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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATTTCTAAAAAATCTTGGAGCAGACGAGGTTCTTGACTATCACTCTACGGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCGgtaagtcctattcaatcttctctaaaatctcagtatgactgtctcgtgactaacttggatcatttcaaaaggcgaagcttatttgaacggctcttgattgtaataatctagctttgttgcgatgtgattgtgagcag

Basic information

species Physcomitrella patens
transcript PP1S47_72V6.1
intron # 3
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|37832723|gb|BJ590735.1|BJ590735
EST:     GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCG                         GTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
genomic: GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCGgtaagtccta ... ttgtgagcagGTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
EST: gi|67579076|gb|BJ951227.1|BJ951227
EST:     GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCG                         GTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
genomic: GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCGgtaagtccta ... ttgtgagcagGTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
EST: gi|162237338|gb|FC412446.1|FC412446
EST:     GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCG                         GTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
genomic: GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCGgtaagtccta ... ttgtgagcagGTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
EST: gi|67726911|gb|BJ977170.1|BJ977170
EST:     GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCG                         GTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
genomic: GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCGgtaagtccta ... ttgtgagcagGTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
EST: gi|18336208|gb|BJ168230.1|BJ168230
EST:     GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCG                         GTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
genomic: GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCGgtaagtccta ... ttgtgagcagGTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
EST: gi|37834963|gb|BJ592975.1|BJ592975
EST:     GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCG                         GTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGAAGGTGTGCTTG
genomic: GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCGgtaagtccta ... ttgtgagcagGTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
EST: gi|162237337|gb|FC412445.1|FC412445
EST:     GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCG                         GTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
genomic: GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCGgtaagtccta ... ttgtgagcagGTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
EST: gi|18362523|gb|BJ194594.1|BJ194594
EST:     GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCG                         GTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
genomic: GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCGgtaagtccta ... ttgtgagcagGTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
EST: gi|162224246|gb|FC399505.1|FC399505
EST:     GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCG                         GTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
genomic: GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCGgtaagtccta ... ttgtgagcagGTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
EST: gi|37839438|gb|BJ597446.1|BJ597446
EST:     GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCG                         GTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
genomic: GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCGgtaagtccta ... ttgtgagcagGTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
EST: gi|37837652|gb|BJ595660.1|BJ595660
EST:     GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCG                         GTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
genomic: GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCGgtaagtccta ... ttgtgagcagGTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
EST: gi|37839797|gb|BJ597805.1|BJ597805
EST:     GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCG                         GTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
genomic: GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCGgtaagtccta ... ttgtgagcagGTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
EST: gi|37839869|gb|BJ597877.1|BJ597877
EST:     GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCG                         GTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
genomic: GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCGgtaagtccta ... ttgtgagcagGTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
EST: gi|162209638|gb|FC385942.1|FC385942
EST:     GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCG                         GTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
genomic: GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCGgtaagtccta ... ttgtgagcagGTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
EST: gi|37838329|gb|BJ596337.1|BJ596337
EST:     GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCG                         GTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
genomic: GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCGgtaagtccta ... ttgtgagcagGTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
EST: gi|162261652|gb|FC438085.1|FC438085
EST:     GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCG                         GTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
genomic: GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCGgtaagtccta ... ttgtgagcagGTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
EST: gi|67697068|gb|BJ957301.1|BJ957301
EST:     GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCG                         GTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
genomic: GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCGgtaagtccta ... ttgtgagcagGTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
EST: gi|37846181|gb|BJ604189.1|BJ604189
EST:     GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCG                         GTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
genomic: GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCGgtaagtccta ... ttgtgagcagGTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
EST: gi|37852801|gb|BJ610809.1|BJ610809
EST:     GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCG                         GTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
genomic: GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCGgtaagtccta ... ttgtgagcagGTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
EST: gi|37835120|gb|BJ593132.1|BJ593132
EST:     GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCG                         GTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
genomic: GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCGgtaagtccta ... ttgtgagcagGTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
EST: gi|37848625|gb|BJ606633.1|BJ606633
EST:     GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCG                         GTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
genomic: GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCGgtaagtccta ... ttgtgagcagGTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
EST: gi|37828733|gb|BJ586745.1|BJ586745
EST:     GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCG                         GTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
genomic: GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCGgtaagtccta ... ttgtgagcagGTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
EST: gi|37822006|gb|BJ580072.1|BJ580072
EST:     GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCG                         GTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGAAGGTGTGCTTG
genomic: GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCGgtaagtccta ... ttgtgagcagGTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
EST: gi|162224247|gb|FC399506.1|FC399506
EST:     GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCG                         GTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG
genomic: GGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCGgtaagtccta ... ttgtgagcagGTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTG

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), 24 (downstream exon)
Score: 13

GAATTTCTAAAAAATCTTGGAGCAGACGAGGTTCTTGACTATCACTCTACGGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCGgtaagtccta ... ttgtgagcagGTGAAGGCCCAACTAAAGGAGTCAAAGTGTTGAAGGATGGAGGTGTGCTTGTGTCCATTCTTACCAAAGACCCTGCCTTCCGGCATGTTGTGCAATCAAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAATTTCTAAAAAATCTTGGAGCAGACGAGGTTCTTGACTATCACTCTACGGATTATACCCAGAAGCCCGAACGCTATGACGTTGTCTATGACACTGTCGgtaagtcctattcaatcttctctaaaatctcagtatgactgtctcgtgactaacttggatcatttcaaaaggcgaagcttatttgaacggctcttgattgtaataatctagctttgttgcgatgtgattgtgagcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC