LOCUS       NM_012135               1643 bp    mRNA    linear   PRI 08-JUN-2024
DEFINITION  Homo sapiens family with sequence similarity 50 member B (FAM50B),
            mRNA.
ACCESSION   NM_012135
VERSION     NM_012135.3
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 1643)
  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   2  (bases 1 to 1643)
  AUTHORS   Fragoza,R., Das,J., Wierbowski,S.D., Liang,J., Tran,T.N., Liang,S.,
            Beltran,J.F., Rivera-Erick,C.A., Ye,K., Wang,T.Y., Yao,L., Mort,M.,
            Stenson,P.D., Cooper,D.N., Wei,X., Keinan,A., Schimenti,J.C.,
            Clark,A.G. and Yu,H.
  TITLE     Extensive disruption of protein interactions by genetic variants
            across the allele frequency spectrum in human populations
  JOURNAL   Nat Commun 10 (1), 4141 (2019)
   PUBMED   31515488
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 1643)
  AUTHORS   Kolarova,J., Tangen,I., Bens,S., Gillessen-Kaesbach,G., Gutwein,J.,
            Kautza,M., Rydzanicz,M., Stephani,U., Siebert,R., Ammerpohl,O. and
            Caliebe,A.
  TITLE     Array-based DNA methylation analysis in individuals with
            developmental delay/intellectual disability and normal molecular
            karyotype
  JOURNAL   Eur J Med Genet 58 (8), 419-425 (2015)
   PUBMED   26003415
REFERENCE   4  (bases 1 to 1643)
  AUTHORS   Sahni,N., Yi,S., Taipale,M., Fuxman Bass,J.I.,
            Coulombe-Huntington,J., Yang,F., Peng,J., Weile,J., Karras,G.I.,
            Wang,Y., Kovacs,I.A., Kamburov,A., Krykbaeva,I., Lam,M.H.,
            Tucker,G., Khurana,V., Sharma,A., Liu,Y.Y., Yachie,N., Zhong,Q.,
            Shen,Y., Palagi,A., San-Miguel,A., Fan,C., Balcha,D., Dricot,A.,
            Jordan,D.M., Walsh,J.M., Shah,A.A., Yang,X., Stoyanova,A.K.,
            Leighton,A., Calderwood,M.A., Jacob,Y., Cusick,M.E.,
            Salehi-Ashtiani,K., Whitesell,L.J., Sunyaev,S., Berger,B.,
            Barabasi,A.L., Charloteaux,B., Hill,D.E., Hao,T., Roth,F.P.,
            Xia,Y., Walhout,A.J.M., Lindquist,S. and Vidal,M.
  TITLE     Widespread macromolecular interaction perturbations in human
            genetic disorders
  JOURNAL   Cell 161 (3), 647-660 (2015)
   PUBMED   25910212
REFERENCE   5  (bases 1 to 1643)
  AUTHORS   Green,B.B., Kappil,M., Lambertini,L., Armstrong,D.A., Guerin,D.J.,
            Sharp,A.J., Lester,B.M., Chen,J. and Marsit,C.J.
  TITLE     Expression of imprinted genes in placenta is associated with infant
            neurobehavioral development
  JOURNAL   Epigenetics 10 (9), 834-841 (2015)
   PUBMED   26198301
REFERENCE   6  (bases 1 to 1643)
  AUTHORS   Beygo,J., Ammerpohl,O., Gritzan,D., Heitmann,M., Rademacher,K.,
            Richter,J., Caliebe,A., Siebert,R., Horsthemke,B. and Buiting,K.
  TITLE     Deep bisulfite sequencing of aberrantly methylated loci in a
            patient with multiple methylation defects
  JOURNAL   PLoS One 8 (10), e76953 (2013)
   PUBMED   24130816
  REMARK    Erratum:[PLoS One. 2013;8(12).
            doi:10.1371/annotation/8a05c514-48b6-4dd9-b322-273b575cbd95]
            Publication Status: Online-Only
REFERENCE   7  (bases 1 to 1643)
  AUTHORS   Zhang,A., Skaar,D.A., Li,Y., Huang,D., Price,T.M., Murphy,S.K. and
            Jirtle,R.L.
  TITLE     Novel retrotransposed imprinted locus identified at human 6p25
  JOURNAL   Nucleic Acids Res 39 (13), 5388-5400 (2011)
   PUBMED   21421564
REFERENCE   8  (bases 1 to 1643)
  AUTHORS   Venkatesan,K., Rual,J.F., Vazquez,A., Stelzl,U., Lemmens,I.,
            Hirozane-Kishikawa,T., Hao,T., Zenkner,M., Xin,X., Goh,K.I.,
            Yildirim,M.A., Simonis,N., Heinzmann,K., Gebreab,F., Sahalie,J.M.,
            Cevik,S., Simon,C., de Smet,A.S., Dann,E., Smolyar,A.,
            Vinayagam,A., Yu,H., Szeto,D., Borick,H., Dricot,A., Klitgord,N.,
            Murray,R.R., Lin,C., Lalowski,M., Timm,J., Rau,K., Boone,C.,
            Braun,P., Cusick,M.E., Roth,F.P., Hill,D.E., Tavernier,J.,
            Wanker,E.E., Barabasi,A.L. and Vidal,M.
  TITLE     An empirical framework for binary interactome mapping
  JOURNAL   Nat Methods 6 (1), 83-90 (2009)
   PUBMED   19060904
REFERENCE   9  (bases 1 to 1643)
  AUTHORS   Sedlacek,Z., Munstermann,E., Dhorne-Pollet,S., Otto,C., Bock,D.,
            Schutz,G. and Poustka,A.
  TITLE     Human and mouse XAP-5 and XAP-5-like (X5L) genes: identification of
            an ancient functional retroposon differentially expressed in testis
  JOURNAL   Genomics 61 (2), 125-132 (1999)
   PUBMED   10534398
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from BI488606.1, BC001261.1 and
            DB566944.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 23, 2018 this sequence version replaced NM_012135.2.
            
            Summary: This gene contains an intronless ORF that arose from
            ancestral retroposition. The encoded protein is related to a plant
            protein that plays a role in the circadian clock. This gene is
            adjacent to a differentially methylated region (DMR) and is
            imprinted and paternally expressed in many tissues. [provided by
            RefSeq, Nov 2015].
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR3476690.704028.1, BC001261.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            imprinted gene         :: PMID: 21421564
            MANE Ensembl match     :: ENST00000648326.1/ ENSP00000496837.1
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-15                BI488606.1         9-23
            16-1636             BC001261.1         1-1621
            1637-1643           DB566944.1         446-452
FEATURES             Location/Qualifiers
     source          1..1643
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="6"
                     /map="6p25.2"
     gene            1..1643
                     /gene="FAM50B"
                     /gene_synonym="D6S2654E; X5L"
                     /note="family with sequence similarity 50 member B"
                     /db_xref="GeneID:26240"
                     /db_xref="HGNC:HGNC:18789"
                     /db_xref="MIM:614686"
     exon            1..114
                     /gene="FAM50B"
                     /gene_synonym="D6S2654E; X5L"
                     /inference="alignment:Splign:2.1.0"
     exon            115..1643
                     /gene="FAM50B"
                     /gene_synonym="D6S2654E; X5L"
                     /inference="alignment:Splign:2.1.0"
     CDS             138..1115
                     /gene="FAM50B"
                     /gene_synonym="D6S2654E; X5L"
                     /note="XAP5-like protein; XAP5 like"
                     /codon_start=1
                     /product="protein FAM50B"
                     /protein_id="NP_036267.1"
                     /db_xref="CCDS:CCDS4487.1"
                     /db_xref="GeneID:26240"
                     /db_xref="HGNC:HGNC:18789"
                     /db_xref="MIM:614686"
                     /translation="MAQYKGTMREAGRAMHLLKKRERQREQMEVLKQRIAEETILKSQ
                     VDKRFSAHYDAVEAELKSSTVGLVTLNDMKARQEALVRERERQLAKRQHLEEQRLQQE
                     RQREQEQRRERKRKISCLSFALDDLDDQADAAEARRAGNLGKNPDVDTSFLPDRDREE
                     EENRLREELRQEWEAQREKVKDEEMEVTFSYWDGSGHRRTVRVRKGNTVQQFLKKALQ
                     GLRKDFLELRSAGVEQLMFIKEDLILPHYHTFYDFIIARARGKSGPLFSFDVHDDVRL
                     LSDATMEKDESHAGKVVLRSWYEKNKHIFPASRWEAYDPEKKWDKYTIR"
     regulatory      1220..1225
                     /regulatory_class="polyA_signal_sequence"
                     /gene="FAM50B"
                     /gene_synonym="D6S2654E; X5L"
                     /note="hexamer: AATAAA"
     polyA_site      1247
                     /gene="FAM50B"
                     /gene_synonym="D6S2654E; X5L"
                     /note="major polyA site"
     regulatory      1621..1626
                     /regulatory_class="polyA_signal_sequence"
                     /gene="FAM50B"
                     /gene_synonym="D6S2654E; X5L"
                     /note="hexamer: AATAAA"
     polyA_site      1643
                     /gene="FAM50B"
                     /gene_synonym="D6S2654E; X5L"
                     /note="major polyA site"
ORIGIN      
        1 acttcctgtg tccacggctg tcgcgagagc ccggggcgag tgggcctctg ctcgtgggtg
       61 gttctcgtgg aggtcagctc ccgcgtgtct ccgctcgaca gggtgcttgg gcagagccca
      121 tcgggtaggc gcgggccatg gcgcagtaca agggcaccat gcgcgaggca ggccgtgcca
      181 tgcacctcct caagaagcgc gaaaggcagc gggagcagat ggaggtgctg aagcagcgca
      241 tcgccgagga gaccatcctc aagtcgcagg tggacaagag gttctcggcg cattacgacg
      301 ccgtggaggc cgagctgaag tccagcacgg tgggcctggt gaccctgaac gacatgaagg
      361 cccggcagga ggccctggtc agggagcgcg agcggcagct ggccaagcgc cagcacctgg
      421 aggagcagcg gctgcagcag gagcggcagc gggagcagga gcagcggcgc gagcgcaagc
      481 gtaagatctc ctgcctgtcc tttgcactag acgacctcga tgaccaggcc gacgcggccg
      541 aggccaggcg cgccggaaac ctgggcaaga accccgacgt ggacaccagc ttcctgccag
      601 accgcgaccg cgaggaggag gagaaccggc tccgagagga gctgcgccaa gagtgggagg
      661 cgcagcgcga gaaagtgaag gacgaggaga tggaggtcac cttcagctac tgggacggct
      721 cgggccaccg gcgcacggtg cgggtgcgca agggcaacac ggtgcagcag ttcctgaaga
      781 aggcgctgca ggggctgcgc aaggacttcc tggagctgcg ctccgccggc gtggagcagc
      841 tcatgttcat caaggaggac ctcatcctgc cgcactacca caccttctac gacttcatca
      901 tcgccagggc gaggggcaag agcgggccgc tcttcagctt cgatgtgcac gatgacgtgc
      961 gcctgctcag cgacgccacc atggagaagg acgagtcgca cgcgggcaag gtggtgctgc
     1021 gcagctggta cgagaagaac aagcacatct tccccgccag ccgctgggag gcctatgacc
     1081 ccgagaagaa gtgggacaag tacaccatcc gctaacaccc gcctgccaga gcggaaaccg
     1141 ggggtggggg gagacactca tttctaggcc ccatcaccag tcacttgatt tcgtgacctt
     1201 gatttcttcc cccaaattta ataaagacag agggttctca tgattcacat tggttgtgct
     1261 attgctgatg ttatgctttg gttgcttggt tggtcttttc tgagtatttt agtgttgcca
     1321 cctggatttg ctgcattgct ctgctgagct gtattgaaac catgactggg cccactgtca
     1381 gacagaaatt agaataggag gcacattttt tacctggtgg ttatgagcat ggacttgggg
     1441 gccacagtga ctgagtttga ttcccgacac agcctcctcc ttgctgtgta gttttgggta
     1501 agcttattaa acccccatgc ctcagtttgg tcacctgtaa aaggaaataa caagagcact
     1561 tactttataa gattgatgtg agtattaagt gaattaatat ttgtaaaacg cttagctctt
     1621 aataaatgtt tctgttgtta tta
//
