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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgacttacattgtgaaacggaggaagtatgtgaattgctcctttagtttggttcctaacatgctatctgaatgtcttcaaaatattttctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAGTCAGCTGATCCAGATATCCAGTTAATCTGCGATGATTCAAACATATTCA

Basic information

species Oryza sativa
transcript LOC_Os02g42314.1
intron # 2
splice site 3'
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|88333562|gb|CI656634.1|CI656634
EST:     AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG                         GCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
genomic: AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAGgtcagttcta ... ctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
EST: gi|88717712|gb|CI741222.1|CI741222
EST:     AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG                         GCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
genomic: AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAGgtcagttcta ... ctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
EST: gi|88334413|gb|CI642658.1|CI642658
EST:     AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGAACAGATGCAG                         GCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
genomic: AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAGgtcagttcta ... ctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
EST: gi|9865085|gb|AU100835.1|AU100835
EST:     AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG                         GCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
genomic: AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAGgtcagttcta ... ctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
EST: gi|88581898|gb|CI699113.1|CI699113
EST:     AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG                         GCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
genomic: AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAGgtcagttcta ... ctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
EST: gi|88386007|gb|CI570642.1|CI570642
EST:     AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG                         GCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
genomic: AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAGgtcagttcta ... ctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
EST: gi|88676847|gb|CI730960.1|CI730960
EST:     AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG                         GCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
genomic: AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAGgtcagttcta ... ctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
EST: gi|88387401|gb|CI582919.1|CI582919
EST:     AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG                         GCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
genomic: AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAGgtcagttcta ... ctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
EST: gi|88595265|gb|CI714086.1|CI714086
EST:     AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG                         GCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
genomic: AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAGgtcagttcta ... ctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
EST: gi|55438029|gb|CV732308.1|CV732308
EST:     AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG                         GCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
genomic: AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAGgtcagttcta ... ctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
EST: gi|313080048|gb|HO213368.1|HO213368
EST:     AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG                         GCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
genomic: AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAGgtcagttcta ... ctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
EST: gi|88308370|gb|CI649585.1|CI649585
EST:     AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG                         GCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
genomic: AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAGgtcagttcta ... ctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
EST: gi|88342554|gb|CI637130.1|CI637130
EST:     AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG                         GCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
genomic: AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAGgtcagttcta ... ctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
EST: gi|88337710|gb|CI632212.1|CI632212
EST:     AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG                         GCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
genomic: AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAGgtcagttcta ... ctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
EST: gi|86905439|gb|CI285402.1|CI285402
EST:     AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG                         GCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
genomic: AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAGgtcagttcta ... ctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
EST: gi|88729548|gb|CI751351.1|CI751351
EST:     AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG                         GCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
genomic: AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAGgtcagttcta ... ctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
EST: gi|163919981|gb|EG714923.1|EG714923
EST:     AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG                         GCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
genomic: AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAGgtcagttcta ... ctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
EST: gi|88730413|gb|CI754026.1|CI754026
EST:     AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG                         GCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
genomic: AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAGgtcagttcta ... ctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
EST: gi|88393637|gb|CI619929.1|CI619929
EST:     AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG                         GCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
genomic: AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAGgtcagttcta ... ctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
EST: gi|88348941|gb|CI653985.1|CI653985
EST:     AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG                         GCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
genomic: AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAGgtcagttcta ... ctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
EST: gi|88595236|gb|CI714057.1|CI714057
EST:     AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG                         GCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
genomic: AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAGgtcagttcta ... ctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
EST: gi|88692966|gb|CI736541.1|CI736541
EST:     AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGAACAGATGCAG                         GCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
genomic: AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAGgtcagttcta ... ctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
EST: gi|88760639|gb|CI770195.1|CI770195
EST:     AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG                         GCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
genomic: AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAGgtcagttcta ... ctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
EST: gi|33823074|gb|CF337340.1|CF337340
EST:     AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG                         GCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
genomic: AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAGgtcagttcta ... ctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
EST: gi|88345516|gb|CI629777.1|CI629777
EST:     AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG                         GCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
genomic: AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAGgtcagttcta ... ctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
EST: gi|88729270|gb|CI752780.1|CI752780
EST:     AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCACATGCAG                         GCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
genomic: AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAGgtcagttcta ... ctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
EST: gi|88383885|gb|CI631775.1|CI631775
EST:     AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG                         GCATCTACAGCTAGGCTCTTTCAGGAGTATAAGGAGGTGCAGCGAGAAAAG
genomic: AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAGgtcagttcta ... ctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
EST: gi|86900317|gb|CI296360.1|CI296360
EST:     AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG                         GCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
genomic: AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAGgtcagttcta ... ctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
EST: gi|88592549|gb|CI710658.1|CI710658
EST:     AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG                         GCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG
genomic: AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAGgtcagttcta ... ctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAG

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: 70 (upstream exon), 75 (downstream exon)
Score: 58

AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAGgtcagttcta ... ctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAGTCAGCTGATCCAGATATCCAGTTAATCTGCGATGATTCAAACATATTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtttggttcctaacatgctatctgaatgtcttcaaaatattttctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAGTCAGCTGATCCAGATATCCAGTTAATCTGCGATGATTCAAACATATTCA
         tcctaac  putative branch site (score: 58)
                                         ttttctatc  putative PPT
                                ttcaaaatattttcta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgacttacattgtgaaacggaggaagtatgtgaattgctcctttagtttggttcctaacatgctatctgaatgtcttcaaaatattttctatcgaaagGCATCTAGAGCTAGGCTCTTTAAGGAGTATAAGGAGGTGCAGCGAGAAAAGTCAGCTGATCCAGATATCCAGTTAATCTGCGATGATTCAAACATATTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT