_172230.3
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 3038)
  AUTHORS   Song,Z., Thepsuwan,P., Hur,W.S., Torres,M., Wu,S.A., Wei,X.,
            Tushi,N.J., Wei,J., Ferraresso,F., Paton,A.W., Paton,J.C.,
            Zheng,Z., Zhang,K., Fang,D., Kastrup,C.J., Jaiman,S., Flick,M.J.
            and Sun,S.
  TITLE     Regulation of hepatic inclusions and fibrinogen biogenesis by
            SEL1L-HRD1 ERAD
  JOURNAL   Nat Commun 15 (1), 9244 (2024)
   PUBMED   39455574
  REMARK    GeneRIF: Regulation of hepatic inclusions and fibrinogen biogenesis
            by SEL1L-HRD1 ERAD.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3038)
  AUTHORS   Xiang,Z., Hou,G., Zheng,S., Lu,M., Li,T., Lin,Q., Liu,H., Wang,X.,
            Guan,T., Wei,Y., Zhang,W., Zhang,Y., Liu,C., Li,L., Lei,Q.Y. and
            Hu,Y.
  TITLE     ER-associated degradation ligase HRD1 links ER stress to DNA damage
            repair by modulating the activity of DNA-PKcs
  JOURNAL   Proc Natl Acad Sci U S A 121 (37), e2403038121 (2024)
   PUBMED   39226359
  REMARK    GeneRIF: ER-associated degradation ligase HRD1 links ER stress to
            DNA damage repair by modulating the activity of DNA-PKcs.
REFERENCE   3  (bases 1 to 3038)
  AUTHORS   Zhao,X., Liu,D., Zhao,Y., Wang,Z., Wang,Y., Chen,Z., Ning,S.,
            Wang,G., Meng,L., Yao,J. and Tian,X.
  TITLE     HRD1-induced TMEM2 ubiquitination promotes ER stress-mediated
            apoptosis through a non-canonical pathway in intestinal
            ischemia/reperfusion
  JOURNAL   Cell Death Dis 15 (2), 154 (2024)
   PUBMED   38378757
  REMARK    GeneRIF: HRD1-induced TMEM2 ubiquitination promotes ER
            stress-mediated apoptosis through a non-canonical pathway in
            intestinal ischemia/reperfusion.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 3038)
  AUTHORS   Umphred-Wilson,K. and Adoro,S.
  TITLE     Hypomorphic human SEL1L and HRD1 variants uncouple multilayered
            ER-associated degradation machinery
  JOURNAL   J Clin Invest 134 (2), e175448 (2024)
   PUBMED   38226624
  REMARK    GeneRIF: Hypomorphic human SEL1L and HRD1 variants uncouple
            multilayered ER-associated degradation machinery.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 3038)
  AUTHORS   Wang,H.H., Lin,L.L., Li,Z.J., Wei,X., Askander,O., Cappuccio,G.,
            Hashem,M.O., Hubert,L., Munnich,A., Alqahtani,M., Pang,Q.,
            Burmeister,M., Lu,Y., Poirier,K., Besmond,C., Sun,S.,
            Brunetti-Pierri,N., Alkuraya,F.S. and Qi,L.
  TITLE     Hypomorphic variants of SEL1L-HRD1 ER-associated degradation are
            associated with neurodevelopmental disorders
  JOURNAL   J Clin Invest 134 (2), e170054 (2024)
   PUBMED   37943610
  REMARK    GeneRIF: Hypomorphic variants of SEL1L-HRD1 ER-associated
            degradation are associated with neurodevelopmental disorders.
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 3038)
  AUTHORS   Kikkert,M., Doolman,R., Dai,M., Avner,R., Hassink,G., van
            Voorden,S., Thanedar,S., Roitelman,J., Chau,V. and Wiertz,E.
  TITLE     Human HRD1 is an E3 ubiquitin ligase involved in degradation of
            proteins from the endoplasmic reticulum
  JOURNAL   J Biol Chem 279 (5), 3525-3534 (2004)
   PUBMED   14593114
  REMARK    GeneRIF: Human HRD1 is an E3 ubiquitin ligase involved in
            degradation of proteins from the endoplasmic reticulum
REFERENCE   7  (bases 1 to 3038)
  AUTHORS   Amano,T., Yamasaki,S., Yagishita,N., Tsuchimochi,K., Shin,H.,
            Kawahara,K., Aratani,S., Fujita,H., Zhang,L., Ikeda,R., Fujii,R.,
            Miura,N., Komiya,S., Nishioka,K., Maruyama,I., Fukamizu,A. and
            Nakajima,T.
  TITLE     Synoviolin/Hrd1, an E3 ubiquitin ligase, as a novel pathogenic
            factor for arthropathy
  JOURNAL   Genes Dev 17 (19), 2436-2449 (2003)
   PUBMED   12975321
REFERENCE   8  (bases 1 to 3038)
  AUTHORS   Nadav,E., Shmueli,A., Barr,H., Gonen,H., Ciechanover,A. and
            Reiss,Y.
  TITLE     A novel mammalian endoplasmic reticulum ubiquitin ligase homologous
            to the yeast Hrd1
  JOURNAL   Biochem Biophys Res Commun 303 (1), 91-97 (2003)
   PUBMED   12646171
  REMARK    GeneRIF: endogenous hHrd1 resides in the ER and has a
            ubiquitin-ligase activity
REFERENCE   9  (bases 1 to 3038)
  AUTHORS   Kaneko,M., Ishiguro,M., Niinuma,Y., Uesugi,M. and Nomura,Y.
  TITLE     Human HRD1 protects against ER stress-induced apoptosis through
            ER-associated degradation
  JOURNAL   FEBS Lett 532 (1-2), 147-152 (2002)
   PUBMED   12459480
  REMARK    GeneRIF: HRD1 protects against endoplasmic reticulum stress-induced
            apoptosis through endoplasmic reticulum-associated degradation.
REFERENCE   10 (bases 1 to 3038)
  AUTHORS   Simpson,J.C., Wellenreuther,R., Poustka,A., Pepperkok,R. and
            Wiemann,S.
  TITLE     Systematic subcellular localization of novel proteins identified by
            large-scale cDNA sequencing
  JOURNAL   EMBO Rep 1 (3), 287-292 (2000)
   PUBMED   11256614
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AL834262.1, BC030530.1 and
            AA864844.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Jun 2, 2019 this sequence version replaced NM_172230.2.
            
            Summary: This gene encodes a protein involved in endoplasmic
            reticulum (ER)-associated degradation. The encoded protein removes
            unfolded proteins, accumulated during ER stress, by retrograde
            transport to the cytosol from the ER. This protein also uses the
            ubiquitin-proteasome system for additional degradation of unfolded
            proteins. Sequence analysis identified two transcript variants that
            encode different isoforms. [provided by RefSeq, May 2011].
            
            Transcript Variant: This variant (2) uses a different splice site
            than variant 1 and encodes the longer isoform (b).
            
            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 :: BC030530.1, SRR7346977.1229991.1
                                           [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000377190.8/ ENSP00000366395.3
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-46                AL834262.1         14-59
            47-2586             BC030530.1         1-2540
            2587-2596           AA864844.1         441-450             c
            2597-3038           BC030530.1         2551-2992
FEATURES             Location/Qualifiers
     source          1..3038
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="11"
                     /map="11q13.1"
     gene            1..3038
                     /gene="SYVN1"
                     /gene_synonym="DER3; HRD1"
                     /note="synoviolin 1"
                     /db_xref="GeneID:84447"
                     /db_xref="HGNC:HGNC:20738"
                     /db_xref="MIM:608046"
     exon            1..64
                     /gene="SYVN1"
                     /gene_synonym="DER3; HRD1"
                     /inference="alignment:Splign:2.1.0"
     exon            65..213
                     /gene="SYVN1"
                     /gene_synonym="DER3; HRD1"
                     /inference="alignment:Splign:2.1.0"
     CDS             82..1935
                     /gene="SYVN1"
                     /gene_synonym="DER3; HRD1"
                     /EC_number="2.3.2.27"
                     /note="isoform b is encoded by transcript variant 2; E3
                     ubiquitin-protein ligase synoviolin; HMG-coA reductase
                     degradation 1 homolog; synovial apoptosis inhibitor 1,
                     synoviolin; RING-type E3 ubiquitin transferase synoviolin"
                     /codon_start=1
                     /product="E3 ubiquitin-protein ligase synoviolin isoform
                     b"
                     /protein_id="NP_757385.1"
                     /db_xref="CCDS:CCDS31605.1"
                     /db_xref="GeneID:84447"
                     /db_xref="HGNC:HGNC:20738"
                     /db_xref="MIM:608046"
                     /translation="MFRTAVMMAASLALTGAVVAHAYYLKHQFYPTVVYLTKSSPSMA
                     VLYIQAFVLVFLLGKVMGKVFFGQLRAAEMEHLLERSWYAVTETCLAFTVFRDDFSPR
                     FVALFTLLLFLKCFHWLAEDRVDFMERSPNISWLFHCRIVSLMFLLGILDFLFVSHAY
                     HSILTRGASVQLVFGFEYAILMTMVLTIFIKYVLHSVDLQSENPWDNKAVYMLYTELF
                     TGFIKVLLYMAFMTIMIKVHTFPLFAIRPMYLAMRQFKKAVTDAIMSRRAIRNMNTLY
                     PDATPEELQAMDNVCIICREEMVTGAKRLPCNHIFHTSCLRSWFQRQQTCPTCRMDVL
                     RASLPAQSPPPPEPADQGPPPAPHPPPLLPQPPNFPQGLLPPFPPGMFPLWPPMGPFP
                     PVPPPPSSGEAVAPPSTSAAALSRPSGAATTTAAGTSATAASATASGPGSGSAPEAGP
                     APGFPFPPPWMGMPLPPPFAFPPMPVPPAGFAGLTPEELRALEGHERQHLEARLQSLR
                     NIHTLLDAAMLQINQYLTVLASLGPPRPATSVNSTEETATTVVAAASSTSIPSSEATT
                     PTPGASPPAPEMERPPAPESVGTEEMPEDGEPDAAELRRRRLQKLESPVAH"
     exon            214..306
                     /gene="SYVN1"
                     /gene_synonym="DER3; HRD1"
                     /inference="alignment:Splign:2.1.0"
     exon            307..459
                     /gene="SYVN1"
                     /gene_synonym="DER3; HRD1"
                     /inference="alignment:Splign:2.1.0"
     exon            460..508
                     /gene="SYVN1"
                     /gene_synonym="DER3; HRD1"
                     /inference="alignment:Splign:2.1.0"
     exon            509..612
                     /gene="SYVN1"
                     /gene_synonym="DER3; HRD1"
                     /inference="alignment:Splign:2.1.0"
     exon            613..739
                     /gene="SYVN1"
                     /gene_synonym="DER3; HRD1"
                     /inference="alignment:Splign:2.1.0"
     exon            740..839
                     /gene="SYVN1"
                     /gene_synonym="DER3; HRD1"
                     /inference="alignment:Splign:2.1.0"
     exon            840..905
                     /gene="SYVN1"
                     /gene_synonym="DER3; HRD1"
                     /inference="alignment:Splign:2.1.0"
     exon            906..1022
                     /gene="SYVN1"
                     /gene_synonym="DER3; HRD1"
                     /inference="alignment:Splign:2.1.0"
     exon            1023..1186
                     /gene="SYVN1"
                     /gene_synonym="DER3; HRD1"
                     /inference="alignment:Splign:2.1.0"
     exon            1187..1315
                     /gene="SYVN1"
                     /gene_synonym="DER3; HRD1"
                     /inference="alignment:Splign:2.1.0"
     exon            1316..1489
                     /gene="SYVN1"
                     /gene_synonym="DER3; HRD1"
                     /inference="alignment:Splign:2.1.0"
     exon            1490..1676
                     /gene="SYVN1"
                     /gene_synonym="DER3; HRD1"
                     /inference="alignment:Splign:2.1.0"
     exon            1677..1828
                     /gene="SYVN1"
                     /gene_synonym="DER3; HRD1"
                     /inference="alignment:Splign:2.1.0"
     exon            1829..3038
                     /gene="SYVN1"
                     /gene_synonym="DER3; HRD1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3018..3023
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SYVN1"
                     /gene_synonym="DER3; HRD1"
                     /note="hexamer: AATAAA"
     polyA_site      3038
                     /gene="SYVN1"
                     /gene_synonym="DER3; HRD1"
                     /note="major polyA site"
ORIGIN      
        1 gttgttaacc ggaggggcag ccgcagtcgc gcggattgag cgggctcgcg gcgctgggtt
       61 cctggtctcc gggccagggc aatgttccgc acggcagtga tgatggcggc cagcctggcg
      121 ctgaccgggg ctgtggtggc tcacgcctac tacctcaaac accagttcta ccccactgtg
      181 gtgtacctga ccaagtccag ccccagcatg gcagtcctgt acatccaggc ctttgtcctt
      241 gtcttccttc tgggcaaggt gatgggcaag gtgttctttg ggcaactgag ggcagcagag
      301 atggagcacc ttctggaacg ttcctggtac gccgtcacag agacttgtct ggccttcacc
      361 gtttttcggg atgacttcag cccccgcttt gttgcactct tcactcttct tctcttcctc
      421 aaatgtttcc actggctggc tgaggaccgt gtggacttta tggaacgcag ccccaacatc
      481 tcctggctct ttcactgccg cattgtctct cttatgttcc tcctgggcat cctggacttc
      541 ctcttcgtca gccacgccta tcacagcatc ctgacccgtg gggcctctgt gcagctggtg
      601 tttggctttg agtatgccat cctgatgacg atggtgctca ccatcttcat caagtatgtg
      661 ctgcactccg tggacctcca gagtgagaac ccctgggaca acaaggctgt gtacatgctc
      721 tacacagagc tgtttacagg cttcatcaag gttctgctgt acatggcctt catgaccatc
      781 atgatcaagg tgcacacctt cccactcttt gccatccggc ccatgtacct ggccatgaga
      841 cagttcaaga aagctgtgac agatgccatc atgtctcgcc gagccatccg caacatgaac
      901 accctgtatc cagatgccac cccagaggag ctccaggcaa tggacaatgt ctgcatcatc
      961 tgccgagaag agatggtgac tggtgccaag agactgccct gcaaccacat tttccatacc
     1021 agctgcctgc gctcctggtt ccagcggcag cagacctgcc ccacctgccg tatggatgtc
     1081 cttcgtgcat cgctgccagc gcagtcacca ccacccccgg agcctgcgga tcaggggcca
     1141 ccccctgccc cccacccccc accactcttg cctcagcccc ccaacttccc ccagggcctc
     1201 ctgcctcctt ttcctccagg catgttccca ctgtggcccc ccatgggccc ctttccacct
     1261 gtcccgcctc cccccagctc aggagaggct gtggctcctc catccaccag tgcagcagcc
     1321 ctttctcggc ccagtggagc agctacaacc acagctgctg gcaccagtgc tactgctgct
     1381 tctgccacag catctggccc aggctctggc tctgccccag aggctggccc tgcccctggt
     1441 ttccccttcc ctcctccctg gatgggtatg cccctgcctc caccctttgc cttcccccca
     1501 atgcctgtgc cccctgcggg ctttgctggg ctgaccccag aggagctacg agctctggag
     1561 ggccatgagc ggcagcacct ggaggcccgg ctgcagagcc tgcgtaacat ccacacactg
     1621 ctggacgccg ccatgctgca gatcaaccag tacctcaccg tgctggcctc cttggggccc
     1681 ccccggcctg ccacttcagt caactccact gaggagactg ccactacagt tgttgctgct
     1741 gcctcctcca ccagcatccc tagctcagag gccacgaccc caaccccagg agcctcccca
     1801 ccagcccctg aaatggaaag gcctccagct cctgagtcag tgggcacaga ggagatgcct
     1861 gaggatggag agcccgatgc agcagagctc cgccggcgcc gcctgcagaa gctggagtct
     1921 cctgttgccc actgacactg ccccagccca gccccagcct ctgctctttt gagcagccct
     1981 cgctggaaca tgtcctgcca ccaagtgcca gctccctctc tgtctgcacc agggagtagt
     2041 acccccagct ctgagaaaga ggcggcatcc cctaggccaa gtggaaagag gctggggttc
     2101 ccatttgact ccagtcccag gcagccatgg ggatctcggg tcagttccag ccttcctctc
     2161 caactcttca gccctgtgtt ctgctggggc catgaaggca gaaggtttag cctctgagaa
     2221 gccctcttct tcccccaccc ctttccagga gaaggggctg cccctccaag ccctacttgt
     2281 atgtgcggag tcacactgca gtgccgaaca gtattagctc ccgttcccaa gtgtggactc
     2341 cagaggggct ggaggcaagc tatgaacttg ctcgctggcc cacccctaag actggtaccc
     2401 atttcctttt cttaccctga tctccccaga agcctcttgt ggtggtggct gtgcccccta
     2461 tgccctgtgg catttctgcg tcttactggc aaccacacaa ctcagggaaa ggaatgcctg
     2521 ggagtggggg tgcaggcggg cagcactgag ggaccctgcc ccgcccctcc ccccaggccc
     2581 ctttcctctg cagcttctca agtgagactg acctgtctca cccagcagcc actgcccagc
     2641 cgcactccag gcaagggcca gtgcgcctgc tcctgaccac tgcaatccca gcgcccaagg
     2701 aaggccactt ctcaactggc agaacttctg aagtttagaa ttggaattac ttccttacta
     2761 gtgtcttttg gcttaaattt tgtcttttga agttgaatgc ttaatcccgg gaaagaggaa
     2821 caggagtgcc agactcctgg tctttccagt ttagaaaagg ctctgtgcca aggagggacc
     2881 acaggagctg ggacctgcct gcccctgtct tttccccttg gttttgtgtt acaagagttg
     2941 ttggagacag tttcagatga ttatttaatt tgtaaatatt gtacaaattt taatagctta
     3001 aattgtatat acagccaaat aaaaacttgc attaacaa
//
