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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGAACAAAAACTAGCAGACATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactgaaaattctaacttgagtgtcgggttgtgttactaatttcattattactctatgatctacatataccagacactatggcctgctctatcct...

Basic information

species Physcomitrella patens
transcript PP1S207_28V6.1
intron # 8
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|162264592|gb|FC440888.1|FC440888
EST:     ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
EST: gi|37827125|gb|BJ585137.1|BJ585137
EST:     ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
EST: gi|162175834|gb|FC352136.1|FC352136
EST:     ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
EST: gi|18340498|gb|BJ172526.1|BJ172526
EST:     ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
EST: gi|7287402|gb|AW599889.1|AW599889
EST:     GAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: GAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
EST: gi|162217120|gb|FC392484.1|FC392484
EST:     ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
EST: gi|162191630|gb|FC367675.1|FC367675
EST:     ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
EST: gi|162191631|gb|FC367676.1|FC367676
EST:     ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
EST: gi|37840412|gb|BJ598420.1|BJ598420
EST:     ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
EST: gi|37826709|gb|BJ584721.1|BJ584721
EST:     ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
EST: gi|37827937|gb|BJ585949.1|BJ585949
EST:     ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
EST: gi|37828408|gb|BJ586420.1|BJ586420
EST:     ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
EST: gi|208374509|gb|DC944979.1|DC944979
EST:     ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
EST: gi|37839229|gb|BJ597237.1|BJ597237
EST:     ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
EST: gi|208352669|gb|DC921403.1|DC921403
EST:     ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
EST: gi|37851612|gb|BJ609620.1|BJ609620
EST:     TGCAGATGAAGNTGCAGTATACTGCAAGGAGAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: TGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
EST: gi|7583861|gb|AW699764.1|AW699764
EST:     GTGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
EST: gi|67720060|gb|BJ970319.1|BJ970319
EST:     ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
EST: gi|162217121|gb|FC392485.1|FC392485
EST:     ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
EST: gi|37837900|gb|BJ595908.1|BJ595908
EST:     ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
EST: gi|162263697|gb|FC439622.1|FC439622
EST:     ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
EST: gi|7286362|gb|AW598903.1|AW598903
EST:     GAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: GAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
EST: gi|37848687|gb|BJ606695.1|BJ606695
EST:     ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
EST: gi|208353452|gb|DC946316.1|DC946316
EST:     ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
EST: gi|67697251|gb|BJ957484.1|BJ957484
EST:     ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
EST: gi|208378223|gb|DC918844.1|DC918844
EST:     ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
EST: gi|37845126|gb|BJ603134.1|BJ603134
EST:     ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
EST: gi|37826854|gb|BJ584866.1|BJ584866
EST:     ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
EST: gi|162272680|gb|FC448306.1|FC448306
EST:     ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
EST: gi|208365594|gb|DC944092.1|DC944092
EST:     ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
EST: gi|37845996|gb|BJ604004.1|BJ604004
EST:     ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
EST: gi|37824831|gb|BJ582897.1|BJ582897
EST:     ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAG                         TGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA
genomic: ATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTA

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: 30 (upstream exon), 35 (downstream exon)
Score: 12

GTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGAACAAAAACTAGCAGACATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactg ... ctgtgtacagTGCATTGCCCAAAATTATCAAGACAGGTTTCGCTGCCATCAATTTAATTTATTTCTTCACAGCTGGTCCTGATGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGAACAAAAACTAGCAGACATGCCTGCAGATGAAGCTGCAGTATACTGCAAGGAGAATGATCTCGTCAGgtgtgtactgaaaattctaacttgagtgtcgggttgtgttactaatttcattattactctatgatctacatataccagacactatggcctgctctatcct

- - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA