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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAGGATTTAAGGAGCTCTTTTTGACCGCCTTCCCTGTGGATTAATTTATCCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAGgtacagatctcgtgatttccctgtttactggtgttagttttaggaaccttgatgctttggtttagggctatggttaattgcaatttattgaaatttcaatatgtcaatattgtgcag

Basic information

species Oryza sativa
transcript LOC_Os12g04204.2
intron # 3
splice site 5'
intron type U2

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|4716350|gb|AU057466.1|AU057466
EST:     CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAG                         TTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
genomic: CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAGgtacagatct ... tattgtgcagTTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
EST: gi|29672671|gb|CB668946.1|CB668946
EST:     CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAG                         TTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
genomic: CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAGgtacagatct ... tattgtgcagTTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
EST: gi|29665113|gb|CB661388.1|CB661388
EST:     CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAG                         TTGGTTTGCTTCCATTACAAGCAACTGT
genomic: CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAGgtacagatct ... tattgtgcagTTGGTTTGCTTCCATTACAAGCAACTGT
EST: gi|29681110|gb|CB677385.1|CB677385
EST:     CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAG                         TTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
genomic: CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAGgtacagatct ... tattgtgcagTTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
EST: gi|29672792|gb|CB669067.1|CB669067
EST:     CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAG                         TTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
genomic: CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAGgtacagatct ... tattgtgcagTTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
EST: gi|29667260|gb|CB663535.1|CB663535
EST:     CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAG                         TTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
genomic: CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAGgtacagatct ... tattgtgcagTTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
EST: gi|33683584|gb|CF311823.1|CF311823
EST:     CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAG                         TTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
genomic: CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAGgtacagatct ... tattgtgcagTTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
EST: gi|29667261|gb|CB663536.1|CB663536
EST:     GCTCAGTTTGAG                         TTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
genomic: GCTCAGTTTGAGgtacagatct ... tattgtgcagTTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
EST: gi|29675181|gb|CB671456.1|CB671456
EST:     CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAG                         TTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
genomic: CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAGgtacagatct ... tattgtgcagTTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
EST: gi|29642048|gb|CB647055.1|CB647055
EST:     ACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAG                         TTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
genomic: ACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAGgtacagatct ... tattgtgcagTTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
EST: gi|29645640|gb|CB650647.1|CB650647
EST:     CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAG                         TTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
genomic: CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAGgtacagatct ... tattgtgcagTTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
EST: gi|88273326|gb|CI388782.1|CI388782
EST:     CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAG                         TTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
genomic: CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAGgtacagatct ... tattgtgcagTTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
EST: gi|29642088|gb|CB647095.1|CB647095
EST:     GTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAG                         TTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
genomic: GTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAGgtacagatct ... tattgtgcagTTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
EST: gi|29681391|gb|CB677666.1|CB677666
EST:     CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAG                         TTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
genomic: CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAGgtacagatct ... tattgtgcagTTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
EST: gi|29667029|gb|CB663304.1|CB663304
EST:     CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAG                         TTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
genomic: CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAGgtacagatct ... tattgtgcagTTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
EST: gi|33675075|gb|CF303314.1|CF303314
EST:     CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAG                         TTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
genomic: CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAGgtacagatct ... tattgtgcagTTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
EST: gi|29661293|gb|CB657568.1|CB657568
EST:     CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAG                         TTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTACTA
genomic: CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAGgtacagatct ... tattgtgcagTTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
EST: gi|29675125|gb|CB671400.1|CB671400
EST:     CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAG                         TTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
genomic: CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAGgtacagatct ... tattgtgcagTTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
EST: gi|29640820|gb|CB645827.1|CB645827
EST:     CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAG                         TTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
genomic: CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAGgtacagatct ... tattgtgcagTTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
EST: gi|29657161|gb|CB653436.1|CB653436
EST:     CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAG                         TTGGTTTGCTTCCATTACAAGCAACTGTCCGAGAACATTTTATTTGTAATA
genomic: CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAGgtacagatct ... tattgtgcagTTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
EST: gi|29667028|gb|CB663303.1|CB663303
EST:     CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAG                         TTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
genomic: CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAGgtacagatct ... tattgtgcagTTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
EST: gi|29640827|gb|CB645834.1|CB645834
EST:     CCTAGCACAGGAACTACGGATTACTTGCTGCTTGACCTGCTCAGTTTGAG                         TTGGTTTGCTTCCATTACAAGCAACTGTCCA
genomic: CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAGgtacagatct ... tattgtgcagTTGGTTTGCTTCCATTACAAGCAACTGTCCA
EST: gi|29643071|gb|CB648078.1|CB648078
EST:     CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAG                         TTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
genomic: CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAGgtacagatct ... tattgtgcagTTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
EST: gi|14574815|gb|AU197330.1|AU197330
EST:     CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAG                         TTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA
genomic: CCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAGgtacagatct ... tattgtgcagTTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATA

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: 67 (upstream exon), 62 (downstream exon)
Score: 23

CGAGGATTTAAGGAGCTCTTTTTGACCGCCTTCCCTGTGGATTAATTTATCCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAGgtacagatct ... tattgtgcagTTGGTTTGCTTCCATTACAAGCAACTGTCCAAGAACATTTTATTTGTAATACGAACATTTATAAACCAGAGAAATTGAAGCTTGTTGTATGGGATTGGTC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAGGATTTAAGGAGCTCTTTTTGACCGCCTTCCCTGTGGATTAATTTATCCTAGTACAGGAACTACAGATTACTTGCTGCTTGACCTGCTCAGTTTGAGgtacagatctcgtgatttccctgtttactggtgttagttttaggaaccttgatgctttggtttagggctatggttaattgcaatttattgaaatttcaatatgtcaatattgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT