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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTGATGCTAAAGCTGGGGAGGTTCCCATTGCCTATGTTGTTCGGTCACCTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctgatttggaagttggaaccttgtttaattgggattgtagactagtggaactttttagcagcatgagacaatttgggtaaagctcgtccagata...

Basic information

species Oryza sativa
transcript LOC_Os03g05780.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g05780.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G122787_T06 (Zea mays), 5'ss of exon 6
TCCTGATGCTAAAGCTGGGGAGGTTCCCATTGCCTATGTTGTTCGGTCACCTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctgatttggaagttggaacc--ttgttta-attgggattgtaga---ctagtggaact--ttttagcagcatgagacaatttgggtaaagctcgtccagata-------------------------------------------------------------------------------
 || |||||| ||||||| || ||||| ||||| || || ||  ||||  |||| ||||| ||||| |||||||||||||| |||||||||||||| |||||||| ||   | ||||  |     |  ||||||  ||||| |  ||  |   ||    | ||   | | |  || |||  ||  ||   ||||  |  |     ||                                                                                
CCCCGATGCTGAAGCTGGTGAAGTTCCTATTGCTTACGTCGTAAGGTCCTCTGAGAGTTCTTTGACTGAAGTTGATGTCCAGAAATTTATTGAAAAGCAGgtgagcctatgtaggaacctttgctcaattgtttccattggcaaagtctaactctctcagtaccggtctcactagtatgcaacgttt---gtaattcctgagtgaattaacattactctgtatttatccttcaactgatacagccatgttaatacatagctgattttgttcatgaactaccttgtag

upper sequence: LOC_Os03g05780.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA11G20020.2 (Glycine max), 5'ss of exon 6
TCCTGATGCTAAAGCTGGGGAGGTTCCCATTGCCTATGTTGTTCGGTCACCTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctgatttgga------------agttggaaccttgttta-attgggattgtagactagtggaactttttagcagcatgagacaatttgggtaaagctcgtccagata
|||||||| | | ||||| |||||||| ||||||||||||||||| |||||  | |||||| |||| ||||  ||  | || || |||||||  || ||||| ||    |  |  |            || | || | ||| ||  ||  | ||| |       ||    ||||| | ||| ||  |||  ||   | |  || ||  | |  
TCCTGATGATGAGGCTGGTGAGGTTCCAATTGCCTATGTTGTTCGCTCACCCAATAGTTCACTGACTGAAGAAGAAATTCAGAAGTTTATTGCTAAGCAGgtaagagaaagataaagaataaagaatgagcttgatctttgattgcatctgaattattagtctatgtgcatttttggtagc-tgttacacattt--ttacacttgtttacag-

upper sequence: LOC_Os03g05780.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA12G08460.1 (Glycine max), 5'ss of exon 6
TCCTGATGCTAAAGCTGGGGAGGTTCCCATTGCCTATGTTGTTCGGTCACCTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctgatttggaagttggaacctt-gtttaat---tgggattgtagactagtggaactttttagcagcatgagacaatt---tgggtaaagctcgtccagata
|||||||| | | ||||| |||||||| ||||||||||||||||| |||||  | |||||  |||| ||||  ||  | || || |||||||  || ||||| ||    |  |     ||  |   |  | || ||   || |    |   |  |   |   | || |||   |  |  | ||       | |  || ||  | |  
TCCTGATGATGAGGCTGGTGAGGTTCCAATTGCCTATGTTGTTCGCTCACCCAATAGTTCGCTGACTGAAGAAGAAATTCAGAAGTTTATTGCTAAGCAGgtaagataaagataaggattaaagaatgagcttgatctttgagcgcatctgcatgattagtctatttgcatttttcggtagttactcattttatacttgtttatag-

upper sequence: LOC_Os03g05780.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA13G39770.2 (Glycine max), 5'ss of exon 4
TCCTGATGCTAAAGCTGGGGAGGTTCCCATTGCCTATGTTGTTCGGTCACCTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctgatttggaagttggaaccttgtttaattgggattgt-agactagtggaactttttagcagc-atgagacaatttggg-taaagctcgtccagata
|||||||||| ||||||| ||||||||  |||||||||| ||||| |||||  | |||||| | ||||| |  ||||| |||||||||||||  || ||||| ||    |  |  |   || | | | || | | | | ||| |  || |  |   |  |||     |  | || || |       ||||    || |  |  
TCCTGATGCTGAAGCTGGTGAGGTTCCAGTTGCCTATGTCGTTCGTTCACCCAATAGTTCACTCACAGAGGAAGATGTTCAAAAATTTATTGCTAAGCAGgtaagagaaaaataaacaatg-agcttggtctgacttgcattcttggaattataagatctttggcttgtgaagaaacgaagcaaactaaatggggttctaa--

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|88243085|gb|CI244207.1|CI244207
EST:     CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAG                         GTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
genomic: CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctga ... gcattatcagGTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
EST: gi|88541159|gb|CI468411.1|CI468411
EST:     GACAGTTCATTGACAGGAAGTTGATGTCCCAAAATTTATTGAAAAACAG                         GTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
genomic: GACAGTTCATTGACA-GAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctga ... gcattatcagGTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
EST: gi|88527486|gb|CI455651.1|CI455651
EST:     CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGTAAAACAG                         GTGGCGTAGTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
genomic: CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctga ... gcattatcagGTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
EST: gi|88540328|gb|CI470364.1|CI470364
EST:     CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAG                         GTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
genomic: CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctga ... gcattatcagGTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
EST: gi|88544598|gb|CI472712.1|CI472712
EST:     TTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAG                         GTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
genomic: TTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctga ... gcattatcagGTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
EST: gi|86494866|gb|CI137499.1|CI137499
EST:     CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAG                         GTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
genomic: CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctga ... gcattatcagGTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
EST: gi|88531291|gb|CI459756.1|CI459756
EST:     CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAG                         GTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGGCGTGCC
genomic: CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctga ... gcattatcagGTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAG-CGTGCC
EST: gi|86601911|gb|CI258587.1|CI258587
EST:     CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAG                         GTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
genomic: CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctga ... gcattatcagGTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
EST: gi|86858919|gb|CI275128.1|CI275128
EST:     CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAG                         GTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
genomic: CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctga ... gcattatcagGTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
EST: gi|6449606|gb|AU081548.1|AU081548
EST:     CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAG                         GTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCCGTGCC
genomic: CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctga ... gcattatcagGTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGC-GTGCC
EST: gi|86495388|gb|CI138021.1|CI138021
EST:     CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAG                         GTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
genomic: CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctga ... gcattatcagGTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
EST: gi|88274772|gb|CI395178.1|CI395178
EST:     CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTTAAAAACAG                         GTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
genomic: CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctga ... gcattatcagGTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
EST: gi|6449607|gb|AU081549.1|AU081549
EST:     CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAG                         GTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
genomic: CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctga ... gcattatcagGTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
EST: gi|88236772|gb|CI235974.1|CI235974
EST:     CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAG                         GTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
genomic: CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctga ... gcattatcagGTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
EST: gi|3766917|gb|AU031027.1|AU031027
EST:     CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAG                         GTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
genomic: CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctga ... gcattatcagGTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
EST: gi|88549315|gb|CI479196.1|CI479196
EST:     CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAG                         GTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
genomic: CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctga ... gcattatcagGTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
EST: gi|88217352|gb|CI217201.1|CI217201
EST:     CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAG                         GTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
genomic: CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctga ... gcattatcagGTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
EST: gi|25044725|gb|AJ420708.1|AJ420708
EST:     CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAG                         GTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
genomic: CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctga ... gcattatcagGTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
EST: gi|66918181|gb|CX105029.1|CX105029
EST:     CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAG                         GTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCA
genomic: CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctga ... gcattatcagGTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCA
EST: gi|87015891|gb|CI279643.1|CI279643
EST:     CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAG                         GTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
genomic: CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctga ... gcattatcagGTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
EST: gi|86493702|gb|CI136335.1|CI136335
EST:     CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAG                         GTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
genomic: CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctga ... gcattatcagGTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
EST: gi|11026437|gb|AU163038.1|AU163038
EST:     NTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAG                         GTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
genomic: CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctga ... gcattatcagGTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
EST: gi|88526135|gb|CI452514.1|CI452514
EST:     TGACAGGTTCAGTGACAGAACTTGATGTCCAAAAATTTATTGAAAAACAG                         GTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
genomic: TGACA-GTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctga ... gcattatcagGTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
EST: gi|88545001|gb|CI474528.1|CI474528
EST:     CGGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAG                         GTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGGGTGCCC
genomic: CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctga ... gcattatcagGTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
EST: gi|218482819|gb|FG952971.1|FG952971
EST:     CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAG                         GTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
genomic: CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctga ... gcattatcagGTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
EST: gi|88245220|gb|CI245069.1|CI245069
EST:     CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAG                         GTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
genomic: CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctga ... gcattatcagGTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
EST: gi|86500396|gb|CI143029.1|CI143029
EST:     CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAG                         GTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
genomic: CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctga ... gcattatcagGTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
EST: gi|86496707|gb|CI139340.1|CI139340
EST:     CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAG                         GTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC
genomic: CTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctga ... gcattatcagGTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 55 (downstream exon)
Score: 35

TCCTGATGCTAAAGCTGGGGAGGTTCCCATTGCCTATGTTGTTCGGTCACCTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctga ... gcattatcagGTGGCGTACTACAAAAGATTGAAGAGAGTTACCTTTGTGGGCAGCGTGCCCAAATCAGCTTCAGGAAAGATTCTGAGAAGGCAGCTTATCGCCCAAGTGA




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTGATGCTAAAGCTGGGGAGGTTCCCATTGCCTATGTTGTTCGGTCACCTGACAGTTCATTGACAGAAGTTGATGTCCAAAAATTTATTGAAAAACAGgtgaggctgatttggaagttggaaccttgtttaattgggattgtagactagtggaactttttagcagcatgagacaatttgggtaaagctcgtccagata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT