LOCUS       NM_001002862            3093 bp    mRNA    linear   PRI 06-APR-2024
DEFINITION  Homo sapiens derlin 3 (DERL3), transcript variant 2, mRNA.
ACCESSION   NM_001002862
VERSION     NM_001002862.3
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 3093)
  AUTHORS   Kondo,S., Okabe,A., Nakagawa,T., Matsusaka,K., Fukuyo,M.,
            Rahmutulla,B., Dochi,H., Mizokami,H., Kitagawa,Y., Kurokawa,T.,
            Mima,M., Endo,K., Sugimoto,H., Wakisaka,N., Misawa,K., Yoshizaki,T.
            and Kaneda,A.
  TITLE     Repression of DERL3 via DNA methylation by Epstein-Barr virus
            latent membrane protein 1 in nasopharyngeal carcinoma
  JOURNAL   Biochim Biophys Acta Mol Basis Dis 1869 (2), 166598 (2023)
   PUBMED   36372158
  REMARK    GeneRIF: Repression of DERL3 via DNA methylation by Epstein-Barr
            virus latent membrane protein 1 in nasopharyngeal carcinoma.
REFERENCE   2  (bases 1 to 3093)
  AUTHORS   Geng,M., Xu,K., Meng,L., Xu,J., Jiang,C., Guo,Y., Ren,X., Li,X.,
            Peng,Y., Wang,S., Huang,F., Zhang,J., Wang,X., Zhu,W. and Lu,S.
  TITLE     Up-regulated DERL3 in fibroblast-like synoviocytes exacerbates
            inflammation of rheumatoid arthritis
  JOURNAL   Clin Immunol 220, 108579 (2020)
   PUBMED   32866644
  REMARK    GeneRIF: Up-regulated DERL3 in fibroblast-like synoviocytes
            exacerbates inflammation of rheumatoid arthritis.
REFERENCE   3  (bases 1 to 3093)
  AUTHORS   Luck,K., Kim,D.K., Lambourne,L., Spirohn,K., Begg,B.E., Bian,W.,
            Brignall,R., Cafarelli,T., Campos-Laborie,F.J., Charloteaux,B.,
            Choi,D., Cote,A.G., Daley,M., Deimling,S., Desbuleux,A., Dricot,A.,
            Gebbia,M., Hardy,M.F., Kishore,N., Knapp,J.J., Kovacs,I.A.,
            Lemmens,I., Mee,M.W., Mellor,J.C., Pollis,C., Pons,C.,
            Richardson,A.D., Schlabach,S., Teeking,B., Yadav,A., Babor,M.,
            Balcha,D., Basha,O., Bowman-Colin,C., Chin,S.F., Choi,S.G.,
            Colabella,C., Coppin,G., D'Amata,C., De Ridder,D., De Rouck,S.,
            Duran-Frigola,M., Ennajdaoui,H., Goebels,F., Goehring,L., Gopal,A.,
            Haddad,G., Hatchi,E., Helmy,M., Jacob,Y., Kassa,Y., Landini,S.,
            Li,R., van Lieshout,N., MacWilliams,A., Markey,D., Paulson,J.N.,
            Rangarajan,S., Rasla,J., Rayhan,A., Rolland,T., San-Miguel,A.,
            Shen,Y., Sheykhkarimli,D., Sheynkman,G.M., Simonovsky,E., Tasan,M.,
            Tejeda,A., Tropepe,V., Twizere,J.C., Wang,Y., Weatheritt,R.J.,
            Weile,J., Xia,Y., Yang,X., Yeger-Lotem,E., Zhong,Q., Aloy,P.,
            Bader,G.D., De Las Rivas,J., Gaudet,S., Hao,T., Rak,J.,
            Tavernier,J., Hill,D.E., Vidal,M., Roth,F.P. and Calderwood,M.A.
  TITLE     A reference map of the human binary protein interactome
  JOURNAL   Nature 580 (7803), 402-408 (2020)
   PUBMED   32296183
REFERENCE   4  (bases 1 to 3093)
  AUTHORS   Li,Y., Liu,H., Chen,H., Shao,J., Su,F., Zhang,S., Cai,X. and He,X.
  TITLE     DERL3 functions as a tumor suppressor in gastric cancer
  JOURNAL   Comput Biol Chem 84, 107172 (2020)
   PUBMED   31862624
  REMARK    GeneRIF: DERL3 is both a tumor suppressor of and a methylation
            biomarker for gastric cancer.
REFERENCE   5  (bases 1 to 3093)
  AUTHORS   Shibata,M., Kanda,M., Tanaka,H., Umeda,S., Miwa,T., Shimizu,D.,
            Hayashi,M., Inaishi,T., Miyajima,N., Adachi,Y., Takano,Y.,
            Nakanishi,K., Takeuchi,D., Noda,S., Kodera,Y. and Kikumori,T.
  TITLE     Overexpression of Derlin 3 is associated with malignant phenotype
            of breast cancer cells
  JOURNAL   Oncol Rep 38 (3), 1760-1766 (2017)
   PUBMED   28713959
  REMARK    GeneRIF: DERL3 promotes malignant phenotype in BC cells.
REFERENCE   6  (bases 1 to 3093)
  AUTHORS   Oda,Y., Okada,T., Yoshida,H., Kaufman,R.J., Nagata,K. and Mori,K.
  TITLE     Derlin-2 and Derlin-3 are regulated by the mammalian unfolded
            protein response and are required for ER-associated degradation
  JOURNAL   J Cell Biol 172 (3), 383-393 (2006)
   PUBMED   16449189
  REMARK    GeneRIF: Findings indicate that Derlin-3 provides the missing link
            between EDEM and p97 in the process of degrading misfolded
            glycoproteins.
REFERENCE   7  (bases 1 to 3093)
  AUTHORS   Oh,J.H., Yang,J.O., Hahn,Y., Kim,M.R., Byun,S.S., Jeon,Y.J.,
            Kim,J.M., Song,K.S., Noh,S.M., Kim,S., Yoo,H.S., Kim,Y.S. and
            Kim,N.S.
  TITLE     Transcriptome analysis of human gastric cancer
  JOURNAL   Mamm Genome 16 (12), 942-954 (2005)
   PUBMED   16341674
REFERENCE   8  (bases 1 to 3093)
  AUTHORS   Lilley,B.N. and Ploegh,H.L.
  TITLE     A membrane protein required for dislocation of misfolded proteins
            from the ER
  JOURNAL   Nature 429 (6994), 834-840 (2004)
   PUBMED   15215855
REFERENCE   9  (bases 1 to 3093)
  AUTHORS   Collins,J.E., Wright,C.L., Edwards,C.A., Davis,M.P., Grinham,J.A.,
            Cole,C.G., Goward,M.E., Aguado,B., Mallya,M., Mokrab,Y.,
            Huckle,E.J., Beare,D.M. and Dunham,I.
  TITLE     A genome annotation-driven approach to cloning the human ORFeome
  JOURNAL   Genome Biol 5 (10), R84 (2004)
   PUBMED   15461802
REFERENCE   10 (bases 1 to 3093)
  AUTHORS   Dunham,I., Shimizu,N., Roe,B.A., Chissoe,S., Hunt,A.R.,
            Collins,J.E., Bruskiewich,R., Beare,D.M., Clamp,M., Smink,L.J.,
            Ainscough,R., Almeida,J.P., Babbage,A., Bagguley,C., Bailey,J.,
            Barlow,K., Bates,K.N., Beasley,O., Bird,C.P., Blakey,S.,
            Bridgeman,A.M., Buck,D., Burgess,J., Burrill,W.D., O'Brien,K.P. et
            al.
  TITLE     The DNA sequence of human chromosome 22
  JOURNAL   Nature 402 (6761), 489-495 (1999)
   PUBMED   10591208
  REMARK    Erratum:[Nature 2000 Apr 20;404(6780):904]
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AL389876.1, BC057830.1,
            AK092582.1, AP000350.1 and CA313370.1.
            
            On Jun 2, 2019 this sequence version replaced NM_001002862.2.
            
            Summary: The protein encoded by this gene belongs to the derlin
            family, and resides in the endoplasmic reticulum (ER). Proteins
            that are unfolded or misfolded in the ER must be refolded or
            degraded to maintain the homeostasis of the ER. This protein
            appears to be involved in the degradation of misfolded
            glycoproteins in the ER. Several alternatively spliced transcript
            variants encoding different isoforms have been identified for this
            gene. [provided by RefSeq, Oct 2008].
            
            Transcript Variant: This variant (2) is alternatively spliced at
            the 3' end compared to transcript variant 1, resulting in a
            slightly shorter isoform (2) with a distinct C-terminus compared to
            isoform 1.
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data because no quality transcript was available
            for the full length of the gene. The extent of this transcript is
            supported by transcript alignments.
            
            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 :: CB996137.1, CB960259.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000318109.12/ ENSP00000315303.8
            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
            1-465               AL389876.1         7-471
            466-862             BC057830.1         465-861
            863-1192            AK092582.1         14-343
            1193-2823           AP000350.1         28817-30447         c
            2824-3093           CA313370.1         17-286              c
FEATURES             Location/Qualifiers
     source          1..3093
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="22"
                     /map="22q11.23"
     gene            1..3093
                     /gene="DERL3"
                     /gene_synonym="C22orf14; derlin-3; IZP6; LLN2"
                     /note="derlin 3"
                     /db_xref="GeneID:91319"
                     /db_xref="HGNC:HGNC:14236"
                     /db_xref="MIM:610305"
     exon            1..112
                     /gene="DERL3"
                     /gene_synonym="C22orf14; derlin-3; IZP6; LLN2"
                     /inference="alignment:Splign:2.1.0"
     CDS             20..727
                     /gene="DERL3"
                     /gene_synonym="C22orf14; derlin-3; IZP6; LLN2"
                     /note="isoform 2 is encoded by transcript variant 2;
                     DERtrin 3; der1-like protein 3; degradation in endoplasmic
                     reticulum protein 3; Der1-like domain family, member 3"
                     /codon_start=1
                     /product="derlin-3 isoform 2"
                     /protein_id="NP_001002862.1"
                     /db_xref="CCDS:CCDS33615.1"
                     /db_xref="GeneID:91319"
                     /db_xref="HGNC:HGNC:14236"
                     /db_xref="MIM:610305"
                     /translation="MAWQGLAAEFLQVPAVTRAYTAACVLTTAAVQLELLSPFQLYFN
                     PHLVFRKFQVWRLVTNFLFFGPLGFSFFFNMLFVFRYCRMLEEGSFRGRTADFVFMFL
                     FGGVLMTLLGLLGSLFFLGQALMAMLVYVWSRRSPRVRVNFFGLLTFQAPFLPWALMG
                     FSLLLGNSILVDLLGIAVGHIYYFLEDVFPNQPGGKRLLQTPGFLKLLLDAPAEDPNY
                     LPLPEEQPGPHLPPPQQ"
     exon            113..178
                     /gene="DERL3"
                     /gene_synonym="C22orf14; derlin-3; IZP6; LLN2"
                     /inference="alignment:Splign:2.1.0"
     exon            179..252
                     /gene="DERL3"
                     /gene_synonym="C22orf14; derlin-3; IZP6; LLN2"
                     /inference="alignment:Splign:2.1.0"
     exon            253..346
                     /gene="DERL3"
                     /gene_synonym="C22orf14; derlin-3; IZP6; LLN2"
                     /inference="alignment:Splign:2.1.0"
     exon            347..542
                     /gene="DERL3"
                     /gene_synonym="C22orf14; derlin-3; IZP6; LLN2"
                     /inference="alignment:Splign:2.1.0"
     exon            543..633
                     /gene="DERL3"
                     /gene_synonym="C22orf14; derlin-3; IZP6; LLN2"
                     /inference="alignment:Splign:2.1.0"
     exon            634..3093
                     /gene="DERL3"
                     /gene_synonym="C22orf14; derlin-3; IZP6; LLN2"
                     /inference="alignment:Splign:2.1.0"
     regulatory      843..848
                     /regulatory_class="polyA_signal_sequence"
                     /gene="DERL3"
                     /gene_synonym="C22orf14; derlin-3; IZP6; LLN2"
                     /note="hexamer: AATAAA"
     polyA_site      862
                     /gene="DERL3"
                     /gene_synonym="C22orf14; derlin-3; IZP6; LLN2"
                     /note="major polyA site"
     regulatory      3060..3065
                     /regulatory_class="polyA_signal_sequence"
                     /gene="DERL3"
                     /gene_synonym="C22orf14; derlin-3; IZP6; LLN2"
                     /note="hexamer: AAGAAA"
     polyA_site      3093
                     /gene="DERL3"
                     /gene_synonym="C22orf14; derlin-3; IZP6; LLN2"
                     /note="major polyA site"
ORIGIN      
        1 gcgtgcttga gaaggttcaa tggcgtggca gggactagcg gccgagttcc tgcaggtgcc
       61 ggcggtgacg cgggcttaca ccgcagcctg tgtcctcacc accgccgcgg tgcagctgga
      121 gctcctcagc ccctttcaac tctacttcaa cccgcacctt gtgttccgga agttccaggt
      181 ctggaggctc gtcaccaact tcctcttctt cgggcccctg ggattcagct tcttcttcaa
      241 catgctcttc gtgttccgct actgccgcat gctggaagag ggctccttcc gcggccgcac
      301 ggccgacttc gtcttcatgt ttctcttcgg gggcgtcctt atgaccctgc tgggactcct
      361 gggcagcctg ttcttcctgg gccaggccct catggccatg ctggtgtacg tgtggagccg
      421 ccgcagccct cgggtgaggg tcaacttctt cggcctgctc actttccagg caccgttcct
      481 gccttgggcg ctcatgggct tctcgctgct gctgggcaac tccatcctcg tggacctgct
      541 ggggattgcg gtgggccata tctactactt cctggaggac gtcttcccca accagcctgg
      601 aggcaagagg ctcctgcaga cccctggctt cctaaagctg ctcctggatg cccctgcaga
      661 agaccccaat tacctgcccc tccctgagga acagccagga ccccatctgc cacccccgca
      721 gcagtgaccc ccacccaggg ccaggcctaa gaggcttctg gcagcttcca tcctacccat
      781 gacccctact tggggcagaa aaaacccatc ctaaaggctg ggcccatgca agggcccacc
      841 tgaataaaca gaatgagctg cagtctcttg gcccacagca ctggcttccc catctcacct
      901 ggccacatcc ttctatgcct gccccgtcct cactcagtgt ggcctctcag cccaactgca
      961 ggtggtagga taggggtgcc cacagagggc aaagaaactg cccatggttg cctggcagag
     1021 ctttgagctc acaggttgcc aggcagagct tttgagctca caggtgacag gctcagggtt
     1081 ctcatcctgg ccccaccagg gccttgggca agtcctgccc accataggcc tctgctacct
     1141 gccagtcagc ggggaagttc accagatttc ggctgctggg gccaggacag gcgtctccta
     1201 ggttgtgcca aaccagccta cagatgttcc tgccagtggt gccttcaggc tgatgccaat
     1261 ctagcctctc ctgtctctca tcagccaccc tgacaggtgg gcgtatgcct catttttcat
     1321 ctggtgatgc caaagcccca tggattcagg tgcagaagag ggccaggact aggtcttctg
     1381 ccctttctat gacctcagag cctaagtttt caccttagca gagttctgag actgggtgag
     1441 gcagggactt ctggaaggtt ctgttcctgc cctttttagc tgaggacgtg tgtgagcctt
     1501 atccgacccc tgtggctcat ttttctcttc tgacctggca gctttccttg ttgttctaag
     1561 cctgtccatg ttgtggttta tttctggatg ctcagtggca cggggcctcc tccaaagaca
     1621 ggttgtcatt ttcatggtaa caacactgtt ctctgttgag tctgccctcc gtgttgtagc
     1681 cagaccttgt ggagatggct ttgcggcggt gtgagctggc ggtcaggagt gagggcccag
     1741 ccttcccggc acctcccagc caggtggccc tgcccgacct gtggggtgag gcagccaagg
     1801 ttccttccat ccccccagtt gtggagacac agggctgcct caccctttca ttgccgaggt
     1861 tcctacctca tggacagaac aaacacctca gcaatgaaac ctgttcatgt ctaagagcag
     1921 ctgggctggg aatcttcccc tttgttcaag gccttccagt aaggcccagc tgtccccttg
     1981 ctgtgcatgg ggctctgggg agttccactc tttgatggag ggcagaggcc ctgagtgcaa
     2041 actccctggg aagagtccca tgctaacatg tgctcaaagg agccctcctc tcacatctca
     2101 gcgaccaaga accccaatcc ctaatcagag ctctgcctct gccccacatg gggccctacc
     2161 ccacttccag ggagcacagc agcctctgac cctagccctg ccctggcagc atgggacctg
     2221 ccaacagctg agggtggcag cagtctgtgc tgggatctgt gcccggatct gtgcccattc
     2281 tcttcagtaa ggctggagct gcgagccagt ttgctgccct cccagatcct gtgtccattc
     2341 tgaagaatgg ggacacctcc ctattacaga tgagaacaga ggggacatga actccttgga
     2401 ggcagggctg ggaagggacc ctgggctgtg tctcctccct gtaccgtgtc aactccaaga
     2461 gctggcacca ggccgggagg gctattccca tattcctcac agctggcttg taaggcagga
     2521 gctggcccag gccacagcac ctgctggggt gggaaagggc cccagctgac ctggctatgg
     2581 gtgccactgg agctagaaca gccctcctgc acccaggctg gcgacagccc agcagtgccc
     2641 acacaggact gggccctccg caggggactt cagagcagca aggccccagc tggcagtagc
     2701 ctgaccatct ggacacagca gagccagggc ggcccaggga cggcaggaga gctcgcggca
     2761 ccttcctgag gccaagcaag gggagcaggg ttagggctgt tcctgaaagg cagagagcct
     2821 cttgccctga gcctcacagc tactcttctc agctctctgg gtctggaagg agaacaggct
     2881 gaggggagct gagaggagct gaggtgctac ccggagcccc attcaccccc acctgcccac
     2941 ttgggaatct gaggcagagg agggtgaggc ctgtgtgcca accttgttca cataccacct
     3001 tcgtcccccc aggccccggc cccactcctg gctctcatta tttttatgtt aaaactttga
     3061 agaaattgaa catgacctgt tgaagaaatt gaa
//
