LOCUS       NM_001284417            2710 bp    mRNA    linear   PRI 08-JUN-2024
DEFINITION  Homo sapiens LysM domain containing 4 (LYSMD4), transcript variant
            2, mRNA.
ACCESSION   NM_001284417 XM_005254864
VERSION     NM_001284417.2
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 2710)
  AUTHORS   Wojczynski,M.K., Li,M., Bielak,L.F., Kerr,K.F., Reiner,A.P.,
            Wong,N.D., Yanek,L.R., Qu,L., White,C.C., Lange,L.A.,
            Ferguson,J.F., He,J., Young,T., Mosley,T.H., Smith,J.A., Kral,B.G.,
            Guo,X., Wong,Q., Ganesh,S.K., Heckbert,S.R., Griswold,M.E.,
            O'Leary,D.H., Budoff,M., Carr,J.J., Taylor,H.A. Jr., Bluemke,D.A.,
            Demissie,S., Hwang,S.J., Paltoo,D.N., Polak,J.F., Psaty,B.M.,
            Becker,D.M., Province,M.A., Post,W.S., O'Donnell,C.J., Wilson,J.G.,
            Harris,T.B., Kavousi,M., Cupples,L.A., Rotter,J.I., Fornage,M.,
            Becker,L.C., Peyser,P.A., Borecki,I.B. and Reilly,M.P.
  TITLE     Genetics of coronary artery calcification among African Americans,
            a meta-analysis
  JOURNAL   BMC Med Genet 14, 75 (2013)
   PUBMED   23870195
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2710)
  CONSRTM   GENDEP Investigators; MARS Investigators; STAR*D Investigators
  TITLE     Common genetic variation and antidepressant efficacy in major
            depressive disorder: a meta-analysis of three genome-wide
            pharmacogenetic studies
  JOURNAL   Am J Psychiatry 170 (2), 207-217 (2013)
   PUBMED   23377640
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AK056718.1, AK290296.1, BC084545.1, KF459559.1 and AC022692.11.
            
            On Jun 2, 2019 this sequence version replaced NM_001284417.1.
            
            Transcript Variant: This variant (2) differs in the 5' UTR, lacks
            two alternate exons in the coding region, and initiates translation
            at an alternate upstream start codon, compared to variant 1. The
            encoded isoform (b) is shorter and has a distinct N-terminus,
            compared to isoform a. Variants 2 and 3 encode the same isoform
            (b).
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript alignments.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR1660803.77806.1,
                                           SRR1803611.264799.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2158188 [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000684762.1/ ENSP00000506747.1
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-36                AK056718.1         8-43
            37-496              AK290296.1         30-489
            497-570             BC084545.1         472-545
            571-707             KF459559.1         1-137               c
            708-2710            AC022692.11        166930-168932       c
FEATURES             Location/Qualifiers
     source          1..2710
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="15"
                     /map="15q26.3"
     gene            1..2710
                     /gene="LYSMD4"
                     /note="LysM domain containing 4"
                     /db_xref="GeneID:145748"
                     /db_xref="HGNC:HGNC:26571"
     exon            1..93
                     /gene="LYSMD4"
                     /inference="alignment:Splign:2.1.0"
     exon            94..383
                     /gene="LYSMD4"
                     /inference="alignment:Splign:2.1.0"
     CDS             102..992
                     /gene="LYSMD4"
                     /note="isoform b is encoded by transcript variant 2; lysM
                     and putative peptidoglycan-binding domain-containing
                     protein 4; LysM, putative peptidoglycan-binding, domain
                     containing 4"
                     /codon_start=1
                     /product="lysM and putative peptidoglycan-binding
                     domain-containing protein 4 isoform b"
                     /protein_id="NP_001271346.1"
                     /db_xref="CCDS:CCDS66877.1"
                     /db_xref="GeneID:145748"
                     /db_xref="HGNC:HGNC:26571"
                     /translation="MRHEELLTKTFQGPAVVCGTPTSHVYMFKNGSGDSGDSSEEESH
                     RVVLRPRGKERHKSGVHQPPQAGAGDVVLLQRELAQEDSLNKLALQYGCKVADIKKVN
                     NFIREQDLYALKSVKIPVRNHGILMETHKELKPLLSPSSETTVTVELPEADRAGAGTG
                     AQAGQLMGFFKGIDQDIERAVQSEIFLHESYCMDTSHQPLLPAPPKTPMDGADCGIQW
                     WNAVFIMLLIGIVLPVFYLVYFKIQASGETPNSLNTTVIPNGSMAMGTVPGQAPRLAV
                     AVPAVTSADSQFSQTTQAGS"
     exon            384..2710
                     /gene="LYSMD4"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2682..2687
                     /regulatory_class="polyA_signal_sequence"
                     /gene="LYSMD4"
                     /note="hexamer: AATAAA"
     polyA_site      2710
                     /gene="LYSMD4"
                     /note="major polyA site"
ORIGIN      
        1 gtagccaatc cgcaggcgcg gtggcagctg cgggtcgcgg gtcgcgggtc gcgagtcgcc
       61 ggtcgccggt cgcggcggag cctgggcgct gagtgaagaa aatgaggcac gaggaattgt
      121 taaccaagac cttccaaggc ccagctgttg tgtgtgggac tccgaccagc cacgtataca
      181 tgtttaagaa tggcagtggg gactcggggg actcttctga agaagagtct caccgtgtgg
      241 ttttgcggcc ccggggcaag gagcgccaca agagcggtgt ccaccagcct ccccaggcgg
      301 gagcaggtga cgtggtgctg ctgcagcggg agctggccca ggaggacagc ctcaacaagc
      361 tggcgctgca gtatggctgc aaagttgcag atatcaagaa agtcaacaac ttcatcagag
      421 aacaagactt atatgctttg aaatctgtta agattccagt gagaaaccat gggatcctga
      481 tggagaccca caaagaactg aaaccccttc tgagcccgtc ttccgagacc acagtgaccg
      541 tggaactgcc agaggcagac agagcaggcg cgggcaccgg tgcccaggcc ggccaactga
      601 tgggcttctt taaggggatt gaccaggata ttgagcgtgc agtgcagtca gaaatctttc
      661 tacatgaaag ttactgcatg gacacctccc atcagccact gctcccggca cctccgaaga
      721 cgcctatgga tggtgcagat tgtggcattc agtggtggaa tgctgttttc atcatgctgc
      781 tgattggtat tgtcttgcct gtcttttatt tggtctactt taaaatacaa gctagtggtg
      841 agacccctaa tagcttgaac acaactgtca tccccaatgg ctcgatggca atgggtacag
      901 ttccagggca agcccccaga ctagcagttg cagtgccagc cgtcacttct gcagacagcc
      961 agttcagtca gaccacccaa gcggggagct aagctttgtt tttaaagact aggcccagct
     1021 ttagcaattg gctgttgatg tgcctcagct gtcactggcg atgtcctagg ggtgctgcat
     1081 tttgcttccg gggaaggatg gacacttttc agaagtcact gcagtattcc caattgcact
     1141 ggccctgggc atggccttac ccagtctaag ctggcaggat ctaaaacagc agcgacctcg
     1201 gcccctatcc agagaggtgc agcaagagag ccatttccct gtgacattta gtggactggc
     1261 cagttcatag cagcactgtg aggaccccca agttggacgt gctcggaggg aaagatttat
     1321 ggcctctgtc gagggacctg cagcgtgaga gccagtggca tctgcgcggc ttgcctggct
     1381 cttgctgtat cctcacttcc tgtggagcgg ggattggctc tgagaaggag tgttctctgt
     1441 ctgcctggca aaggtgctgt ggaataggct tggcatgcca ccctgtttta gagagtgaca
     1501 gttacagttg taacaagcct acttcatatt ggccccctca gttagccttt ttgaggcaat
     1561 gccatttcta gagttgaaaa agccctggac ccaaactgcg gcactgttga ataaagggca
     1621 gtcctactcc tgtcctttta gagtggctta gtgtgacaca caggcatctc ccaggccaag
     1681 cacacacagg ctgcgcccag ttccgcagga gccgtcccac agcgtggctc tctggattct
     1741 cccacttgtc ctccttggaa ggagctcttg ctggccagtg tttggagggg aggatgagtg
     1801 cctgtcactg aggcctcact atggttggcg tctgaagctg ggcggtcgtc aggcctgtgc
     1861 tgagagccgc agcccctgtg cacacctaac acagggcgct ccccctgctg cttccctggc
     1921 tcagttcttc ggagctccag agtgagaagg ccgcttcgtc ctttttctct gggtgatgcc
     1981 cttagaataa cactatatgc aatgtaactc acaatgttcc aggaccaaag acttgatgga
     2041 ggggctagag gcgacccttg ttgtaaaagg cgatcagaac acctgaggga ggaaggggct
     2101 tgcagttttc ccagcccttc tcgctgccaa ggcagcagtg gtgctgtgga tgggctgggg
     2161 actgcgggac agagcctgct actacttggg agttggtgct gccctgtggc atggaggggt
     2221 gggaggggct gagatggctg ctggcccggc ctccaagagt tctggacagg aggcagacac
     2281 tgcccagatg ctcggtggag ggacagtgat ggcctttgac tcatgaggcc tggagaaaag
     2341 tatcaaaggt ctcaccatgt aagagtgatt tccgatttct ctcctttcag ttgtgtgaaa
     2401 aaacagctgg cctgggttcc attagcaaat taaatcatct tcaatcttaa attagaaacc
     2461 agaatgatct tcaggataaa aagaacttct gaatctctgc aataggaaat gtttcgatca
     2521 tgcaagtgct ttcccagcca aatgtctgtg ctctctgtgt cactgagggc cacaggttcc
     2581 tctaacatct gtcactgtca cttcaccagg caggccttgg agttccatga caaaatcact
     2641 tttgtcagac aaagaatgta tcctttactt ttctcaaatg gaataaaatt atttcttctg
     2701 tggaggaaaa
//
