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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTTCGGAAACTACGGGATTCCCTACTCATCGGCCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAGgtgatgttcatgccctaattggggacagtggctgatcaccttgaggtctttagggtttgtgagggttgtctagcgcttggtagcgtggagggacgggcct...

Basic information

species Physcomitrella patens
transcript PP1S245_32V6.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S245_32V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ38251 (Selaginella moellendorffii), 5'ss of exon 1
---------TATTTCGGAAACTACGGGATTCCCTACTCATCGGCCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAGgtgatgttcatgccctaattggggacagtggctgatcaccttgaggtctttagggtttgtgagggttgtctagcgcttggtagcgtggagggacgggcct
         || |||||    || || ||    | |||  |    ||||| ||||||||||||||||| || || || ||||||||||| ||||| |    |    |    |         |  ||  || |  |     |    || |||| || |   |  |  | ||||  ||                 
ATGCCGCAGTACTTCGGGGGATATGGCATCAATTTCTCGGCCTTGCCGTTTGAGCAGAATTATCGCTGCTATTCCGCCTCCTTCATCGACAAGgtaagagactcttctctctc--------tctctc-tctctctcgctccacccggttttgcgacgtgcgcttctc-cttgccag-----------------

upper sequence: PP1S245_32V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ14970 (Selaginella moellendorffii), 5'ss of exon 1
---------TATTTCGGAAACTACGGGATTCCCTACTCATCGGCCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAGgtgatgttcatgccctaattggggacagtggctgatcaccttgaggtctttagggtttgtgagggttgtctagcgcttggtagcgtggagggacgggcct
         || |||||    || || ||    | |||  |    ||||| ||||||||||||||||| || || || ||||||||||| ||||| |    |    |    |      |     | | |        |  |  |     |||  ||                                     
ATGCCGCAGTACTTCGGGGGATATGGCATCAATTTCTCGGCCTTGCCGTTTGAGCAGAATTATCGCTGCTATTCCGCCTCCTTCATCGACAAGgtaagagactcttctctctctctcgctccacccggttttgcgacgtgcgcttctccttgccag-------------------------------------
















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|100385818|gb|BY951012.1|BY951012
EST:     CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAG                         CCGCATTTGGAAAATGGAGATAAAG
genomic: CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAGgtgatgttca ... gtggatgcagCCGCATTTGGAAAATGGAGATAAAG
EST: gi|100406597|gb|BY955683.1|BY955683
EST:     CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAG                         CCGCATTTGGAAAATGGAGATAAAG
genomic: CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAGgtgatgttca ... gtggatgcagCCGCATTTGGAAAATGGAGATAAAG
EST: gi|100418696|gb|BY975696.1|BY975696
EST:     CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAG                         CCGCATTTGGAAAATGGAGATAAAG
genomic: CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAGgtgatgttca ... gtggatgcagCCGCATTTGGAAAATGGAGATAAAG
EST: gi|208387770|gb|DC941339.1|DC941339
EST:     CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAG                         CCGCATTTGGAAAATGGAGATAAAG
genomic: CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAGgtgatgttca ... gtggatgcagCCGCATTTGGAAAATGGAGATAAAG
EST: gi|100415871|gb|BY956965.1|BY956965
EST:     CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAG                         CCGCATTTGGAAAATGGAGATAAAG
genomic: CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAGgtgatgttca ... gtggatgcagCCGCATTTGGAAAATGGAGATAAAG
EST: gi|67508675|gb|BJ941536.1|BJ941536
EST:     CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAG                         CCGCATTTGGAAAATGGAGATAAAG
genomic: CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAGgtgatgttca ... gtggatgcagCCGCATTTGGAAAATGGAGATAAAG
EST: gi|100448950|gb|CJ973249.1|CJ973249
EST:     CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAG                         CCGCATTTGGAAAATGGAGATAAAG
genomic: CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAGgtgatgttca ... gtggatgcagCCGCATTTGGAAAATGGAGATAAAG
EST: gi|208349271|gb|DC906385.1|DC906385
EST:     CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAG                         CCGCATTTGGAAAATGGAGATAAAG
genomic: CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAGgtgatgttca ... gtggatgcagCCGCATTTGGAAAATGGAGATAAAG
EST: gi|208346232|gb|DC905221.1|DC905221
EST:     CCCCGTTCGAGCAGAATTATCGCTGTTACGCAGCTTCCTTCATCGATAAG                         CCGCATTTGGAAAATGGAGATAAAG
genomic: CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAGgtgatgttca ... gtggatgcagCCGCATTTGGAAAATGGAGATAAAG
EST: gi|208352262|gb|DC906337.1|DC906337
EST:     CCCCGTTCGAGCAGAATTATTGCTGTTACTCAGCTTCCTTCATCGATAAG                         CCGCATTTGGAAAATGGAGATAAAG
genomic: CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAGgtgatgttca ... gtggatgcagCCGCATTTGGAAAATGGAGATAAAG
EST: gi|208366055|gb|DC935844.1|DC935844
EST:     CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAG                         CCGCATTTGGAAAATGGAGATAAAG
genomic: CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAGgtgatgttca ... gtggatgcagCCGCATTTGGAAAATGGAGATAAAG
EST: gi|208372135|gb|DC940317.1|DC940317
EST:     CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAG                         CCGCATTTGGAAAATGGAGATAAAG
genomic: CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAGgtgatgttca ... gtggatgcagCCGCATTTGGAAAATGGAGATAAAG
EST: gi|18358101|gb|BJ190160.1|BJ190160
EST:     CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAG                         CCGCATTTGGAAAATGGAGATAAAG
genomic: CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAGgtgatgttca ... gtggatgcagCCGCATTTGGAAAATGGAGATAAAG
EST: gi|208390049|gb|DC938104.1|DC938104
EST:     CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAG                         CCGCATTTGGAAAATGGAGATAAAG
genomic: CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAGgtgatgttca ... gtggatgcagCCGCATTTGGAAAATGGAGATAAAG
EST: gi|100419714|gb|BY957686.1|BY957686
EST:     CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAG                         CCGCATTTGGAAAATGGAGATAAAG
genomic: CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAGgtgatgttca ... gtggatgcagCCGCATTTGGAAAATGGAGATAAAG
EST: gi|208358250|gb|DC930691.1|DC930691
EST:     CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAG                         CCGCATTTGGAAAATGGAGATAAAG
genomic: CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAGgtgatgttca ... gtggatgcagCCGCATTTGGAAAATGGAGATAAAG
EST: gi|208357678|gb|DC934130.1|DC934130
EST:     CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAG                         CCGCATTTGGAAAATGGAGATAAAG
genomic: CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAGgtgatgttca ... gtggatgcagCCGCATTTGGAAAATGGAGATAAAG
EST: gi|100442532|gb|BY963226.1|BY963226
EST:     CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAG                         CCGCATTTGGAAAATGGAGATAAAG
genomic: CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAGgtgatgttca ... gtggatgcagCCGCATTTGGAAAATGGAGATAAAG
EST: gi|100366066|gb|BY967268.1|BY967268
EST:     CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAG                         CCGCATTTGGAAAATGGAGATAAAG
genomic: CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAGgtgatgttca ... gtggatgcagCCGCATTTGGAAAATGGAGATAAAG
EST: gi|208366022|gb|DC935839.1|DC935839
EST:     CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAG                         CCGCATTTGGAAAATGGAGATAAAG
genomic: CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAGgtgatgttca ... gtggatgcagCCGCATTTGGAAAATGGAGATAAAG
EST: gi|100386786|gb|BY970327.1|BY970327
EST:     CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAG                         CCGCATTTGGAAAATGGAGATAAAG
genomic: CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAGgtgatgttca ... gtggatgcagCCGCATTTGGAAAATGGAGATAAAG
EST: gi|208374981|gb|DC956391.1|DC956391
EST:     TTCATCGATAAG                         CCGCATTTGGAAAATGGAGATAAAG
genomic: TTCATCGATAAGgtgatgttca ... gtggatgcagCCGCATTTGGAAAATGGAGATAAAG
EST: gi|208356440|gb|DC934430.1|DC934430
EST:     CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAG                         CCGCATTTGGAAAATGGAGATAAAG
genomic: CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAGgtgatgttca ... gtggatgcagCCGCATTTGGAAAATGGAGATAAAG
EST: gi|208386327|gb|DC932823.1|DC932823
EST:     CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAG                         CCGCATTTGGAAAATGGAGATAAAG
genomic: CCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAGgtgatgttca ... gtggatgcagCCGCATTTGGAAAATGGAGATAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATTTCGGAAACTACGGGATTCCCTACTCATCGGCCCCGTTCGAGCAGAATTATCGCTGTTACTCAGCTTCCTTCATCGATAAGgtgatgttcatgccctaattggggacagtggctgatcaccttgaggtctttagggtttgtgagggttgtctagcgcttggtagcgtggagggacgggcct

- - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT