LOCUS       NM_153346               4614 bp    mRNA    linear   PRI 20-FEB-2025
DEFINITION  Homo sapiens BEN domain containing 2 (BEND2), transcript variant 1,
            mRNA.
ACCESSION   NM_153346
VERSION     NM_153346.5
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 4614)
  AUTHORS   Lehman,N.L.
  TITLE     Early ependymal tumor with MN1-BEND2 fusion: a mostly cerebral
            tumor of female children with a good prognosis that is distinct
            from classical astroblastoma
  JOURNAL   J Neurooncol 161 (3), 425-439 (2023)
   PUBMED   36604386
  REMARK    GeneRIF: Early ependymal tumor with MN1-BEND2 fusion: a mostly
            cerebral tumor of female children with a good prognosis that is
            distinct from classical astroblastoma.
            Review article
REFERENCE   2  (bases 1 to 4614)
  AUTHORS   Lucas,C.G., Gupta,R., Wu,J., Shah,K., Ravindranathan,A.,
            Barreto,J., Gener,M., Ginn,K.F., Prall,O.W.J., Xu,H., Kee,D.,
            Ko,H.S., Yaqoob,N., Zia,N., Florez,A., Cha,S., Perry,A.,
            Clarke,J.L., Chang,S.M., Berger,M.S. and Solomon,D.A.
  TITLE     EWSR1-BEND2 fusion defines an epigenetically distinct subtype of
            astroblastoma
  JOURNAL   Acta Neuropathol 143 (1), 109-113 (2022)
   PUBMED   34825267
  REMARK    GeneRIF: EWSR1-BEND2 fusion defines an epigenetically distinct
            subtype of astroblastoma.
REFERENCE   3  (bases 1 to 4614)
  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 4614)
  AUTHORS   Yamasaki,K., Nakano,Y., Nobusawa,S., Okuhiro,Y., Fukushima,H.,
            Inoue,T., Murakami,C., Hirato,J., Kunihiro,N., Matsusaka,Y.,
            Honda-Kitahara,M., Ozawa,T., Shiraishi,K., Kohno,T., Ichimura,K.
            and Hara,J.
  TITLE     Spinal cord astroblastoma with an EWSR1-BEND2 fusion classified as
            a high-grade neuroepithelial tumour with MN1 alteration
  JOURNAL   Neuropathol Appl Neurobiol 46 (2), 190-193 (2020)
   PUBMED   31863478
  REMARK    GeneRIF: Spinal cord astroblastoma with an EWSR1-BEND2 fusion
            classified as a high-grade neuroepithelial tumour with MN1
            alteration.
REFERENCE   5  (bases 1 to 4614)
  AUTHORS   Pineau,C., Hikmet,F., Zhang,C., Oksvold,P., Chen,S., Fagerberg,L.,
            Uhlen,M. and Lindskog,C.
  TITLE     Cell Type-Specific Expression of Testis Elevated Genes Based on
            Transcriptomics and Antibody-Based Proteomics
  JOURNAL   J Proteome Res 18 (12), 4215-4230 (2019)
   PUBMED   31429579
REFERENCE   6  (bases 1 to 4614)
  AUTHORS   Burford,A., Mackay,A., Popov,S., Vinci,M., Carvalho,D., Clarke,M.,
            Izquierdo,E., Avery,A., Jacques,T.S., Ingram,W.J., Moore,A.S.,
            Frawley,K., Hassall,T.E., Robertson,T. and Jones,C.
  TITLE     The ten-year evolutionary trajectory of a highly recurrent
            paediatric high grade neuroepithelial tumour with MN1:BEND2 fusion
  JOURNAL   Sci Rep 8 (1), 1032 (2018)
   PUBMED   29348602
  REMARK    Publication Status: Online-Only
REFERENCE   7  (bases 1 to 4614)
  AUTHORS   Bahi-Buisson,N., Girard,B., Gautier,A., Nectoux,J., Fichou,Y.,
            Saillour,Y., Poirier,K., Chelly,J. and Bienvenu,T.
  TITLE     Epileptic encephalopathy in a girl with an interstitial deletion of
            Xp22 comprising promoter and exon 1 of the CDKL5 gene
  JOURNAL   Am J Med Genet B Neuropsychiatr Genet 153B (1), 202-207 (2010)
   PUBMED   19455595
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            BX952865.1, BC037301.2, AK128155.1 and AL096763.14.
            This sequence is a reference standard in the RefSeqGene project.
            
            On May 17, 2019 this sequence version replaced NM_153346.4.
            
            Summary: This gene encodes a protein which has two BEN domains in
            the C-terminus. These domains are found in proteins which
            participate in protein and DNA interactions which occur during
            chromatin restructuring or transcription. Alternative splicing
            results in multiple transcript variants. [provided by RefSeq, Aug
            2011].
            
            Transcript Variant: This variant (1) represents the longer
            transcript and encodes the longer isoform (1).
            
            Sequence Note: The RefSeq transcript and protein were derived from
            transcript and 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##
            Transcript exon combination :: BC037301.2, AK128155.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1968968, SAMEA2161674
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000380033.9/ ENSP00000369372.4
            RefSeq Select criteria :: based on expression
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-161               BX952865.1         20-180
            162-1888            BC037301.2         160-1886
            1889-2117           AK128155.1         1889-2117
            2118-2321           BC037301.2         2116-2319
            2322-3849           AL096763.14        2524-4051           c
            3850-4614           BC037301.2         3848-4612
FEATURES             Location/Qualifiers
     source          1..4614
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="X"
                     /map="Xp22.13"
     gene            1..4614
                     /gene="BEND2"
                     /gene_synonym="CXorf20"
                     /note="BEN domain containing 2"
                     /db_xref="GeneID:139105"
                     /db_xref="HGNC:HGNC:28509"
     exon            1..161
                     /gene="BEND2"
                     /gene_synonym="CXorf20"
                     /inference="alignment:Splign:2.1.0"
     CDS             137..2536
                     /gene="BEND2"
                     /gene_synonym="CXorf20"
                     /note="isoform 1 is encoded by transcript variant 1"
                     /codon_start=1
                     /product="BEN domain-containing protein 2 isoform 1"
                     /protein_id="NP_699177.2"
                     /db_xref="CCDS:CCDS14184.1"
                     /db_xref="GeneID:139105"
                     /db_xref="HGNC:HGNC:28509"
                     /translation="MSERTQEQDFVIITVDDSDDNNDCSIEMVEVSETADNSTNDIAD
                     DSTYVTADNPTDDTATQPNFPGGNDGHHRPLQMSYGSGSVTQAGVQWHDHSSLQPQPL
                     GLKQFFHLSLPSSWDDRRTPPCPVAHGDQIVSQINHPVHLRRYSYNSEEVDFPKRGRF
                     YTPEVQSSISPPAERQETHAWASPAVTSLESAACHELQEADLSESLSYPRIVSSSSLQ
                     QYVAQGGSFPCFGMPWNFISGGAESTNAVISFANATTAVPMAVLSRRESSLANNPGVV
                     NYSALPENENVGPGRALSSFCFHPNLEMPERPANSSKNSTETANYPTLMGNYNGQNTA
                     SLSVFIPPYFAEKIILTEMPGTTETNVENNSQTVYYPALSGNTSAPYPASSYLPITSN
                     FESGPQMSYGTMSYSTEMKNNCDQDDASASACLTPDFALLPLNILVKVDTNTENSVNT
                     MNRSTLLDSDSGQDSSSSSVCIPPKYGYLGDPKRNVRVLKIHLLAVQNMAKPKQAACY
                     LVRILFSKEILISSSVDIHLKDSQSLDPNKMAALREYLATTFPTCDLHEHGKDWQDCI
                     SGINSMIYCLCSEGKSTPKTVRKNKKRTNRVASASADRNDQRGRDGGEGCSWMFQPMN
                     NSKMREKRNLQPNSNAIPEGMREPSTDNPEEPGEAWSYFGRPWRNIRMPCSVLTLAKT
                     KSCASLSARYLIQKLFTKDVLVQSNVYGNLKHGLCALDPNKISALREFLQENYPICDL
                     SENGRDWKSCVTSINSGIRSLRHDVRRAEARSQSLPAVTPPELEQESKPGDPDATDPS
                     T"
     exon            162..374
                     /gene="BEND2"
                     /gene_synonym="CXorf20"
                     /inference="alignment:Splign:2.1.0"
     exon            375..512
                     /gene="BEND2"
                     /gene_synonym="CXorf20"
                     /inference="alignment:Splign:2.1.0"
     exon            513..628
                     /gene="BEND2"
                     /gene_synonym="CXorf20"
                     /inference="alignment:Splign:2.1.0"
     exon            629..1043
                     /gene="BEND2"
                     /gene_synonym="CXorf20"
                     /inference="alignment:Splign:2.1.0"
     exon            1044..1169
                     /gene="BEND2"
                     /gene_synonym="CXorf20"
                     /inference="alignment:Splign:2.1.0"
     exon            1170..1316
                     /gene="BEND2"
                     /gene_synonym="CXorf20"
                     /inference="alignment:Splign:2.1.0"
     exon            1317..1424
                     /gene="BEND2"
                     /gene_synonym="CXorf20"
                     /inference="alignment:Splign:2.1.0"
     exon            1425..1565
                     /gene="BEND2"
                     /gene_synonym="CXorf20"
                     /inference="alignment:Splign:2.1.0"
     exon            1566..1766
                     /gene="BEND2"
                     /gene_synonym="CXorf20"
                     /inference="alignment:Splign:2.1.0"
     exon            1767..1888
                     /gene="BEND2"
                     /gene_synonym="CXorf20"
                     /inference="alignment:Splign:2.1.0"
     exon            1889..2117
                     /gene="BEND2"
                     /gene_synonym="CXorf20"
                     /inference="alignment:Splign:2.1.0"
     exon            2118..2321
                     /gene="BEND2"
                     /gene_synonym="CXorf20"
                     /inference="alignment:Splign:2.1.0"
     exon            2322..4614
                     /gene="BEND2"
                     /gene_synonym="CXorf20"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4592..4597
                     /regulatory_class="polyA_signal_sequence"
                     /gene="BEND2"
                     /gene_synonym="CXorf20"
                     /note="hexamer: AATAAA"
     polyA_site      4614
                     /gene="BEND2"
                     /gene_synonym="CXorf20"
                     /note="major polyA site"
ORIGIN      
        1 attgtgcctc ggacaacgag tgtacgcagt taccacacag ttaccaagca gttacctcag
       61 agccgcggcg cagacgtagg cctcaggtct cgggcctcag gtctcgggcc tcagagccag
      121 accccgccat ctcacgatgt cagagaggac ccaggaacag gattttgtta ttataactgt
      181 cgacgacagt gatgataaca atgattgcag tattgagatg gtggaagttt ctgaaacagc
      241 agataattcc actaatgaca tagcagatga ttccacttat gtcacagcag ataatcccac
      301 tgatgacaca gccacacaac caaattttcc aggcggcaat gatggccatc accgtccact
      361 ccaaatgtca tatgggtctg gctctgtcac ccaggctgga gtgcagtggc atgatcacag
      421 ctcactgcag cctcaacctc ttggactcaa gcaattcttc cacctcagcc ttcccagtag
      481 ctgggatgac aggcgcacgc caccatgccc agtagcccat ggtgaccaaa tagtttcaca
      541 gataaaccac ccagtacatt taagaagata cagttacaac tcagaggaag tggattttcc
      601 aaaaagagga agattctata ctccagaggt acagtctagc atatcaccac cagcggaaag
      661 gcaggaaacc catgcctggg ccagccctgc tgtaacatct cttgagtcag cagcatgtca
      721 tgaactgcag gaagcagacc tcagtgagag tttatcatat cccagaattg tctcctcaag
      781 ttcattacag cagtatgtcg cacaaggtgg ctcatttcct tgtttcggta tgccatggaa
      841 ctttatcagt ggaggtgctg aaagtaccaa tgctgtcatc tcatttgcca atgctactac
      901 agcagtacct atggcagttc tgtcacgaag agaatccagt ctggcaaata accctggtgt
      961 ggtgaattac tctgctctac cagaaaatga aaatgtgggc ccaggtagag ccttgtcatc
     1021 tttctgcttc catcccaatt tggaaatgcc agaaagacca gcaaacagca gtaaaaacag
     1081 cactgagaca gcgaattatc caactttaat gggaaattac aatggccaaa atactgcctc
     1141 tttatctgtc ttcatccctc cctattttgc tgagaaaatt atacttactg aaatgccagg
     1201 aacaacagaa accaacgtgg aaaataactc tcagacagtg tattacccag ctttatcggg
     1261 aaatacgagt gccccatatc cagcctcttc atatcttccc atcacttcta attttgaatc
     1321 tggcccacaa atgagttatg ggacaatgag ttactcaact gaaatgaaaa ataactgtga
     1381 ccaagatgat gcttcagcat ctgcctgcct cactcccgat tttgcactgt tacctctgaa
     1441 tattttggta aaagtagaca ccaacacgga aaacagcgtc aacacaatga atcgctcaac
     1501 tttattggac agtgacagtg gccaggattc ttcctcatca tctgtctgta tccctcccaa
     1561 gtatggctat cttggtgatc caaaaagaaa tgtcagagta cttaaaatcc atttgctggc
     1621 cgtacaaaat atggccaaac ctaagcaagc agcctgctac ttggttcgta ttttgttctc
     1681 caaggaaatc ctgattagca gctcagtgga tatccatttg aaagacagcc aatccctcga
     1741 cccgaacaaa atggctgcat tgagagaata tctggcaaca acttttccca cctgtgattt
     1801 gcatgaacat ggaaaagact ggcaggactg tatttctggt atcaattcta tgatctactg
     1861 tttatgttct gaaggcaaga gtactccaaa aactgttcgc aaaaataaaa aacgtaccaa
     1921 ccgtgttgca tcggcatctg cagatagaaa tgaccaaagg ggcagagatg gtggtgaagg
     1981 ctgttcttgg atgtttcagc caatgaataa ctccaaaatg agagaaaaga ggaacttgca
     2041 gccaaacagt aatgctatcc ctgaaggaat gcgagaacct tccactgata atccagagga
     2101 acctggtgaa gcatggagct attttggaag accatggaga aatatacgga tgccatgttc
     2161 agtactgact ttggcaaaaa ctaagtcttg cgcaagcctg tcggctagat accttattca
     2221 gaaactcttc acaaaagatg tcctggtcca aagtaacgtc tatggcaatc tgaagcatgg
     2281 cctgtgtgcc cttgacccca ataagattag tgctctccga gagttcctcc aagaaaacta
     2341 cccaatttgt gatctctcgg aaaatggaag agactggaag tcgtgtgtga cctccatcaa
     2401 cagcggtatc cgtagcctta gacatgacgt cagaagggct gaagccaggt ctcagtcgct
     2461 tccagcagtg acccctccag agctggagca ggagtcaaag ccaggagatc ccgacgccac
     2521 tgacccaagc acctgaacgg cagctgccaa actttttttt tttttttaac tgttaagact
     2581 attttgtaag tttctcaagt tctaattcca aaatcagcct gctgtactgg cagagtagtt
     2641 tgcattgaca cctgtagtaa tcgccaaacc tctttttctg ctcataaagg aggtagaatc
     2701 acattaggaa gatacgtaat gtttcatctg tggatttgat gacaacctct gattgaggga
     2761 atggtagtaa actcctcatg ggcttgtgac ccatggcttt gacttagata attgacatta
     2821 atatactttg tttttttgat aaggtagaga aagaaattca atagaaagta aggagccact
     2881 cagtcaaata atataattcg tataaaactt gacaagtctt tttatttttg tgacttgtga
     2941 gatagtttaa gatattttta tgtgaccaat ttgtagaatg aatacatatt ttcaaagtta
     3001 tcttttcaaa attcaacttt tagagtattt tagcaaaata tatgtatagt ttataatata
     3061 gaagtatagc tttataaaga tattaaggat ttatttttta aaataattct ctgaatagtt
     3121 tgctgtagta gttgccttca gcttaataaa accatagtac ttctacatac atctttataa
     3181 gttaggctat gcctacaaag gtcttaaaaa gtagataatt taccgggtgt agtggctcac
     3241 acctgtaatc ccagcacttt gggaggccga gacgggtgga tcacctgagg tcaggggttc
     3301 gagaccagcc tggccaacat gacgaaaccc catctctact aaaaatacaa aaaaagtagc
     3361 caggcatggt ggcaagcacc tgtagtccca gttactcggg tggctgaggc aggagaatca
     3421 cttgaacctg ggaggtggag actgcagtga gccgagattg tgccactgca ctcgagcctg
     3481 ggtgacagag tgagactccg tctcgggaaa agaaaaaaaa gaagtagata attaaaaaaa
     3541 tcttgcataa aaaaaaatct tccataaagg gcaaaaaggc tttaacttcc attattcaga
     3601 tttaatccaa ctaagatagt ctttggcttc attcactgtt cagtttcaca agttttttac
     3661 aactactagt aacagagcta atacagaata gtaatccaca ttataaacat agatcaaaat
     3721 accacatcat accccataaa tacatgcagt tattatttgt caattaaaaa taaaattttt
     3781 ttaaaagaaa agtacagttc gaccctaggc aagaagaaat ttcaaattgt atatgcatat
     3841 tttgaatttg gtttatattt tgtggtatct gaaatattcc ctggactaga agcaaaacca
     3901 cagaaacaaa actttacatt tagaaaaaaa tttcaagact tctattgcta actttattac
     3961 attagtggtt tttagaagtt atttagagca gtcttgtctg atagaacttt ccaccatgat
     4021 ggaaatgtaa ataaatatac cacattaaaa atataaattt gcaatgtcca ataggctcgt
     4081 atggctattg agcatttaag atgtaattaa ttagacagag gaagtaaatt taacattttc
     4141 tctcatttta gctaattaga atttaaagtg aaatagccac aagtggatag tggctactgt
     4201 gttggatggc acagttcaaa atgcctctta tttataaaaa aaagtgttta aaagtggttc
     4261 ccatggcttg aagaggaata atatacacat aacttcttta aaatcacatt ttgtttgaga
     4321 tggagatctt gctatattgc ccaggcttat ctggaactcc tgggctcaag agggaggatc
     4381 acatttgact ggacaaaata cattttataa aggtgttttg tattttatgt taaagtggaa
     4441 ttgtgtcttc aaaattgtgt cttcaaaatt tcacaagtta atactattac tgtattagtc
     4501 caatgttaaa cattttaaat gcctgctcat aagactcatt tttgataaat aaatgtatct
     4561 ttaatgtttt gtttcccaaa tagatacaat aaataaacat ttaaaatgcc ttaa
//
