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2020-10-26 19:19:48, GGRNA : RefSeq release 60 (20130726)

LOCUS       NM_001134418            3082 bp    mRNA    linear   PRI 17-APR-2013
DEFINITION  Homo sapiens leprecan-like 1 (LEPREL1), transcript variant 2, mRNA.
ACCESSION   NM_001134418
VERSION     NM_001134418.1  GI:197313661
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 3082)
  AUTHORS   Mordechai,S., Gradstein,L., Pasanen,A., Ofir,R., El Amour,K.,
            Levy,J., Belfair,N., Lifshitz,T., Joshua,S., Narkis,G.,
            Elbedour,K., Myllyharju,J. and Birk,O.S.
  TITLE     High myopia caused by a mutation in LEPREL1, encoding prolyl
            3-hydroxylase 2
  JOURNAL   Am. J. Hum. Genet. 89 (3), 438-445 (2011)
   PUBMED   21885030
  REMARK    GeneRIF: High myopia is caused by a mutation in LEPREL1, encoding
            prolyl 3-hydroxylase 2.
REFERENCE   2  (bases 1 to 3082)
  AUTHORS   Fernandes,R.J., Farnand,A.W., Traeger,G.R., Weis,M.A. and Eyre,D.R.
  TITLE     A role for prolyl 3-hydroxylase 2 in post-translational
            modification of fibril-forming collagens
  JOURNAL   J. Biol. Chem. 286 (35), 30662-30669 (2011)
   PUBMED   21757687
  REMARK    GeneRIF: P3H2 has preferred substrate sequences among the classes
            of 3Hyp sites in clade A collagen chains
REFERENCE   3  (bases 1 to 3082)
  AUTHORS   Shah,R., Smith,P., Purdie,C., Quinlan,P., Baker,L., Aman,P.,
            Thompson,A.M. and Crook,T.
  TITLE     The prolyl 3-hydroxylases P3H2 and P3H3 are novel targets for
            epigenetic silencing in breast cancer
  JOURNAL   Br. J. Cancer 100 (10), 1687-1696 (2009)
   PUBMED   19436308
  REMARK    GeneRIF: The restriction of silencing in P3H2 to breast carcinomas,
            and its association with oestrogen-receptor-positive cases,
            suggests that P3H2 may be a breast-cancer-specific tumour
            suppressor.
REFERENCE   4  (bases 1 to 3082)
  AUTHORS   Tiainen,P., Pasanen,A., Sormunen,R. and Myllyharju,J.
  TITLE     Characterization of recombinant human prolyl 3-hydroxylase
            isoenzyme 2, an enzyme modifying the basement membrane collagen IV
  JOURNAL   J. Biol. Chem. 283 (28), 19432-19439 (2008)
   PUBMED   18487197
  REMARK    GeneRIF: P3H2 is responsible for the hydroxylation of collagen IV,
            which has the highest 3-hydroxyproline content of all collagens. It
            is thus possible that P3H2 mutations may lead to a disease with
            changes in basement membranes.
REFERENCE   5  (bases 1 to 3082)
  AUTHORS   Vranka,J.A., Sakai,L.Y. and Bachinger,H.P.
  TITLE     Prolyl 3-hydroxylase 1, enzyme characterization and identification
            of a novel family of enzymes
  JOURNAL   J. Biol. Chem. 279 (22), 23615-23621 (2004)
   PUBMED   15044469
REFERENCE   6  (bases 1 to 3082)
  AUTHORS   Jarnum,S., Kjellman,C., Darabi,A., Nilsson,I., Edvardsen,K. and
            Aman,P.
  TITLE     LEPREL1, a novel ER and Golgi resident member of the Leprecan
            family
  JOURNAL   Biochem. Biophys. Res. Commun. 317 (2), 342-351 (2004)
   PUBMED   15063763
REFERENCE   7  (bases 1 to 3082)
  AUTHORS   Thelin-Jarnum,S., Lassen,C., Panagopoulos,I., Mandahl,N. and
            Aman,P.
  TITLE     Identification of genes differentially expressed in TLS-CHOP
            carrying myxoid liposarcomas
  JOURNAL   Int. J. Cancer 83 (1), 30-33 (1999)
   PUBMED   10449603
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DA720646.1, BC005029.1,
            AC016966.19, BU621129.1 and BU737886.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            Summary: This gene encodes a member of the prolyl 3-hydroxylase
            subfamily of 2-oxo-glutarate-dependent dioxygenases. These enzymes
            play a critical role in collagen chain assembly, stability and
            cross-linking by catalyzing post-translational 3-hydroxylation of
            proline residues. Mutations in this gene are associated with
            nonsyndromic severe myopia with cataract and vitreoretinal
            degeneration, and downregulation of this gene may play a role in
            breast cancer. Alternatively spliced transcript variants encoding
            multiple isoforms have been observed for this gene. [provided by
            RefSeq, Dec 2011].
            
            Transcript Variant: This variant (2) differs in the 5' UTR, lacks a
            portion of the 5' coding region and initiates translation at a
            downstream, in-frame start codon, compared to variant 1. The
            encoded isoform (b) has a shorter N-terminus, compared to isoform
            a.
            
            ##Evidence-Data-START##
            Transcript exon combination :: BC005029.1 [ECO:0000332]
            RNAseq introns              :: mixed/partial sample support
                                           ERS025081, ERS025082 [ECO:0000350]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-172               DA720646.1         1-172
            173-450             BC005029.1         1-278
            451-451             AC016966.19        36592-36592         c
            452-2346            BC005029.1         280-2174
            2347-2963           BU621129.1         17-633              c
            2964-3082           BU737886.1         1-119               c
FEATURES             Location/Qualifiers
     source          1..3082
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="3"
                     /map="3q28"
     gene            1..3082
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /note="leprecan-like 1"
                     /db_xref="GeneID:55214"
                     /db_xref="HGNC:19317"
                     /db_xref="MIM:610341"
     exon            1..235
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /inference="alignment:Splign:1.39.8"
     misc_feature    224..226
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /note="upstream in-frame stop codon"
     exon            236..388
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /inference="alignment:Splign:1.39.8"
     CDS             299..1882
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /EC_number="1.14.11.7"
                     /note="isoform b is encoded by transcript variant 2;
                     prolyl 3-hydroxylase 3; prolyl 3-hydroxylase 2; myxoid
                     liposarcoma-associated protein 4"
                     /codon_start=1
                     /product="prolyl 3-hydroxylase 2 isoform b"
                     /protein_id="NP_001127890.1"
                     /db_xref="GI:197313662"
                     /db_xref="CCDS:CCDS46981.1"
                     /db_xref="GeneID:55214"
                     /db_xref="HGNC:19317"
                     /db_xref="MIM:610341"
                     /translation="
MEMQQNIENYRATAGVEALQLVDREAKPHMESYNAGVKHYEADDFEMAIRHFEQALREYFVEDTECRTLCEGPQRFEEYEYLGYKAGLYEAIADHYMQVLVCQHECVRELATRPGRLSPIENFLPLHYDYLQFAYYRVGEYVKALECAKAYLLCHPDDEDVLDNVDYYESLLDDSIDPASIEAREDLTMFVKRHKLESELIKSAAEGLGFSYTEPNYWIRYGGRQDENRVPSGVNVEGAEVHGFSMGKKLSPKIDRDLREGGPLLYENITFVYNSEQLNGTQRVLLDNVLSEEQCRELHSVASGIMLVGDGYRGKTSPHTPNEKFEGATVLKALKSGYEGRVPLKSARLFYDISEKARRIVESYFMLNSTLYFSYTHMVCRTALSGQQDRRNDLSHPIHADNCLLDPEANECWKEPPAYTFRDYSALLYMNDDFEGGEFIFTEMDAKTVTASIKPKCGRMISFSSGGENPHGVKAVTKGKRCAVALWFTLDPLYRELERIQADEVIAILDQEQQGKHELNINPKDEL
"
     misc_feature    1169..1765
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /note="Prolyl 4-hydroxylase alpha subunit homologues;
                     Region: P4Hc; smart00702"
                     /db_xref="CDD:197834"
     misc_feature    1484..1765
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /note="2OG-Fe(II) oxygenase superfamily; Region:
                     2OG-FeII_Oxy_3; pfam13640"
                     /db_xref="CDD:205817"
     variation       367
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:34128856"
     exon            389..578
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /inference="alignment:Splign:1.39.8"
     variation       451
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:1719600"
     exon            579..710
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /inference="alignment:Splign:1.39.8"
     exon            711..853
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /inference="alignment:Splign:1.39.8"
     variation       727
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:34558237"
     exon            854..943
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /inference="alignment:Splign:1.39.8"
     variation       924
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:35904452"
     exon            944..984
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /inference="alignment:Splign:1.39.8"
     variation       977
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:35737596"
     exon            985..1079
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /inference="alignment:Splign:1.39.8"
     exon            1080..1207
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /inference="alignment:Splign:1.39.8"
     variation       1132
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:35257648"
     variation       1207
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /replace="a"
                     /replace="t"
                     /db_xref="dbSNP:34111865"
     exon            1208..1303
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /inference="alignment:Splign:1.39.8"
     variation       1263
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:35072845"
     exon            1304..1454
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /inference="alignment:Splign:1.39.8"
     exon            1455..1572
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /inference="alignment:Splign:1.39.8"
     variation       1559
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:34620268"
     variation       1562
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:35067805"
     exon            1573..1648
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /inference="alignment:Splign:1.39.8"
     exon            1649..1789
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /inference="alignment:Splign:1.39.8"
     variation       1762
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:1061534"
     exon            1790..3066
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /inference="alignment:Splign:1.39.8"
     STS             2408..2597
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /standard_name="RH93767"
                     /db_xref="UniSTS:87517"
     STS             2573..2714
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
                     /standard_name="STS-N21495"
                     /db_xref="UniSTS:21296"
     polyA_signal    2941..2946
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
     polyA_site      2963
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
     polyA_signal    3045..3050
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
     polyA_site      3066
                     /gene="LEPREL1"
                     /gene_synonym="MCVD; MLAT4; P3H2"
ORIGIN      
agaagaccacagaaatgcctccaggaggcaggctgggatccagggtccaaccaatattcttgtgagagtgtgaagccaaggaacacgaaagaggggaacaccttggctaagaatgtattcgtgacagaggagaaggggaggaacaggaagcctccagctagtcgtttggaatctggcaaccatttctgtcagctttctcattcctagattgatgcagattgcttaattccttgagcttaaccagctcgaaaaagcagtggaagcagctcacacatttttcgtggctaaccctgagcacatggaaatgcagcagaacattgagaattacagggcgacagctggtgttgaagcattgcagttggtagacagagaagccaagccacacatggagagttacaatgcaggagttaaacattatgaggctgatgactttgagatggctatcaggcacttcgaacaagccttaagagaatatttcgttgaagatacagaatgccggaccctatgtgaggggcctcagagatttgaagaatatgagtatttagggtataaggctggtctgtatgaagctattgcagatcactacatgcaggtgcttgtttgtcagcatgaatgtgtgagggaacttgccacccgccctggccgcctctctcccatcgagaattttcttcctctgcactatgattacctacagtttgcctactatcgagttggtgagtatgtgaaagccctggagtgtgccaaagcctatcttctatgccatccagatgatgaggatgtcctagacaatgtggattactatgagagtctgctggatgatagcattgacccggcatccattgaggccagagaggatttaacaatgtttgtgaaacgtcataagctggagtctgagctgataaaatcagctgcagaaggtctggggttttcatacactgaaccgaattattggatcagatatggaggacgacaggatgagaatcgggtcccttcaggagtgaacgtagagggagcagaagttcatggattctcaatgggaaaaaagctatcacccaagatagatcgagacctaagagaaggtggtcctctactctatgagaacatcacattcgtctacaactcggagcagctgaacgggactcagcgggttctcctggataacgtcctgtcggaagaacagtgccgggagctccacagcgtggccagtggaatcatgcttgttggtgatggatacagaggaaaaacttcaccccatacacccaatgaaaagtttgaaggtgcaactgtcctgaaagcactcaaatctggttatgaaggtcgagtcccactgaagagcgctcgtctgttttatgacatcagcgaaaaggctcgaaggattgtagaatcttattttatgctgaactcaactctgtatttttcctatacacacatggtctgccgaacagccctgtctggtcagcaggatagaagaaatgacctcagtcatcccatccatgctgacaactgtttgttggatccagaggccaacgaatgctggaaggagcctcctgcttacacatttcgagactatagtgctctcctatatatgaatgatgactttgaaggaggagaattcatattcacagagatggatgctaagactgtgactgcctctataaaaccaaaatgtgggcgcatgatcagcttctcatctggaggagagaaccctcatggggtgaaggcagtcaccaagggaaagaggtgtgctgtggctctgtggttcaccttggacccactttatagagaattggagcgaatacaggctgatgaagtgattgcaattctggatcaagaacagcaagggaagcatgaactgaatatcaaccctaaagatgagctataaaaatgagaaagaatgttctatcaaatatttatttaaattgttaatcttatgagaacctttttatttttgtacagagccatggtataaattaacaggttaatgtcagtcatcagatcttccttctcttcctaaggatgcttgtgttgcctcaatctatcaatctatctttcttgttttgggttgttttctctctctctctctctctctctcttcttagagacatggtctaaccatgttgtctaggatatagggcagtggctattcacagatgtgatgatagcacactggagcctcaaactcttaggctcaggcgatccttcaagcctcccggggagctgggaccacaggcacgtgccaccacacccagctctctttcttggtttttcatcatttcatgtatctatcaaagcccagttcacctcctcccccaaacacacacacacacacacacacacacacacacacacacaattaagttgctgcaaattcaaaagcttagagagaataagcttcttggtggtgaaactacaactctcacgtgtgctccagttctaaaattaacctgtgcctggtctctgaagccctttcttgctctgtgcctttcagccacatccttaggtgctaacggccatgagctccgactctccaaagtgagctccactttgggtctgaggagcccctggcagagtccacgctgcctcaggtatcatgggcgtaatgatcacccaggctccgggagatctcatggatgattactgtatgagacagaggggacttcagtctttccagggccttggtggaatttttggctctggtgttttcgccagacaataaacttacactggaagctttgattcaccctccacagtactccagaaaggactgtcctataagttgtacactttaaaaggtcatgtagaggttgtagtagaatggcttttcaccctggtgactttggaagaaactcttgaatactgcctgcatccgggcaccatggccaggttgcctaggagtggggtccactgatgaaaagaggtgttttgtacttacataagaaaaataaatttctgattgattttaaccgtcatctgcttatattttgggggcccctcctcattgctgctatccagcacacagatttgtgcttgtgtctgatttgtttaataaagggaggcttattttaaaaaaaaaaaaaaaaaa
//

Annotations:

ANNOTATIONS from NCBI Entrez Gene (20130726):
            GeneID:55214 -> Molecular function: GO:0005506 [iron ion binding] evidence: IEA
            GeneID:55214 -> Molecular function: GO:0016702 [oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen] evidence: IEA
            GeneID:55214 -> Molecular function: GO:0019797 [procollagen-proline 3-dioxygenase activity] evidence: IDA
            GeneID:55214 -> Molecular function: GO:0031418 [L-ascorbic acid binding] evidence: IEA
            GeneID:55214 -> Biological process: GO:0008285 [negative regulation of cell proliferation] evidence: IDA
            GeneID:55214 -> Biological process: GO:0019511 [peptidyl-proline hydroxylation] evidence: IDA
            GeneID:55214 -> Biological process: GO:0030198 [extracellular matrix organization] evidence: TAS
            GeneID:55214 -> Biological process: GO:0032963 [collagen metabolic process] evidence: IDA
            GeneID:55214 -> Cellular component: GO:0005604 [basement membrane] evidence: ISS
            GeneID:55214 -> Cellular component: GO:0005783 [endoplasmic reticulum] evidence: IDA
            GeneID:55214 -> Cellular component: GO:0005788 [endoplasmic reticulum lumen] evidence: TAS
            GeneID:55214 -> Cellular component: GO:0005794 [Golgi apparatus] evidence: IDA
ANNOTATIONS from NCBI Entrez Gene (20130726):
            NP_001127890 -> EC 1.14.11.7

by @meso_cacase at DBCLS
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