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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaatatttcccaccacaggggtagctcaagtggatagacactcaatgttactactgctcagttctcgtgaatgtcttaagatagtggttagtgagaagcatcctaccattaaaattcgtatctcttgaaattttaatatgagtggaccattggatgcagCTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCTTGTACAGAGGACTATCCACTCCATGTCATGAATCCTTACGGCCGCACCA

Basic information

species Physcomitrella patens
transcript PP1S101_67V6.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S101_67V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA08G02690.2 (Glycine max), 3'ss of exon 3
gtgagaatatttcccaccacaggggtagctcaagtggatagacactcaatgttactactgctcagttctcgtgaatgtcttaagatagtggttagtgagaagcatcctaccattaaaattcgtatctcttgaaattttaatatgagtggaccattggatgcagCTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCTTGTACAGAGGACTATCCACTCCATGTCATGAATCCTTACGGCCGCACCA
                                         ||  |  |   | |||   |    |  |    | ||||||  |  | ||||||   |     ||  |   | | |  ||  ||| |||||||                     ||  | |||||||||||||||||||||||||| || || ||    ||  ||   || || ||||| || || |  ||  |    |  |  || || || || || ||||
-----------------------------------------accttttactctcctatcccctgctattttgaagtgtcttgtggaattggttacgcaatctgattatttaactgat-tttatatttcttgaa---------------------tgatttcagCTTGTGTTCTCATCTTCAGCAACTGTATATGGGTGGCCAAAGGAGGTCCCATGTACCGAAGAGTTCCCTTTGTCAGCAACAAACCCATATGGACGAACCA

upper sequence: PP1S101_67V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA05G36850.1 (Glycine max), 3'ss of exon 3
gtgagaatatttcccaccacaggggtagctcaagtggatagacactcaatgttactactgctcagttctcgtgaatgtcttaagatagtggtta-gtgagaagcatcctaccattaaaattcg---tatctcttgaaattttaatatgagtggaccattggatgcagCTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCTTGTACAGAGGACTATCCACTCCATGTCATGAATCCTTACGGCCGCACCA
                                                                  | | |  | ||||||  |  | |||||| |    ||  ||  |  | | |   | |    |   | || || |  |  |||   |     | ||  | |||||||||||||||||||||||||| || || ||    ||  ||   || || ||||| || || |  ||  |    |  |  || || || || || ||||
------------------------------------------------------------------ttttg-aagtgtcttgtggaattggttacgcattaattatattttcttgatgctgcaatctgattatttaactgattttatatttctttgaatgatttcagCTTGTGTTCTCATCTTCAGCAACTGTATATGGCTGGCCAAAGGAGGTCCCATGTACCGAAGAGTTCCCTTTGTCAGCAACAAACCCATATGGACGAACCA
















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|100354239|gb|BY945777.1|BY945777
EST:     AAGCACCATTAATCTTATGGATGTCATGTCCAAGAAACA-CTGCNAAAAT                         CTTGTGTTCTCATCTTTCAGCA-CAGTGTACGGACAACCGGAGTGCGTACC
genomic: AAGCACCATTAATCTTATGGATGTCATGTCCAAGAA-CAACTGCAAAAATgtgagaatat ... ttggatgcagCTTGTGTTCTCATCTT-CAGCAACAGTGTACGGACAACCGGAGTGCGTACC
EST: gi|208350330|gb|DC906032.1|DC906032
EST:     TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAAT                         CTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
genomic: TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAATgtgagaatat ... ttggatgcagCTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
EST: gi|208377704|gb|DC932240.1|DC932240
EST:     TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAAT                         CTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
genomic: TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAATgtgagaatat ... ttggatgcagCTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
EST: gi|100449045|gb|CJ973344.1|CJ973344
EST:     TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAAT                         CTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
genomic: TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAATgtgagaatat ... ttggatgcagCTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
EST: gi|18358112|gb|BJ190171.1|BJ190171
EST:     TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAAT                         CTTGTGTTCTCATCTTCAGCAACAGTGTACGGGACAACCGGAGTGCGTAC
genomic: TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAATgtgagaatat ... ttggatgcagCTTGTGTTCTCATCTTCAGCAACAGTGTACGG-ACAACCGGAGTGCGTAC
EST: gi|208375758|gb|DC936698.1|DC936698
EST:     TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAAT                         CTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
genomic: TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAATgtgagaatat ... ttggatgcagCTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
EST: gi|100443377|gb|BY963673.1|BY963673
EST:     TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAAT                         CTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
genomic: TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAATgtgagaatat ... ttggatgcagCTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
EST: gi|100412936|gb|BY992508.1|BY992508
EST:     TAAGCACCATTAATCTTATGGATGTCATGTCCCAGAACAACTGCAAAAAT                         CTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
genomic: TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAATgtgagaatat ... ttggatgcagCTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
EST: gi|100385898|gb|BY951092.1|BY951092
EST:     AAGCACCATTAATCTTATGGATGTCATGTCCAAGAANCA-CTGCAAAAAT                         CTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
genomic: AAGCACCATTAATCTTATGGATGTCATGTCCAAGAA-CAACTGCAAAAATgtgagaatat ... ttggatgcagCTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
EST: gi|100412296|gb|BY956511.1|BY956511
EST:     TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAAT                         CTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGG
genomic: TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAATgtgagaatat ... ttggatgcagCTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGG
EST: gi|208387323|gb|DC933074.1|DC933074
EST:     TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAAT                         CTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
genomic: TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAATgtgagaatat ... ttggatgcagCTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
EST: gi|162192491|gb|FC369121.1|FC369121
EST:     TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAAT                         CTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
genomic: TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAATgtgagaatat ... ttggatgcagCTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
EST: gi|100379480|gb|BY986659.1|BY986659
EST:     TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAAT                         CTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCG
genomic: TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAATgtgagaatat ... ttggatgcagCTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCG
EST: gi|162192001|gb|FC367214.1|FC367214
EST:     TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAAT                         CTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
genomic: TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAATgtgagaatat ... ttggatgcagCTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
EST: gi|208361787|gb|DC935027.1|DC935027
EST:     TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAAT                         CTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
genomic: TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAATgtgagaatat ... ttggatgcagCTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
EST: gi|100412866|gb|BY992475.1|BY992475
EST:     AAGCACCATTAATCTTATGGATGTCATGTCCAAGAAACA-CTGCAAAAAT                         CTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
genomic: AAGCACCATTAATCTTATGGATGTCATGTCCAAGAA-CAACTGCAAAAATgtgagaatat ... ttggatgcagCTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
EST: gi|100351733|gb|BY964522.1|BY964522
EST:     TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAAT                         CTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
genomic: TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAATgtgagaatat ... ttggatgcagCTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
EST: gi|100435311|gb|BY979179.1|BY979179
EST:     TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAAT                         CTTGTGTTCTCATCTTTCAGCA-CAGTGTACGGACAACCGGAGTGCGTACC
genomic: TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAATgtgagaatat ... ttggatgcagCTTGTGTTCTCATCTT-CAGCAACAGTGTACGGACAACCGGAGTGCGTACC
EST: gi|162231058|gb|FC406169.1|FC406169
EST:     TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAAT                         CTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
genomic: TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAATgtgagaatat ... ttggatgcagCTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
EST: gi|100423654|gb|BY976496.1|BY976496
EST:     TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAAT                         CTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
genomic: TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAATgtgagaatat ... ttggatgcagCTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
EST: gi|100369386|gb|BY948074.1|BY948074
EST:     TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAAT                         CTTGTGTTCTCATCTTCAGNCA-CAGTGTACGGACAACCGGAGTGCGTACC
genomic: TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAATgtgagaatat ... ttggatgcagCTTGTGTTCTCATCTTCAG-CAACAGTGTACGGACAACCGGAGTGCGTACC
EST: gi|100436738|gb|BY979501.1|BY979501
EST:     TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAAT                         CTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
genomic: TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAATgtgagaatat ... ttggatgcagCTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
EST: gi|208397832|gb|DC912027.1|DC912027
EST:     TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAAT                         CTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
genomic: TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAATgtgagaatat ... ttggatgcagCTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
EST: gi|100437309|gb|BY961456.1|BY961456
EST:     TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAAT                         CTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
genomic: TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAATgtgagaatat ... ttggatgcagCTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
EST: gi|100365706|gb|BY948371.1|BY948371
EST:     TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAAT                         CTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT
genomic: TAAGCACCATTAATCTTATGGATGTCATGTCCAAGAACAACTGCAAAAATgtgagaatat ... ttggatgcagCTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accattaaaattcgtatctcttgaaattttaatatgagtggaccattggatgcagCTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCTTGTACAGAGGACTATCCACTCCATGTCATGAATCCTTACGGCCGCACCA
                          ttttaat  putative branch site (score: 3)
              tatctcttgaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaatatttcccaccacaggggtagctcaagtggatagacactcaatgttactactgctcagttctcgtgaatgtcttaagatagtggttagtgagaagcatcctaccattaaaattcgtatctcttgaaattttaatatgagtggaccattggatgcagCTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCTTGTACAGAGGACTATCCACTCCATGTCATGAATCCTTACGGCCGCACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA