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LOCUS NM_132004 2983 bp mRNA linear INV 26-DEC-2023 variant A (Vsx1), mRNA. ACCESSION NM_132004 VERSION NM_132004.3 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 2983) 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 2983) 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 2983) 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 2983) 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 2983) 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 2983) 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 2983) 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 2983) 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 2983) 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 2983) 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 2983) 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 2983) 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 2983) 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 2983) 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 2983) 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 2983) 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 2983) 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 2983) 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 2983) 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 2983) 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 2983) 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 2983) 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 2983) 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). On Jul 15, 2014 this sequence version replaced NM_132004.2. ##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..2983 /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..2983 /gene="Vsx1" /locus_tag="Dmel_CG4136" /gene_synonym="CG4136; Chx1; dChx1; Dchx1; DChx1; Dmel\CG4136; dVsx1; DVSX1; lincRNA.S8688; Vsx; Vsx-1" /note="Visual system homeobox 1" /map="5A6-5A7" /db_xref="FLYBASE:FBgn0263511" /db_xref="GeneID:31470" CDS 293..2806 /gene="Vsx1" /locus_tag="Dmel_CG4136" /gene_synonym="CG4136; Chx1; dChx1; Dchx1; DChx1; Dmel\CG4136; dVsx1; DVSX1; lincRNA.S8688; Vsx; Vsx-1" /note="CG4136 gene product from transcript CG4136-RA; CG4136-PA; Vsx1-PA; visual system homeobox 1 ortholog; Chx1" /codon_start=1 /product="visual system homeobox 1, isoform A" /protein_id="NP_572232.2" /db_xref="FLYBASE:FBpp0070747" /db_xref="GeneID:31470" /db_xref="FLYBASE:FBgn0263511" /translation="MQATKMRTPFAIQEILGLGAYQQQATASATPSEAPPSPAATPPP TANTPANGSLSAVQQQQQQQQQQQQQQQQLQQQQQQAIDSLRESRSISPDVSRLSAAA AAAAAAAAHCQLPVFNPANFYAAAGYAAAADPGNAAAAHHHHMTTLAAAAYLRGFLPP GFSTPHEFRGHFQQHFGAQFAEQAAARGQEYASSLANASGDEQSPSKNSSSSGNGGSG GSGSGSGGGNPTSNGLGHLGSPTASNGGSGGGAGVGGSGGGSGTSGSNSSTSGNGGNG GSSGSRSSPAGPHHSAALAAHQHAAAAAAAAHHHAAAAAAAHHAHHAHAQAHAHAHAH VHAHAAHAAHAAHAHAHHAEAFLGAAGGAGGNPNSLLAAHGGDVLVGPGGTGPGGKKK NKRRHGRTIFTSSQLEELEKAFKEAHYPDVSARELLSMKTGLAEDRIQVWYQNRRAKW RKTEKCWGHSTKMAEYGLYGAMVRHSLPLPETIIKSAKEDESVAPWLLGMHKKSLEAA ELLKSDESDRETPTSDDTNTSYSAGSTHNSPISSFSISRLLFDAPPPAAGSAGGKGHH HHHHHHKGHHHAHVHAQAQAHAHMLLHHQQQQQQQQQQQQHHHHLHAAENSLQQQQVA GTGSGSGSGSGSGTGAGSTGPPAHHPYNQQQHLHHLQQLQQQQQQQQQQAQQQQQHHH HQHHHSVHHMHHHNAAAGYAEAAVAAAAAAAAVAAAANARNAAAAAAVAAASASASAA VTIAESEAEEEQDDIEDMELDKDCEVEEDVEPVDNDTNTNNEHDNECDADADVEADVD ADADADPEIDICDDHDEEMRLQEQLLLKVKQEQAHLGSR" misc_feature 1475..1648 /gene="Vsx1" /locus_tag="Dmel_CG4136" /gene_synonym="CG4136; Chx1; dChx1; Dchx1; DChx1; Dmel\CG4136; dVsx1; DVSX1; lincRNA.S8688; Vsx; Vsx-1" /note="Region: Homeodomain; pfam00046" /db_xref="CDD:459649" ORIGIN 1 tcagttcgtt ttcgaacgcc gcaccgaacg ctccagcgct caaaaataca caattagata 61 aaaacaataa aagcaaatcc acaattgcaa cccacacaag tgcgtgagtg aacttttttt 121 cctgtgtaac gtgtacgtgt gcgtgtgctt gccgcagctg ccatgagagt gtgcaataaa 181 tagaaacttg ggaactccaa tcgttttttc gaaaacaaac tgcaaactga caacccaaca 241 aaggggtttc gcatacagtg taccaccaat aatcgaagta ccgtcggcaa aaatgcaggc 301 caccaagatg cgtacgccgt ttgccattca ggagatcctg ggactgggcg cctatcagca 361 gcaggccact gccagtgcca cgccctccga ggcgccaccc tcgccggccg ccacgccgcc 421 gcccacagcg aatacgcccg ctaatggctc gctatccgcc gtacagcagc aacagcagca 481 gcaacagcag cagcagcaac aacagcaaca gctgcagcag caacaacagc aggcgattga 541 tagcctccgc gaatcccgat ccatatcgcc ggatgtctcc agactctcgg ccgctgcagc 601 ggcggcggca gcggctgccg cccactgcca attgcccgtc ttcaatccgg ccaacttcta 661 tgccgccgcc ggctatgccg ctgcagcgga tccgggcaac gcggctgcag cccatcacca 721 ccacatgacc accttggcgg cggccgccta tctccgggga ttcctgccgc ccggattcag 781 cacgccccac gagtttcggg gccacttcca gcagcacttc ggcgctcagt ttgcagaaca 841 agctgccgct cgtggccagg agtacgccag cagtttggcc aatgccagtg gagatgagca 901 gtcgcccagc aagaatagca gttcatcggg caacggcgga tccggcggat cgggatcagg 961 atctggtggc ggcaatccga cctcgaatgg cctcgggcac ctgggctcgc caacggccag 1021 caatggtgga tccggcggtg gagccggtgt gggcggatcg ggcggtggat cgggcacgtc 1081 gggcagcaac tcctcgacat ccggaaacgg cggtaacggc ggcagctccg gcagtcgctc 1141 ctcgcccgct ggtccgcatc actcggccgc actggctgcc catcagcatg cagcggctgc 1201 tgcggccgcc gctcatcatc atgccgctgc cgctgctgcc gcccatcatg ctcaccacgc 1261 ccacgcccag gcgcacgctc atgcccacgc gcatgtccac gcccatgccg ctcacgccgc 1321 ccatgccgcc cacgcccatg cccatcatgc cgaggcattt ctgggagcag cgggcggagc 1381 tggaggcaat cccaatagcc tgctggccgc ccatggtggc gatgttcttg tcggtcctgg 1441 cggcacgggt cccggcggca agaagaagaa caagcgacgc cacggacgca cgatcttcac 1501 cagcagccag ctggaggagc tggagaaggc cttcaaggag gcacactacc cggacgtgag 1561 tgcgcgcgag ctgctgtcca tgaaaactgg cctcgccgag gatcgcattc aggtgtggta 1621 ccagaatcgc cgggccaagt ggcgcaaaac ggagaaatgc tggggccaca gcaccaaaat 1681 ggccgaatac ggattgtatg gagcgatggt gaggcattcg ctgccactgc cggagaccat 1741 catcaagtcg gccaaggagg acgagtcggt ggcgccgtgg ctgctgggca tgcacaagaa 1801 gtcactggag gccgccgagc tgctcaagag cgacgagagt gaccgggaga cgcccacctc 1861 ggacgatacg aacaccagct actcggcggg cagcacccat aattcaccga tctccagttt 1921 ctcgatctcg cgtctcctct ttgacgcccc accgccggcg gcgggttccg ctggtggcaa 1981 gggacaccac caccatcatc accaccacaa gggccaccat catgcccacg ttcatgccca 2041 ggcgcaggcg cacgcccaca tgctgctgca ccaccagcag cagcagcagc aacagcagca 2101 gcagcaacag catcaccatc acttgcacgc cgcagagaat tccttgcagc agcagcaagt 2161 tgctggaacg ggctcgggtt cgggatccgg ttccgggtcg ggaacgggtg cgggctcgac 2221 tgggccacca gcacaccatc cgtacaacca gcagcagcac ctgcaccacc tgcagcaact 2281 gcagcagcag cagcagcagc aacagcagca ggcgcagcag cagcagcagc atcaccacca 2341 ccagcaccac cattcggtgc accatatgca ccaccacaat gctgcggccg gctacgccga 2401 ggcagcggtg gctgctgcag cggccgcagc agctgttgcc gcagcagcaa acgcacggaa 2461 tgcagcggcg gcagcagcgg tggccgcagc ctcagcgtcc gcctccgcag ccgtgaccat 2521 tgcggaatcg gaggcggagg aggagcagga cgacatcgag gacatggaac tggacaagga 2581 ctgtgaggtg gaggaggatg tggagcccgt ggataacgat accaatacca acaacgagca 2641 cgacaacgag tgcgatgcgg atgcggatgt tgaggcggat gtggatgcgg atgcggatgc 2701 cgatcccgag atagacatct gcgacgacca cgacgaggag atgcgtctgc aggagcagct 2761 cctgctgaaa gtgaagcagg agcaggcgca tctggggtcc agatgaaaca tgtacatcga 2821 tgtgttgttc taaggacaac gataaaccta caggattcga aacacatccg gctaaatgca 2881 atgaaccatt ttgtatgcgc aaacgggcga aatttcacgg cccacgatag aaatcgaata 2941 aattaatagc attacatata tgacagaaaa ttaagcaaaa aac