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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAGACGAAGTTGAAGAGGAGACTGAGAAGGACAGAGCTGAAAATGCCGTTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagacctaatcttagttccaacctcggcaattgtcactacctcaatgctatcacttatcattctgaatatcgtactttgtatgataatgcatatgttgagtaacaattcggtacatttgctcactgaaataaccgagttttctgccacgtaacag

Basic information

species Physcomitrella patens
transcript PP1S126_38V6.1
intron # 16
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|37841475|gb|BJ599483.1|BJ599483
EST:     TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAG                         GACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
genomic: TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagaccta ... cacgtaacagGACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
EST: gi|37822678|gb|BJ580744.1|BJ580744
EST:     TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAG                         GACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
genomic: TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagaccta ... cacgtaacagGACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
EST: gi|162166690|gb|FC342659.1|FC342659
EST:     TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAG                         GACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
genomic: TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagaccta ... cacgtaacagGACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
EST: gi|37838652|gb|BJ596660.1|BJ596660
EST:     TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAG                         GACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
genomic: TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagaccta ... cacgtaacagGACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
EST: gi|18341140|gb|BJ173173.1|BJ173173
EST:     TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAG                         GACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
genomic: TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagaccta ... cacgtaacagGACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
EST: gi|37837161|gb|BJ595169.1|BJ595169
EST:     TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAG                         GACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
genomic: TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagaccta ... cacgtaacagGACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
EST: gi|162240202|gb|FC418329.1|FC418329
EST:     TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAG                         GACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
genomic: TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagaccta ... cacgtaacagGACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
EST: gi|37843903|gb|BJ601911.1|BJ601911
EST:     TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAG                         GACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
genomic: TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagaccta ... cacgtaacagGACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
EST: gi|37836149|gb|BJ594157.1|BJ594157
EST:     TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAG                         GACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
genomic: TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagaccta ... cacgtaacagGACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
EST: gi|18332522|gb|BJ164535.1|BJ164535
EST:     TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAG                         GACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
genomic: TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagaccta ... cacgtaacagGACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
EST: gi|37826825|gb|BJ584837.1|BJ584837
EST:     TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAG                         GACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
genomic: TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagaccta ... cacgtaacagGACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
EST: gi|37825141|gb|BJ583207.1|BJ583207
EST:     TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAG                         GACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
genomic: TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagaccta ... cacgtaacagGACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
EST: gi|37826145|gb|BJ584157.1|BJ584157
EST:     TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAG                         GACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
genomic: TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagaccta ... cacgtaacagGACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
EST: gi|162166547|gb|FC343244.1|FC343244
EST:     TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAG                         GACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
genomic: TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagaccta ... cacgtaacagGACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
EST: gi|162260418|gb|FC435044.1|FC435044
EST:     TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAG                         GACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
genomic: TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagaccta ... cacgtaacagGACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
EST: gi|162235625|gb|FC411890.1|FC411890
EST:     TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAG                         GACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
genomic: TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagaccta ... cacgtaacagGACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
EST: gi|162240201|gb|FC418328.1|FC418328
EST:     TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAG                         GACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
genomic: TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagaccta ... cacgtaacagGACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
EST: gi|162168869|gb|FC345343.1|FC345343
EST:     TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAG                         GACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
genomic: TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagaccta ... cacgtaacagGACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
EST: gi|37841177|gb|BJ599185.1|BJ599185
EST:     TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAG                         GACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
genomic: TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagaccta ... cacgtaacagGACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
EST: gi|37834239|gb|BJ592251.1|BJ592251
EST:     TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAG                         GACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
genomic: TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagaccta ... cacgtaacagGACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
EST: gi|37822667|gb|BJ580733.1|BJ580733
EST:     TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAG                         GACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
genomic: TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagaccta ... cacgtaacagGACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
EST: gi|37831437|gb|BJ589449.1|BJ589449
EST:     TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAG                         GACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
genomic: TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagaccta ... cacgtaacagGACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
EST: gi|37849554|gb|BJ607562.1|BJ607562
EST:     TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAG                         GACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
genomic: TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagaccta ... cacgtaacagGACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
EST: gi|37843052|gb|BJ601060.1|BJ601060
EST:     TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAG                         GACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
genomic: TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagaccta ... cacgtaacagGACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
EST: gi|67727873|gb|BJ978132.1|BJ978132
EST:     TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAG                         GACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
genomic: TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagaccta ... cacgtaacagGACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
EST: gi|162196000|gb|FC372691.1|FC372691
EST:     TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAG                         GACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
genomic: TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagaccta ... cacgtaacagGACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
EST: gi|37847752|gb|BJ605760.1|BJ605760
EST:     TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAG                         GACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
genomic: TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagaccta ... cacgtaacagGACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
EST: gi|18334981|gb|BJ166999.1|BJ166999
EST:     TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAG                         GACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
genomic: TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagaccta ... cacgtaacagGACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
EST: gi|37826629|gb|BJ584641.1|BJ584641
EST:     TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAG                         GACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
genomic: TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagaccta ... cacgtaacagGACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
EST: gi|37824151|gb|BJ582217.1|BJ582217
EST:     TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAG                         GACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA
genomic: TTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagaccta ... cacgtaacagGACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAA

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: 31 (upstream exon), 32 (downstream exon)
Score: 15

AGAAGACGAAGTTGAAGAGGAGACTGAGAAGGACAGAGCTGAAAATGCCGTTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagaccta ... cacgtaacagGACGATACGACGGCTTCCGAGCTGGCAGCCGAAGCTGCAGCTAGTGACGAAGTAGCTGACGAGGACGCTTCTTCAGAGAAGGATGAGCTGTAGATTTAGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAGACGAAGTTGAAGAGGAGACTGAGAAGGACAGAGCTGAAAATGCCGTTGAAGACGCTCCTGATTTCCAAAATTTCCAGAATATGAATATGGATCAGgtgagacctaatcttagttccaacctcggcaattgtcactacctcaatgctatcacttatcattctgaatatcgtactttgtatgataatgcatatgttgagtaacaattcggtacatttgctcactgaaataaccgagttttctgccacgtaacag

- - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA