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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtattaagtggttattgtaatagcaaattcgtccagaattacattcacgaggactccttgctatgagtgaacaacactaaatcttatggtggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAATTATCTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATG

Basic information

species Physcomitrella patens
transcript PP1S9_32V6.1
intron # 3
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|208359056|gb|DC957804.1|DC957804
EST:     NTGTGACGTTCNAGGAGGCTCAAGCTCTAGACACTGCNNNNNNNCNTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|100378310|gb|BY949787.1|BY949787
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|208359261|gb|DC939070.1|DC939070
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGGCAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|18342157|gb|BJ174192.1|BJ174192
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|208373441|gb|DC941052.1|DC941052
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|100358635|gb|BY965746.1|BY965746
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|100387784|gb|BY970529.1|BY970529
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|208368227|gb|DC931453.1|DC931453
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|100388020|gb|BY988493.1|BY988493
EST:     TCGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|162265878|gb|FC442465.1|FC442465
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|208357096|gb|DC942730.1|DC942730
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|208393431|gb|DC942515.1|DC942515
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|208396861|gb|DC908181.1|DC908181
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|162265877|gb|FC442464.1|FC442464
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|100397943|gb|BY954009.1|BY954009
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|162280268|gb|FC456285.1|FC456285
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|208387672|gb|DC937237.1|DC937237
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|100444933|gb|BY982761.1|BY982761
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|162240163|gb|FC418290.1|FC418290
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|208384457|gb|DC911543.1|DC911543
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|100405823|gb|BY973872.1|BY973872
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|208368003|gb|DC951014.1|DC951014
EST:     TGNGACGTTCNANGGAGGCTCAAGCTCTAGACACTGNTCTTNTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TGTGACGTTC-AAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|100417073|gb|BY957153.1|BY957153
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|162230915|gb|FC406754.1|FC406754
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|162240162|gb|FC418289.1|FC418289
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|100374498|gb|BY985807.1|BY985807
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|208400060|gb|DC908623.1|DC908623
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|162280269|gb|FC456286.1|FC456286
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|100437426|gb|BY961512.1|BY961512
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGNNAGC-ACTGT-GTCGACAGAGCAGTCAATATTACACCGCTGGAAGATG
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGG--AGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATG
EST: gi|208391737|gb|DC937955.1|DC937955
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|100399961|gb|BY990708.1|BY990708
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|162230914|gb|FC406753.1|FC406753
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|208375442|gb|DC940496.1|DC940496
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|208386854|gb|DC953507.1|DC953507
EST:     NTGTGACG-TC-ANGA-GNTCAAGCTCTAGACACTGTTCTT-TTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|100449088|gb|CJ973387.1|CJ973387
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|100385442|gb|BY969779.1|BY969779
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
EST: gi|100436109|gb|BY979384.1|BY979384
EST:     TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCG                         GGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA
genomic: TTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAA

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: 35 (upstream exon), 29 (downstream exon)
Score: 5

GGATGGTGACACCCAGATTGCCCTTGTGACGTTCAAGGAGGCTCAAGCTCTAGACACTGCTCTTCTTCTTTCGgtgcgaggat ... ggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAATTATCTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacgaggactccttgctatgagtgaacaacactaaatcttatggtggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAATTATCTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATG
                             cactaaa  putative branch site (score: 5)
                                taaatcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattaagtggttattgtaatagcaaattcgtccagaattacattcacgaggactccttgctatgagtgaacaacactaaatcttatggtggttttgcagGGAGCCACTGTTGTCGACAGAGCAGTCAATATTACACCGCTGGAAGATGAATTATCTCCAAGCATCAACTCCATTCCAAGAGATAAAGCATTTGGAAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA