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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCGAAATGCTGGCTGTGATGGGGTGGGACTTCTTGGCATCGCATGGGCTTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagggctgatcattacaagctcaaagtcgtcgatgagctctttggaagactagcagaggaccacagattgaatcccagtggtgaaccctccaga...

Basic information

species Physcomitrella patens
transcript PP1S55_301V6.2
intron # 2
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|100441269|gb|BY962558.1|BY962558
EST:     TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAG                         GAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
genomic: TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagg ... aatttgacagGAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
EST: gi|100367803|gb|BY984790.1|BY984790
EST:     TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAG                         GAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
genomic: TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagg ... aatttgacagGAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
EST: gi|100444954|gb|BY982782.1|BY982782
EST:     TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAG                         GAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
genomic: TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagg ... aatttgacagGAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
EST: gi|18327139|gb|BJ159140.1|BJ159140
EST:     TTTTGGAGGCATGATTTTCGTGCTGGTGTACCGCACCGCCGGTATCTCAG                         GAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
genomic: TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagg ... aatttgacagGAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
EST: gi|18363932|gb|BJ196004.1|BJ196004
EST:     TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAG                         GAGGTCATATTAATCCAGCTGTTACGTTCG
genomic: TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagg ... aatttgacagGAGGTCATATTAATCCAGCTGTTACGTTCG
EST: gi|100446330|gb|CJ970629.1|CJ970629
EST:     TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAG                         GAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
genomic: TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagg ... aatttgacagGAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
EST: gi|100380353|gb|BY986670.1|BY986670
EST:     TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAG                         GAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
genomic: TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagg ... aatttgacagGAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
EST: gi|100450809|gb|CJ974450.1|CJ974450
EST:     TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAG                         GAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
genomic: TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagg ... aatttgacagGAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
EST: gi|100385719|gb|BY987784.1|BY987784
EST:     TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAG                         GAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCANAA
genomic: TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagg ... aatttgacagGAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
EST: gi|18342754|gb|BJ174789.1|BJ174789
EST:     TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAG                         GAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
genomic: TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagg ... aatttgacagGAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
EST: gi|100450101|gb|CJ974094.1|CJ974094
EST:     TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAG                         GAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
genomic: TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagg ... aatttgacagGAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
EST: gi|67720457|gb|BJ970716.1|BJ970716
EST:     TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAG                         GAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
genomic: TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagg ... aatttgacagGAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
EST: gi|18326909|gb|BJ158909.1|BJ158909
EST:     TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAG                         GAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
genomic: TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagg ... aatttgacagGAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
EST: gi|208391222|gb|DC933511.1|DC933511
EST:     TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAG                         GAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
genomic: TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagg ... aatttgacagGAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
EST: gi|100416508|gb|BY975423.1|BY975423
EST:     TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAG                         GAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
genomic: TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagg ... aatttgacagGAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
EST: gi|100436853|gb|BY979558.1|BY979558
EST:     TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAG                         GAGGTCATATTAATCCAGCTGTTACGTTCGGGCT-GCTGTTGGCACGCAAA
genomic: TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagg ... aatttgacagGAGGTCATATTAATCCAGCTGTTACGTTCGG-CTTGCTGTTGGCACGCAAA
EST: gi|162179614|gb|FC355256.1|FC355256
EST:     TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAG                         GAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
genomic: TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagg ... aatttgacagGAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
EST: gi|208352340|gb|DC906151.1|DC906151
EST:     TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAG                         GAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
genomic: TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagg ... aatttgacagGAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
EST: gi|100441166|gb|BY980787.1|BY980787
EST:     TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAG                         GAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
genomic: TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagg ... aatttgacagGAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
EST: gi|162181259|gb|FC357041.1|FC357041
EST:     TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAG                         GAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
genomic: TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagg ... aatttgacagGAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
EST: gi|100438936|gb|BY961878.1|BY961878
EST:     TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAG                         GAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
genomic: TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagg ... aatttgacagGAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
EST: gi|18359721|gb|BJ191782.1|BJ191782
EST:     TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAG                         GAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
genomic: TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagg ... aatttgacagGAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
EST: gi|208377070|gb|DC910844.1|DC910844
EST:     TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAG                         GAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
genomic: TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagg ... aatttgacagGAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
EST: gi|162181095|gb|FC357267.1|FC357267
EST:     TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAG                         GAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
genomic: TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagg ... aatttgacagGAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
EST: gi|18372638|gb|BJ204240.1|BJ204240
EST:     TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAG                         GAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
genomic: TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagg ... aatttgacagGAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
EST: gi|100356719|gb|BY965246.1|BY965246
EST:     TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAG                         GAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
genomic: TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagg ... aatttgacagGAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
EST: gi|100442334|gb|BY981358.1|BY981358
EST:     TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAG                         GAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
genomic: TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagg ... aatttgacagGAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
EST: gi|162246016|gb|FC424388.1|FC424388
EST:     TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAG                         GAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
genomic: TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagg ... aatttgacagGAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
EST: gi|100448690|gb|CJ972989.1|CJ972989
EST:     TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAG                         GAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA
genomic: TTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagg ... aatttgacagGAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAA

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: 34 (upstream exon), 35 (downstream exon)
Score: 214

GTCCGAAATGCTGGCTGTGATGGGGTGGGACTTCTTGGCATCGCATGGGCTTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagg ... aatttgacagGAGGTCATATTAATCCAGCTGTTACGTTCGGCTTGCTGTTGGCACGCAAAATCTCGCTGCCCCGAGCGCTTGCCTACATGATCGCGCAGTGCTTAGGAGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCGAAATGCTGGCTGTGATGGGGTGGGACTTCTTGGCATCGCATGGGCTTTTGGAGGCATGATTTTCGTGCTGGTGTACTGCACCGCCGGTATCTCAGgtacacgagggctgatcattacaagctcaaagtcgtcgatgagctctttggaagactagcagaggaccacagattgaatcccagtggtgaaccctccaga

- - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG