LOCUS       NM_001393391            2465 bp    mRNA    linear   PRI 08-APR-2024
DEFINITION  Homo sapiens membrane spanning 4-domains A4E (MS4A4E), transcript
            variant 2, mRNA.
ACCESSION   NM_001393391
VERSION     NM_001393391.1
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 2465)
  AUTHORS   Bressler,J., Mosley,T.H., Penman,A., Gottesman,R.F., Windham,B.G.,
            Knopman,D.S., Wruck,L.M. and Boerwinkle,E.
  TITLE     Genetic variants associated with risk of Alzheimer's disease
            contribute to cognitive change in midlife: The Atherosclerosis Risk
            in Communities Study
  JOURNAL   Am J Med Genet B Neuropsychiatr Genet 174 (3), 269-282 (2017)
   PUBMED   27781389
  REMARK    GeneRIF: Addition of the minor allele for rs670139 (MS4A4E),
            rs9331896 (CLU), and rs12155159 (NME8) was nominally associated
            with change on the DWRT, DSST, and WFT, respectively, in whites.
            For rs670139 and rs9331896 the association was only significant in
            individuals bearing at least one APOE 4 allele in stratified
            analyses.
REFERENCE   2  (bases 1 to 2465)
  AUTHORS   Ebbert,M.T.W., Boehme,K.L., Wadsworth,M.E., Staley,L.A.,
            Mukherjee,S., Crane,P.K., Ridge,P.G. and Kauwe,J.S.K.
  CONSRTM   Alzheimer's Disease Neuroimaging Initiative; Alzheimer's Disease
            Genetics Consortium
  TITLE     Interaction between variants in CLU and MS4A4E modulates
            Alzheimer's disease risk
  JOURNAL   Alzheimers Dement 12 (2), 121-129 (2016)
   PUBMED   26449541
  REMARK    GeneRIF: We replicated the rs11136000 (CLU)- rs670139 (MS4A4E)
            interaction, demonstrated an association in APOE epsilon4 negative
            subjects, and reported evidence of a possible dominant effect for
            MS4A4E.
REFERENCE   3  (bases 1 to 2465)
  AUTHORS   Ebbert,M.T., Ridge,P.G., Wilson,A.R., Sharp,A.R., Bailey,M.,
            Norton,M.C., Tschanz,J.T., Munger,R.G., Corcoran,C.D. and
            Kauwe,J.S.
  TITLE     Population-based analysis of Alzheimer's disease risk alleles
            implicates genetic interactions
  JOURNAL   Biol Psychiatry 75 (9), 732-737 (2014)
   PUBMED   23954108
REFERENCE   4  (bases 1 to 2465)
  AUTHORS   Hollingworth,P., Harold,D., Sims,R., Gerrish,A., Lambert,J.C.,
            Carrasquillo,M.M., Abraham,R., Hamshere,M.L., Pahwa,J.S.,
            Moskvina,V., Dowzell,K., Jones,N., Stretton,A., Thomas,C.,
            Richards,A., Ivanov,D., Widdowson,C., Chapman,J., Lovestone,S.,
            Powell,J., Proitsi,P., Lupton,M.K., Brayne,C., Rubinsztein,D.C.,
            Gill,M., Lawlor,B., Lynch,A., Brown,K.S., Passmore,P.A., Craig,D.,
            McGuinness,B., Todd,S., Holmes,C., Mann,D., Smith,A.D.,
            Beaumont,H., Warden,D., Wilcock,G., Love,S., Kehoe,P.G.,
            Hooper,N.M., Vardy,E.R., Hardy,J., Mead,S., Fox,N.C., Rossor,M.,
            Collinge,J., Maier,W., Jessen,F., Ruther,E., Schurmann,B., Heun,R.,
            Kolsch,H., van den Bussche,H., Heuser,I., Kornhuber,J.,
            Wiltfang,J., Dichgans,M., Frolich,L., Hampel,H., Gallacher,J.,
            Hull,M., Rujescu,D., Giegling,I., Goate,A.M., Kauwe,J.S.,
            Cruchaga,C., Nowotny,P., Morris,J.C., Mayo,K., Sleegers,K.,
            Bettens,K., Engelborghs,S., De Deyn,P.P., Van Broeckhoven,C.,
            Livingston,G., Bass,N.J., Gurling,H., McQuillin,A., Gwilliam,R.,
            Deloukas,P., Al-Chalabi,A., Shaw,C.E., Tsolaki,M., Singleton,A.B.,
            Guerreiro,R., Muhleisen,T.W., Nothen,M.M., Moebus,S., Jockel,K.H.,
            Klopp,N., Wichmann,H.E., Pankratz,V.S., Sando,S.B., Aasly,J.O.,
            Barcikowska,M., Wszolek,Z.K., Dickson,D.W., Graff-Radford,N.R.,
            Petersen,R.C., van Duijn,C.M., Breteler,M.M., Ikram,M.A.,
            DeStefano,A.L., Fitzpatrick,A.L., Lopez,O., Launer,L.J.,
            Seshadri,S., Berr,C., Campion,D., Epelbaum,J., Dartigues,J.F.,
            Tzourio,C., Alperovitch,A., Lathrop,M., Feulner,T.M., Friedrich,P.,
            Riehle,C., Krawczak,M., Schreiber,S., Mayhaus,M., Nicolhaus,S.,
            Wagenpfeil,S., Steinberg,S., Stefansson,H., Stefansson,K.,
            Snaedal,J., Bjornsson,S., Jonsson,P.V., Chouraki,V.,
            Genier-Boley,B., Hiltunen,M., Soininen,H., Combarros,O.,
            Zelenika,D., Delepine,M., Bullido,M.J., Pasquier,F., Mateo,I.,
            Frank-Garcia,A., Porcellini,E., Hanon,O., Coto,E., Alvarez,V.,
            Bosco,P., Siciliano,G., Mancuso,M., Panza,F., Solfrizzi,V.,
            Nacmias,B., Sorbi,S., Bossu,P., Piccardi,P., Arosio,B., Annoni,G.,
            Seripa,D., Pilotto,A., Scarpini,E., Galimberti,D., Brice,A.,
            Hannequin,D., Licastro,F., Jones,L., Holmans,P.A., Jonsson,T.,
            Riemenschneider,M., Morgan,K., Younkin,S.G., Owen,M.J.,
            O'Donovan,M., Amouyel,P. and Williams,J.
  CONSRTM   Alzheimer's Disease Neuroimaging Initiative; CHARGE consortium;
            EADI1 consortium
  TITLE     Common variants at ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are
            associated with Alzheimer's disease
  JOURNAL   Nat Genet 43 (5), 429-435 (2011)
   PUBMED   21460840
  REMARK    GeneRIF: ABCA7 and the MS4A6A/MS4A4E gene cluster are new
            Alzheimer's disease susceptibility loci.
REFERENCE   5  (bases 1 to 2465)
  AUTHORS   Liang,Y., Buckley,T.R., Tu,L., Langdon,S.D. and Tedder,T.F.
  TITLE     Structural organization of the human MS4A gene cluster on
            Chromosome 11q12
  JOURNAL   Immunogenetics 53 (5), 357-368 (2001)
   PUBMED   11486273
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AP003970.3.
            
            Summary: Most MS4A genes, including MS4A4E, encode proteins with at
            least 4 potential transmembrane domains and N- and C-terminal
            cytoplasmic domains encoded by distinct exons.[supplied by OMIM,
            Apr 2004].
            
            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##
            RNAseq introns :: single sample supports all introns SAMEA2149004
                              [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            inferred exon combination :: based on alignments, homology
            MANE Ensembl match        :: ENST00000651255.1/ ENSP00000499123.1
            RefSeq Select criteria    :: based on manual assertion, expression,
                                         longest protein
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-180               AP003970.3         73276-73455         c
            181-340             AP003970.3         60230-60389         c
            341-374             AP003970.3         58912-58945         c
            375-418             AP003970.3         44889-44932         c
            419-577             AP003970.3         43292-43450         c
            578-679             AP003970.3         38911-39012         c
            680-786             AP003970.3         36032-36138         c
            787-855             AP003970.3         35208-35276         c
            856-2465            AP003970.3         30588-32197         c
FEATURES             Location/Qualifiers
     source          1..2465
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="11"
                     /map="11q12.2"
     gene            1..2465
                     /gene="MS4A4E"
                     /note="membrane spanning 4-domains A4E"
                     /db_xref="GeneID:643680"
                     /db_xref="HGNC:HGNC:14284"
                     /db_xref="MIM:608401"
     exon            1..180
                     /gene="MS4A4E"
                     /inference="alignment:Splign:2.1.0"
     exon            181..340
                     /gene="MS4A4E"
                     /inference="alignment:Splign:2.1.0"
     CDS             197..1192
                     /gene="MS4A4E"
                     /note="isoform 2 is encoded by transcript variant 2;
                     putative membrane-spanning 4-domains subfamily A member
                     4E"
                     /codon_start=1
                     /product="putative membrane-spanning 4-domains subfamily A
                     member 4E isoform 2"
                     /protein_id="NP_001380320.1"
                     /db_xref="CCDS:CCDS91480.1"
                     /db_xref="GeneID:643680"
                     /db_xref="HGNC:HGNC:14284"
                     /db_xref="MIM:608401"
                     /translation="MTTMQGMEQTTPGAGPDVPQLGNIDVIHSYLCKGLQEKFFKRKP
                     KVLGVLCGHKFSTHSVSLSVAAGIRTTKGLVGGSLGKNITSSVLAISGILINAISLTF
                     YSFRYHYCNHDQLSSNCYMTMSILMGTDGMVLLLSVLEFCIAVALSAFGCKVLCCSPS
                     ESKNKIRSNTFMCYLLSIQMQYDGKRLNVDVDSTVWCSGDGQYLEKVYYDILSSWLRI
                     ESIYRVLNGAQAGVQWRDLGSLQPPPPSRLPWPPKVPRVQPLPGRHPVWEVRSVSAWP
                     PIVWDVRSPSAWLPSLESEERLCPAAIPSRKWGAPLPGHHPIWEVRSVSARPPIF"
     exon            341..374
                     /gene="MS4A4E"
                     /inference="alignment:Splign:2.1.0"
     exon            375..418
                     /gene="MS4A4E"
                     /inference="alignment:Splign:2.1.0"
     exon            419..577
                     /gene="MS4A4E"
                     /inference="alignment:Splign:2.1.0"
     exon            578..679
                     /gene="MS4A4E"
                     /inference="alignment:Splign:2.1.0"
     exon            680..786
                     /gene="MS4A4E"
                     /inference="alignment:Splign:2.1.0"
     exon            787..855
                     /gene="MS4A4E"
                     /inference="alignment:Splign:2.1.0"
     exon            856..2465
                     /gene="MS4A4E"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2443..2448
                     /regulatory_class="polyA_signal_sequence"
                     /gene="MS4A4E"
                     /note="hexamer: AATAAA"
     regulatory      2447..2452
                     /regulatory_class="polyA_signal_sequence"
                     /gene="MS4A4E"
                     /note="hexamer: AATAAA"
     polyA_site      2462
                     /gene="MS4A4E"
                     /note="major polyA site"
     polyA_site      2465
                     /gene="MS4A4E"
ORIGIN      
        1 agaagttctc aacacatcct ttaaggttcc aaacatctac tagaaaagga gtgcagattt
       61 aaactgagtg aggtgtggag tgggggaagc tgactgtgtc tggaacaaag aactttgagg
      121 aacttgccca gagccctgca ctcatcagac ctgcagcaga cattgcaggc ctgaagaaag
      181 caccttttct gctgccatga caaccatgca aggaatggaa cagaccactc caggggctgg
      241 ccctgatgtg ccccagctgg gaaacataga tgtcatacat tcatatctgt gtaaaggatt
      301 gcaagagaag ttcttcaaga ggaaacccaa agtccttggg gttttgtgtg gacataagtt
      361 ttcaactcat tcggtatcct tatcagttgc agcaggaatt agaacaacaa aaggtctggt
      421 tggaggtagt ctaggaaaga atatcaccag ttcagtcttg gctatatcag ggatcttaat
      481 caatgcaata agcttgacgt tttattcatt ccgttaccat tactgtaacc acgatcagtt
      541 gtcaagtaat tgttacatga ctatgtccat tttaatgggt acggatggca tggtgctcct
      601 cttaagtgtg ctggaattct gcattgctgt ggccctctct gcctttggat gtaaagtgct
      661 ttgttgtagc cccagtgaga gcaaaaataa aattagaagc aatactttca tgtgctacct
      721 cctttctatt cagatgcaat atgatggaaa gagactaaat gttgatgtcg acagtactgt
      781 atggtgctcc ggagatggac agtatctgga aaaagtctat tatgacattc tatcttcttg
      841 gttgaggatt gaaagtattt atcgagtgct caatggtgcc caggctggag tgcagtggcg
      901 tgatctcggc tccctacaac ctccacctcc cagccgcctg ccttggcctc ccaaagtgcc
      961 gagagtgcag cctctgcccg gccgccaccc cgtctgggaa gtgaggagcg tctctgcctg
     1021 gccgcctatc gtctgggacg tgaggagccc ctctgcctgg ctgcccagtc tggaaagtga
     1081 ggagcgtctc tgcccggctg ccatcccatc taggaagtgg ggagcgcctc ttcccggcca
     1141 ccatcccatc tgggaggtga ggagtgtctc cgcccggccg cccatcttct gagatgtggg
     1201 gagcgccttt gccccaccgc cctgtctggg atgtgaggag cacctctgcc cggccgcgac
     1261 cccgtctggg aggtgaggag cgtctctgcc cagccgcccc atctgagaag ggaggagacc
     1321 ctccgcctgg caaccgcccc gtctgagaag tgaggagccc ctccgcccgg cagccacccc
     1381 gtctgggaag tgaggagcgt ctccgccagg cagccacccc gtccgggagg gaggtggggg
     1441 tcagcccccg ccaggccagc tgccccatcc gggagggagg tggggggggt cagccccccg
     1501 cccggccagc cgccccgtcc gggaggtgag gggcgcctct gcccagccgc ccctactggg
     1561 aagtgaggag cccctctacc cggccagccg ctccgtccgg gagggaggtg ggggggtcag
     1621 accccgcccg gccagccgcc ccgtccggga gggaggtggg gggttcagcc ccccacccgg
     1681 ccagccacca cgtctgggag ggaggtgggg gggtcagccc tctgcccggc cagccgcccc
     1741 gtccgggagg gaggtggggg gttcagcccc ccacccggcc agccgccccg tccgggaggg
     1801 aggtggaggg gtcagccccc cgcccggcca gccgccccgt ccgggaggtg aggggtgcct
     1861 ctgcccagcc gcccctactg ggaagtgagg agcccctctg cccggccacc accccatctg
     1921 ggaagtgtac ccaatagctc attgagaacg ggccatgagg acaatggcgg ttttgtggaa
     1981 tagaaagggg ggaaaggtgg ggaaaagatt gagaaatcgg atggttgcct tgtctgtgtg
     2041 gaaagaagta gacatgggag acttttcatt ttgttctgta ctaagaaaaa ttcttctgcc
     2101 ttgggatcct gttgatctgt gaccttaccc ccaaccctgt gctctctgaa acatgtgctg
     2161 tgtccactca gggttaaatg gattaagggc ggtgcaaggt gtgctttgtt aaacagatgc
     2221 ttgaaggcag catgctcgtt aagagtcatc accactccct aatctcaagt acccagggac
     2281 acaaacacct cggaaggccg cagggtcctc tgcctaggaa aaccagagac ctttgttcac
     2341 ttgtttatct gctgaccttc cctccactat tgtcctatga ccctgccaaa tccccctctg
     2401 tgagaaacac ccaagaatgg tcaataaaaa attaaataaa taaataaata aataaataaa
     2461 aagta
//
