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LOCUS NM_001297968 2373 bp mRNA linear INV 26-DEC-2023 variant B (Vsx2), mRNA. ACCESSION NM_001297968 VERSION NM_001297968.1 DBLINK BioProject: PRJNA164 BioSample: SAMN02803731 KEYWORDS RefSeq. SOURCE Drosophila melanogaster (fruit fly) ORGANISM Drosophila melanogaster Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila; Sophophora. REFERENCE 1 (bases 1 to 2373) AUTHORS Matthews,B.B., Dos Santos,G., Crosby,M.A., Emmert,D.B., St Pierre,S.E., Gramates,L.S., Zhou,P., Schroeder,A.J., Falls,K., Strelets,V., Russo,S.M. and Gelbart,W.M. CONSRTM FlyBase Consortium TITLE Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput Data JOURNAL G3 (Bethesda) 5 (8), 1721-1736 (2015) PUBMED 26109357 REMARK Publication Status: Online-Only REFERENCE 2 (bases 1 to 2373) AUTHORS Crosby,M.A., Gramates,L.S., Dos Santos,G., Matthews,B.B., St Pierre,S.E., Zhou,P., Schroeder,A.J., Falls,K., Emmert,D.B., Russo,S.M. and Gelbart,W.M. CONSRTM FlyBase Consortium TITLE Gene Model Annotations for Drosophila melanogaster: The Rule-Benders JOURNAL G3 (Bethesda) 5 (8), 1737-1749 (2015) PUBMED 26109356 REMARK Publication Status: Online-Only REFERENCE 3 (bases 1 to 2373) AUTHORS Hoskins,R.A., Carlson,J.W., Wan,K.H., Park,S., Mendez,I., Galle,S.E., Booth,B.W., Pfeiffer,B.D., George,R.A., Svirskas,R., Krzywinski,M., Schein,J., Accardo,M.C., Damia,E., Messina,G., Mendez-Lago,M., de Pablos,B., Demakova,O.V., Andreyeva,E.N., Boldyreva,L.V., Marra,M., Carvalho,A.B., Dimitri,P., Villasante,A., Zhimulev,I.F., Rubin,G.M., Karpen,G.H. and Celniker,S.E. TITLE The Release 6 reference sequence of the Drosophila melanogaster genome JOURNAL Genome Res 25 (3), 445-458 (2015) PUBMED 25589440 REFERENCE 4 (bases 1 to 2373) AUTHORS Hoskins,R.A., Carlson,J.W., Kennedy,C., Acevedo,D., Evans-Holm,M., Frise,E., Wan,K.H., Park,S., Mendez-Lago,M., Rossi,F., Villasante,A., Dimitri,P., Karpen,G.H. and Celniker,S.E. TITLE Sequence finishing and mapping of Drosophila melanogaster heterochromatin JOURNAL Science 316 (5831), 1625-1628 (2007) PUBMED 17569867 REFERENCE 5 (bases 1 to 2373) AUTHORS Smith,C.D., Shu,S., Mungall,C.J. and Karpen,G.H. TITLE The Release 5.1 annotation of Drosophila melanogaster heterochromatin JOURNAL Science 316 (5831), 1586-1591 (2007) PUBMED 17569856 REMARK Erratum:[Science. 2007 Sep 7;317(5843):1325] REFERENCE 6 (bases 1 to 2373) AUTHORS Quesneville,H., Bergman,C.M., Andrieu,O., Autard,D., Nouaud,D., Ashburner,M. and Anxolabehere,D. TITLE Combined evidence annotation of transposable elements in genome sequences JOURNAL PLoS Comput Biol 1 (2), 166-175 (2005) PUBMED 16110336 REFERENCE 7 (bases 1 to 2373) AUTHORS Hoskins,R.A., Smith,C.D., Carlson,J.W., Carvalho,A.B., Halpern,A., Kaminker,J.S., Kennedy,C., Mungall,C.J., Sullivan,B.A., Sutton,G.G., Yasuhara,J.C., Wakimoto,B.T., Myers,E.W., Celniker,S.E., Rubin,G.M. and Karpen,G.H. TITLE Heterochromatic sequences in a Drosophila whole-genome shotgun assembly JOURNAL Genome Biol 3 (12), RESEARCH0085 (2002) PUBMED 12537574 REFERENCE 8 (bases 1 to 2373) AUTHORS Kaminker,J.S., Bergman,C.M., Kronmiller,B., Carlson,J., Svirskas,R., Patel,S., Frise,E., Wheeler,D.A., Lewis,S.E., Rubin,G.M., Ashburner,M. and Celniker,S.E. TITLE The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective JOURNAL Genome Biol 3 (12), RESEARCH0084 (2002) PUBMED 12537573 REFERENCE 9 (bases 1 to 2373) AUTHORS Misra,S., Crosby,M.A., Mungall,C.J., Matthews,B.B., Campbell,K.S., Hradecky,P., Huang,Y., Kaminker,J.S., Millburn,G.H., Prochnik,S.E., Smith,C.D., Tupy,J.L., Whitfied,E.J., Bayraktaroglu,L., Berman,B.P., Bettencourt,B.R., Celniker,S.E., de Grey,A.D., Drysdale,R.A., Harris,N.L., Richter,J., Russo,S., Schroeder,A.J., Shu,S.Q., Stapleton,M., Yamada,C., Ashburner,M., Gelbart,W.M., Rubin,G.M. and Lewis,S.E. TITLE Annotation of the Drosophila melanogaster euchromatic genome: a systematic review JOURNAL Genome Biol 3 (12), RESEARCH0083 (2002) PUBMED 12537572 REFERENCE 10 (bases 1 to 2373) AUTHORS Celniker,S.E., Wheeler,D.A., Kronmiller,B., Carlson,J.W., Halpern,A., Patel,S., Adams,M., Champe,M., Dugan,S.P., Frise,E., Hodgson,A., George,R.A., Hoskins,R.A., Laverty,T., Muzny,D.M., Nelson,C.R., Pacleb,J.M., Park,S., Pfeiffer,B.D., Richards,S., Sodergren,E.J., Svirskas,R., Tabor,P.E., Wan,K., Stapleton,M., Sutton,G.G., Venter,C., Weinstock,G., Scherer,S.E., Myers,E.W., Gibbs,R.A. and Rubin,G.M. TITLE Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence JOURNAL Genome Biol 3 (12), RESEARCH0079 (2002) PUBMED 12537568 REFERENCE 11 (bases 1 to 2373) AUTHORS Adams,M.D., Celniker,S.E., Holt,R.A., Evans,C.A., Gocayne,J.D., Amanatides,P.G., Scherer,S.E., Li,P.W., Hoskins,R.A., Galle,R.F., George,R.A., Lewis,S.E., Richards,S., Ashburner,M., Henderson,S.N., Sutton,G.G., Wortman,J.R., Yandell,M.D., Zhang,Q., Chen,L.X., Brandon,R.C., Rogers,Y.H., Blazej,R.G., Champe,M., Pfeiffer,B.D., Wan,K.H., Doyle,C., Baxter,E.G., Helt,G., Nelson,C.R., Gabor,G.L., Abril,J.F., Agbayani,A., An,H.J., Andrews-Pfannkoch,C., Baldwin,D., Ballew,R.M., Basu,A., Baxendale,J., Bayraktaroglu,L., Beasley,E.M., Beeson,K.Y., Benos,P.V., Berman,B.P., Bhandari,D., Bolshakov,S., Borkova,D., Botchan,M.R., Bouck,J., Brokstein,P., Brottier,P., Burtis,K.C., Busam,D.A., Butler,H., Cadieu,E., Center,A., Chandra,I., Cherry,J.M., Cawley,S., Dahlke,C., Davenport,L.B., Davies,P., de Pablos,B., Delcher,A., Deng,Z., Mays,A.D., Dew,I., Dietz,S.M., Dodson,K., Doup,L.E., Downes,M., Dugan-Rocha,S., Dunkov,B.C., Dunn,P., Durbin,K.J., Evangelista,C.C., Ferraz,C., Ferriera,S., Fleischmann,W., Fosler,C., Gabrielian,A.E., Garg,N.S., Gelbart,W.M., Glasser,K., Glodek,A., Gong,F., Gorrell,J.H., Gu,Z., Guan,P., Harris,M., Harris,N.L., Harvey,D., Heiman,T.J., Hernandez,J.R., Houck,J., Hostin,D., Houston,K.A., Howland,T.J., Wei,M.H., Ibegwam,C., Jalali,M., Kalush,F., Karpen,G.H., Ke,Z., Kennison,J.A., Ketchum,K.A., Kimmel,B.E., Kodira,C.D., Kraft,C., Kravitz,S., Kulp,D., Lai,Z., Lasko,P., Lei,Y., Levitsky,A.A., Li,J., Li,Z., Liang,Y., Lin,X., Liu,X., Mattei,B., McIntosh,T.C., McLeod,M.P., McPherson,D., Merkulov,G., Milshina,N.V., Mobarry,C., Morris,J., Moshrefi,A., Mount,S.M., Moy,M., Murphy,B., Murphy,L., Muzny,D.M., Nelson,D.L., Nelson,D.R., Nelson,K.A., Nixon,K., Nusskern,D.R., Pacleb,J.M., Palazzolo,M., Pittman,G.S., Pan,S., Pollard,J., Puri,V., Reese,M.G., Reinert,K., Remington,K., Saunders,R.D., Scheeler,F., Shen,H., Shue,B.C., Siden-Kiamos,I., Simpson,M., Skupski,M.P., Smith,T., Spier,E., Spradling,A.C., Stapleton,M., Strong,R., Sun,E., Svirskas,R., Tector,C., Turner,R., Venter,E., Wang,A.H., Wang,X., Wang,Z.Y., Wassarman,D.A., Weinstock,G.M., Weissenbach,J., Williams,S.M., WoodageT, Worley,K.C., Wu,D., Yang,S., Yao,Q.A., Ye,J., Yeh,R.F., Zaveri,J.S., Zhan,M., Zhang,G., Zhao,Q., Zheng,L., Zheng,X.H., Zhong,F.N., Zhong,W., Zhou,X., Zhu,S., Zhu,X., Smith,H.O., Gibbs,R.A., Myers,E.W., Rubin,G.M. and Venter,J.C. TITLE The genome sequence of Drosophila melanogaster JOURNAL Science 287 (5461), 2185-2195 (2000) PUBMED 10731132 REFERENCE 12 (bases 1 to 2373) AUTHORS Celniker,S., Carlson,J., Wan,K., Pfeiffer,B., Frise,E., George,R., Hoskins,R., Stapleton,M., Pacleb,J., Park,S., Svirskas,R., Smith,E., Yu,C. and Rubin,G. CONSRTM Berkeley Drosophila Genome Project TITLE Drosophila melanogaster release 4 sequence JOURNAL Unpublished REFERENCE 13 (bases 1 to 2373) CONSRTM NCBI Genome Project TITLE Direct Submission JOURNAL Submitted (20-DEC-2023) National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA REFERENCE 14 (bases 1 to 2373) CONSRTM FlyBase TITLE Direct Submission JOURNAL Submitted (13-DEC-2023) FlyBase, Harvard University, Biological Laboratories, 16 Divinity Ave, Cambridge, MA 02138, USA REFERENCE 15 (bases 1 to 2373) CONSRTM FlyBase TITLE Direct Submission JOURNAL Submitted (19-OCT-2022) FlyBase, Harvard University, Biological Laboratories, 16 Divinity Ave, Cambridge, MA 02138, USA REFERENCE 16 (bases 1 to 2373) CONSRTM FlyBase TITLE Direct Submission JOURNAL Submitted (20-APR-2020) FlyBase, Harvard University, Biological Laboratories, 16 Divinity Ave, Cambridge, MA 02138, USA REFERENCE 17 (bases 1 to 2373) CONSRTM FlyBase TITLE Direct Submission JOURNAL Submitted (22-APR-2019) FlyBase, Harvard University, Biological Laboratories, 16 Divinity Ave, Cambridge, MA 02138, USA REFERENCE 18 (bases 1 to 2373) CONSRTM FlyBase TITLE Direct Submission JOURNAL Submitted (24-MAY-2018) FlyBase, Harvard University, Biological Laboratories, 16 Divinity Ave, Cambridge, MA 02138, USA REFERENCE 19 (bases 1 to 2373) CONSRTM FlyBase TITLE Direct Submission JOURNAL Submitted (07-DEC-2016) FlyBase, Harvard University, Biological Laboratories, 16 Divinity Ave, Cambridge, MA 02138, USA REFERENCE 20 (bases 1 to 2373) AUTHORS Celniker,S., Carlson,J., Kennedy,C., Wan,K., Frise,E., Hoskins,R., Park,S., Svirskas,R. and Karpen,G. TITLE Direct Submission JOURNAL Submitted (10-AUG-2006) Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, One #Cyclotron RoadOne Cyclotron Road, MS 64-121, Berkeley, CA 94720, USA REMARK Direct Submission REFERENCE 21 (bases 1 to 2373) AUTHORS Celniker,S., Carlson,J., Wan,K., Frise,E., Hoskins,R., Park,S., Svirskas,R. and Rubin,G. TITLE Direct Submission JOURNAL Submitted (10-AUG-2006) Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, One Cyclotron Road, MS 64-121, Berkeley, CA 94720, USA REMARK Direct Submission REFERENCE 22 (bases 1 to 2373) AUTHORS Smith,C.D., Shu,S., Mungall,C.J. and Karpen,G.H. CONSRTM Drosophila Heterochromatin Genome Project TITLE Direct Submission JOURNAL Submitted (01-AUG-2006) Drosophila Heterochromatin Genome Project, Ernest Orlando Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mailstop 64-121, Berkeley, CA 94720, USA REFERENCE 23 (bases 1 to 2373) AUTHORS Adams,M.D., Celniker,S.E., Gibbs,R.A., Rubin,G.M. and Venter,C.J. TITLE Direct Submission JOURNAL Submitted (21-MAR-2000) Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA COMMENT REVIEWED REFSEQ: This record has been curated by FlyBase. This record is derived from an annotated genomic sequence (NC_004354). ##Genome-Annotation-Data-START## Annotation Provider :: FlyBase Annotation Status :: Full annotation Annotation Version :: Release 6.54 URL :: http://flybase.org ##Genome-Annotation-Data-END## FEATURES Location/Qualifiers source 1..2373 /organism="Drosophila melanogaster" /mol_type="mRNA" /db_xref="taxon:7227" /chromosome="X" /genotype="y[1]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] MstProx[1] GstD5[1] Rh6[1]" gene 1..2373 /gene="Vsx2" /locus_tag="Dmel_CG33980" /gene_synonym="CG15781; CG15782; CG15783; CG33980; Chx2; dChx2; DChx2; Dmel\CG33980; dVsx2; Vsx; vsx2" /note="Visual system homeobox 2" /map="5A3-5A5" /db_xref="FLYBASE:FBgn0263512" /db_xref="GeneID:31469" CDS 222..2159 /gene="Vsx2" /locus_tag="Dmel_CG33980" /gene_synonym="CG15781; CG15782; CG15783; CG33980; Chx2; dChx2; DChx2; Dmel\CG33980; dVsx2; Vsx; vsx2" /note="CG33980 gene product from transcript CG33980-RB; CG33980-PB; Vsx2-PB; Chx2; visual system homeobox 2 ortholog" /codon_start=1 /product="visual system homeobox 2, isoform B" /protein_id="NP_001284897.1" /db_xref="FLYBASE:FBpp0309767" /db_xref="GeneID:31469" /db_xref="FLYBASE:FBgn0263512" /translation="MPQRSPFAIQELLGLAVAAATEAPTDLTTTAGATVAKERQTPTP PKTTNATMATAATSAATAATPTNAAEGNLTSVSEPQQQPQQQQQEQQHHQPHHHQYRE HHQMTMAAASRMAYFNAHAAVAAAFMPHQLAAAVHHHHQHQHQHHPHHHPHHPHGAVG GPPPPPPMQHHHPHHPHHPLLHAQGFPQLKSFAAGAGTCLPGSLAPKDFGMESLNGFG VGPNSKKKKKKRRHSRTIFTSYQLEKLEEAFKEAHYPDVYAREMLSLKTELPEDRIQV WFQNRRAKWRKTEKVWGGSTIMAEYGLYGAMVRHSLPLPDTILKSAKDNDAVAPWLLG MEQKCMHRKSIEAQSALKDDSGVSDHEDSAGSKSAHSEDLSRSRCHALSSSTESLNVV SPAPSSCPTSASTSAPPTSTSGYAGAASSAATTPTGASTTNSSSSPHIELGSPSPQQQ QHLQLQQQQQQQASLYLGAGAVVTGCAPPSYHPLLDAANAAGAGAAASSKDFHMIMNT AVAAAAAAAQQQHQQQQQQQQQATATAPGLHAHNLAAALMEHDPDAFRNNSIACLRAK AQEHQARLLNNGGLFLQVRRFAQGQAQIQDPSDMLKLSEEHNNNSPIPIPPAHSTVNT QVNVKMELTANGGSMKNYEEA" misc_feature 909..1082 /gene="Vsx2" /locus_tag="Dmel_CG33980" /gene_synonym="CG15781; CG15782; CG15783; CG33980; Chx2; dChx2; DChx2; Dmel\CG33980; dVsx2; Vsx; vsx2" /note="Region: Homeodomain; pfam00046" /db_xref="CDD:459649" misc_feature 1887..1937 /gene="Vsx2" /locus_tag="Dmel_CG33980" /gene_synonym="CG15781; CG15782; CG15783; CG33980; Chx2; dChx2; DChx2; Dmel\CG33980; dVsx2; Vsx; vsx2" /note="OAR motif; Region: OAR; pfam03826" /db_xref="CDD:461067" ORIGIN 1 atttgttgtg tgtttttctg cgacgcgtgc cagcgcaaaa tctcaaaacc tccattcgca 61 aatcccattt cgcgtagtct ttacaacatt gcaaaacttg cctttgcttt gttttttttt 121 ttgttttctg ggtttctcaa ttgggactgc atgatgtttt caagcgattt gttttgacaa 181 cggcaatatc tagacgtaaa tcgaaatatt agcaatcgaa aatgccgcag cgttcgccat 241 ttgccattca ggagctgctg ggcttggcgg tggcggcggc cacagaagcg ccaaccgatc 301 tgacgacaac tgccggtgca acggtggcaa aagagcgcca aacgccaacg ccgccaaaga 361 caacaaatgc cacaatggca acagcagcaa catcagcagc tacggcagca acaccaacaa 421 atgcggccga aggcaattta acgagcgttt cggagccaca gcagcagccg cagcagcagc 481 aacaagagca gcagcaccac cagccgcacc accatcagta cagggagcac caccaaatga 541 ccatggcggc cgcctcgcga atggcctact tcaatgccca tgcggcggtg gcagcggcct 601 ttatgcccca ccaactggcc gcggcggtgc accatcatca tcagcatcag caccagcacc 661 atccacacca ccacccgcac cacccacacg gagccgttgg cgggccaccg ccgccgccgc 721 cgatgcagca ccaccacccc caccatccgc accacccgct gctgcacgcg cagggatttc 781 cgcagctgaa aagcttcgcc gccggagccg gaacttgttt gcccggatcg ctggcgccca 841 aggacttcgg catggagagc ttgaatggct tcggtgtggg accgaatagc aaaaagaaga 901 aaaagaagcg acgacacagc cgcaccatat tcaccagcta ccaactggag aaactggagg 961 aggccttcaa ggaagcccat tatcccgatg tctatgcccg cgaaatgctc tcgctgaaga 1021 cagagctgcc cgaggatcgc atacaggtgt ggttccaaaa ccgacgcgcc aagtggcgca 1081 agacggagaa agtctggggc ggcagcacga tcatggccga gtacggtctc tatggggcaa 1141 tggtgcggca ctcgctgcct ctgccggaca cgatccttaa gtcggccaag gataacgatg 1201 cggtggcgcc ctggctacta ggtatggagc agaaatgcat gcatcgcaag tcgattgagg 1261 cgcagtcagc gctcaaggac gactcggggg tgagcgacca cgaggactcg gcgggatcga 1321 agtcggccca ctcggaggat ctttcacgct cccgctgcca cgccctcagc tcctccaccg 1381 aatcactgaa cgtcgtcagt cctgcgccca gtagctgccc cacctccgcc tcaacctcgg 1441 cgccgcccac ctcgacgagc ggctatgcgg gagccgcctc ctcggcggcc accacaccca 1501 caggagcgtc gaccaccaac agctccagca gtccccacat cgagctgggc tcaccttcgc 1561 cgcagcagca gcagcacctg caactgcagc agcagcaaca gcaacaggcg tcgctctact 1621 tgggcgctgg cgcggtggtt actggctgtg ccccgcccag ctatcatccg ctgctggacg 1681 ccgccaatgc cgctggtgcc ggcgcggccg cctccagcaa ggacttccac atgatcatga 1741 acaccgccgt ggcagcggca gcagcagctg ctcagcagca acatcagcaa cagcaacagc 1801 agcagcagca ggccacggcg acagcacctg gactgcatgc ccacaacttg gctgccgccc 1861 tcatggaaca cgatccggat gccttcagaa acaactcaat cgcctgtttg agggccaagg 1921 cgcaggagca ccaggcacga ctcctgaaca acggtgggct cttcctgcag gtgcgtcggt 1981 tcgcccaggg tcaggcgcag atccaggacc caagtgatat gctcaagctc agcgaggagc 2041 acaacaacaa cagcccgatt cccattccac ccgcccactc gactgtcaat acgcaagtca 2101 atgtgaaaat ggagctgacc gccaatgggg gttcaatgaa aaactatgag gaggcctaac 2161 gacagcccca acaagtttaa ttcatctaag ctgcccaatg cgaatgctat gatcccaaaa 2221 aaaaaccaaa ccaaaaatga gaagaaaacc ctttttttta ctagatctaa gaaacattac 2281 atctgtaatc gaaacagtaa ttttaaacag cagcattggc tgcttcaagg tgtaaaaata 2341 cgaaatcgga atattttaat aaattcatca gcg