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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAGgtatgcaatccctgcaataccaggattatttctcttcttaatgcattggaaatggaaacagtgcatattgttatgacctgaatatgtttgtgcatttcct...

Basic information

species Oryza sativa
transcript LOC_Os01g43540.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g43540.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G149704_T02 (Zea mays), 5'ss of exon 6
TTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAGgtatgcaatccctgcaataccaggattatttctcttcttaatgcattggaaatggaaacagtgcatattgttatgacctgaatat-gtttgtgcatttcct-
|| ||||| || |||||||| ||||| || || ||||||||||||||||| ||||||||||||||||||  || || |     ||    |||  |||  ||  |   ||  ||     |   ||  ||| |  ||    ||       ||| ||| |  | || ||| 
TTGAGTGTATCCATTGAAGTACCTGGTGAAGAACCGTACCATTTTCAGCCCCGTCTGTTTTCTAAGgtaaccactctccttgttattttgatgtttttactagtacttgtgttctg--ttacaatggtgtaagttacactgtgtaacctatagttagcaccttgcctt

upper sequence: LOC_Os01g43540.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G105019_T01 (Zea mays), 5'ss of exon 6
TTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAGgtatgcaatccctgcaataccaggat--tatttctcttcttaatgcattggaaatggaa-acagtgcatattgttatgacctgaatatgtttgtgcatttcct
|| ||||| || |||||||| ||||| || || || |||||||||||||| ||||||||||||||||||  || || |     ||    |||  || || || |  | ||    ||  | |     | ||||    || |  ||    | ||||   |  ||| ||   
TTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAGgtaatcactcaccattctattgtgatgttacttttcatacttattatctgttattaaggtaaagtgtgagttttactgtatagcatatagcta-gcacttt--
















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|218485287|gb|FG957632.1|FG957632
EST:     AGCCGTACCATTTTCAGCCTCGTCTG-TTTCTAAG                         ATCATCCCTGAGAAAAGCAGATA-CAAGTGCTATCCACGAAGGTTGAAATA
genomic: AGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAGgtatgcaatc ... tgactatcagATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
EST: gi|25803427|gb|CA759388.1|CA759388
EST:     TCTGTNTTCTAAG                         ATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
genomic: TCTGTTTTCTAAGgtatgcaatc ... tgactatcagATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
EST: gi|29661449|gb|CB657724.1|CB657724
EST:     AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAG                         ATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
genomic: AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAGgtatgcaatc ... tgactatcagATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
EST: gi|87008059|gb|CI297037.1|CI297037
EST:     AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAG                         ATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
genomic: AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAGgtatgcaatc ... tgactatcagATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
EST: gi|29661448|gb|CB657723.1|CB657723
EST:     AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAG                         ATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
genomic: AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAGgtatgcaatc ... tgactatcagATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
EST: gi|58662717|gb|CK051403.1|CK051403
EST:     AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAG                         ATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
genomic: AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAGgtatgcaatc ... tgactatcagATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
EST: gi|58593415|gb|CF991723.1|CF991723
EST:     AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAG                         ATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
genomic: AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAGgtatgcaatc ... tgactatcagATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
EST: gi|25803426|gb|CA759387.1|CA759387
EST:     AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTNGTCTGTTTTCTAAG                         ATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
genomic: AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAGgtatgcaatc ... tgactatcagATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
EST: gi|29660562|gb|CB656837.1|CB656837
EST:     AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAG                         ATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
genomic: AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAGgtatgcaatc ... tgactatcagATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
EST: gi|29625917|gb|CB630928.1|CB630928
EST:     AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAG                         ATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
genomic: AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAGgtatgcaatc ... tgactatcagATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
EST: gi|29625918|gb|CB630929.1|CB630929
EST:     AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAG                         ATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
genomic: AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAGgtatgcaatc ... tgactatcagATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
EST: gi|29669130|gb|CB665405.1|CB665405
EST:     AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAG                         ATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
genomic: AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAGgtatgcaatc ... tgactatcagATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
EST: gi|27578357|gb|CB001052.1|CB001052
EST:     AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAG                         ATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
genomic: AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAGgtatgcaatc ... tgactatcagATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
EST: gi|29660561|gb|CB656836.1|CB656836
EST:     AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAG                         ATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
genomic: AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAGgtatgcaatc ... tgactatcagATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
EST: gi|29655865|gb|CB652140.1|CB652140
EST:     AAGTCCCTGGAGAGGAGCCGTGCCATTTTCAGCCTCGTCTGTTTTCTAAG                         ATCATCCCTGAGAAAAGCAGATCCCAAGTGCTATCCACGAAGGTTGAAATA
genomic: AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAGgtatgcaatc ... tgactatcagATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
EST: gi|163929212|gb|EG713061.1|EG713061
EST:     AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAG                         ATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
genomic: AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAGgtatgcaatc ... tgactatcagATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
EST: gi|4714313|gb|AU058280.1|AU058280
EST:     AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAG                         ATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
genomic: AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAGgtatgcaatc ... tgactatcagATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
EST: gi|163920381|gb|EG714468.1|EG714468
EST:     AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAG                         ATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
genomic: AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAGgtatgcaatc ... tgactatcagATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
EST: gi|33686913|gb|CF315152.1|CF315152
EST:     AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAG                         ATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
genomic: AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAGgtatgcaatc ... tgactatcagATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
EST: gi|58594119|gb|CF992427.1|CF992427
EST:     AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAG                         ATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
genomic: AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAGgtatgcaatc ... tgactatcagATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
EST: gi|218487981|gb|FG959844.1|FG959844
EST:     AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAG                         ATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
genomic: AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAGgtatgcaatc ... tgactatcagATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
EST: gi|29659289|gb|CB655564.1|CB655564
EST:     AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAG                         ATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
genomic: AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAGgtatgcaatc ... tgactatcagATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
EST: gi|29658977|gb|CB655252.1|CB655252
EST:     AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAG                         ATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
genomic: AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAGgtatgcaatc ... tgactatcagATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
EST: gi|29669129|gb|CB665404.1|CB665404
EST:     AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTCTCTAAG                         ATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
genomic: AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAGgtatgcaatc ... tgactatcagATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
EST: gi|29658976|gb|CB655251.1|CB655251
EST:     AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAG                         ATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA
genomic: AAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAGgtatgcaatc ... tgactatcagATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATA

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: 66 (upstream exon), 71 (downstream exon)
Score: 154

TTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAGgtatgcaatc ... tgactatcagATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATAAGACTGGCTAAAGCTGAACAGATTACATGGACCTCACTTGATTATGATA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAGgtatgcaatccctgcaataccaggattatttctcttcttaatgcattggaaatggaaacagtgcatattgttatgacctgaatatgtttgtgcatttcct

- - - - - - - - - - -  TGGAGA
- - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - -  GAGGAG