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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtagatatgctgcattgatattggaatacggtgtgatattctgattcgtaattgattagctgtaaaagaagtaatttcgaatgttgtgtttctttgcagCGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAACCTTGCGGACAAGTCATTGTGGCGTGCTGGAGTTTGTGGCAGAGGAAGG

Basic information

species Physcomitrella patens
transcript PP1S245_32V6.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S245_32V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA08G05030.1 (Glycine max), 3'ss of exon 5
agtagatatgctgcattgatattggaatacggtgtga--tattctgattcgtaattgattagctgtaaaagaagt-aatttcgaatgttgtgtttc-tttgcagCGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAACCTTGCGGACAAGTCATTGTGGCGTGCTGGAGTTTGTGGCAGAGGAAGG
  ||| | ||      |   | ||   |    | |    || | | ||||    |  ||     |    ||   | || ||| ||  |   ||||  |||||||| |||||||  |||||||||||||||||||||||| |||  ||   | |  ||  ||||     ||||||||| || ||||||||  | || ||||||||
gttagttttgtcatggttgaactgtttttttattttgcttacttttattccaggtgaatatatagcttgagttttcaaattctaacatcaagtttaatttgcagCATCTCTGCATATTGATTACCCAATGTTGTTTGAACTCCGTAATGATGCTGCCGAGCGGGTTTCTCATTGTGGGGTTCTGGAGTTCATTGCTGAGGAAGG

upper sequence: PP1S245_32V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA05G34630.2 (Glycine max), 3'ss of exon 5
agtagatatgctgcattgatattggaatacggtgtgat-attctgattcgtaattgat-tagctgtaaaagaagtaatttcgaatgttgtgtttctttgcagCGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAACCTTGCGGACAAGTCATTGTGGCGTGCTGGAGTTTGTGGCAGAGGAAGG
  ||| | ||      |   | ||   |    | || | | | | ||||       || ||  | |  |      || ||| ||  |    ||  |||||||| |||||||  |||||||||||||||||||||||| |||  ||   | |  ||  ||||     ||||||||| || ||||||||  | || ||||||||
gttagttttgtcatggttgaactgttttttattttgcttacttttattccaggcgaatatatatcttgagttttcaaattctaacatcagtttaatttgcagCATCTCTGCATATTGATTACCCAATGTTGTTTGAACTCCGTAATGATGCTGCCGAGCGGGTTTCTCATTGTGGGGTTCTGGAGTTCATTGCTGAGGAAGG
















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:     TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAG                         CGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
genomic: TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAGgtattgttca ... ttctttgcagCGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
EST: gi|100406597|gb|BY955683.1|BY955683
EST:     TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAG                         CGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
genomic: TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAGgtattgttca ... ttctttgcagCGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
EST: gi|100418696|gb|BY975696.1|BY975696
EST:     TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAG                         CGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
genomic: TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAGgtattgttca ... ttctttgcagCGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
EST: gi|208387770|gb|DC941339.1|DC941339
EST:     TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAG                         CGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
genomic: TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAGgtattgttca ... ttctttgcagCGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
EST: gi|100415871|gb|BY956965.1|BY956965
EST:     TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAG                         CGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
genomic: TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAGgtattgttca ... ttctttgcagCGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
EST: gi|67508675|gb|BJ941536.1|BJ941536
EST:     TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAG                         CGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
genomic: TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAGgtattgttca ... ttctttgcagCGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
EST: gi|100448950|gb|CJ973249.1|CJ973249
EST:     TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAG                         CGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
genomic: TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAGgtattgttca ... ttctttgcagCGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
EST: gi|208349271|gb|DC906385.1|DC906385
EST:     TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAN                         CGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
genomic: TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAGgtattgttca ... ttctttgcagCGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
EST: gi|208346232|gb|DC905221.1|DC905221
EST:     TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAG                         CGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
genomic: TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAGgtattgttca ... ttctttgcagCGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
EST: gi|208352262|gb|DC906337.1|DC906337
EST:     TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAG                         CGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
genomic: TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAGgtattgttca ... ttctttgcagCGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
EST: gi|208366055|gb|DC935844.1|DC935844
EST:     TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAG                         CGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
genomic: TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAGgtattgttca ... ttctttgcagCGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
EST: gi|208372135|gb|DC940317.1|DC940317
EST:     TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAG                         CGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
genomic: TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAGgtattgttca ... ttctttgcagCGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
EST: gi|18358101|gb|BJ190160.1|BJ190160
EST:     TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAG                         CGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
genomic: TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAGgtattgttca ... ttctttgcagCGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
EST: gi|208390049|gb|DC938104.1|DC938104
EST:     TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAG                         CGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
genomic: TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAGgtattgttca ... ttctttgcagCGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
EST: gi|100419714|gb|BY957686.1|BY957686
EST:     TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAG                         CGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
genomic: TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAGgtattgttca ... ttctttgcagCGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
EST: gi|208358250|gb|DC930691.1|DC930691
EST:     TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAG                         CGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
genomic: TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAGgtattgttca ... ttctttgcagCGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
EST: gi|208357678|gb|DC934130.1|DC934130
EST:     TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAG                         CGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
genomic: TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAGgtattgttca ... ttctttgcagCGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
EST: gi|100442532|gb|BY963226.1|BY963226
EST:     TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAG                         CGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
genomic: TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAGgtattgttca ... ttctttgcagCGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
EST: gi|100366066|gb|BY967268.1|BY967268
EST:     TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAG                         CGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
genomic: TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAGgtattgttca ... ttctttgcagCGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
EST: gi|208366022|gb|DC935839.1|DC935839
EST:     TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAG                         CGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
genomic: TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAGgtattgttca ... ttctttgcagCGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
EST: gi|100386786|gb|BY970327.1|BY970327
EST:     TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAG                         CGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
genomic: TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAGgtattgttca ... ttctttgcagCGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
EST: gi|208374981|gb|DC956391.1|DC956391
EST:     TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAG                         CGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
genomic: TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAGgtattgttca ... ttctttgcagCGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
EST: gi|208356440|gb|DC934430.1|DC934430
EST:     TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAG                         CGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
genomic: TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAGgtattgttca ... ttctttgcagCGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
EST: gi|208386327|gb|DC932823.1|DC932823
EST:     TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAG                         CGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA
genomic: TGGTTATGCCTCCTTCGGCGCTTGATCGCTTAGgtattgttca ... ttctttgcagCGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgtaattgattagctgtaaaagaagtaatttcgaatgttgtgtttctttgcagCGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAACCTTGCGGACAAGTCATTGTGGCGTGCTGGAGTTTGTGGCAGAGGAAGG
     aattgat  putative branch site (score: 4)
                                          tgtttcttt  putative PPT
                  taaaagaagtaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtagatatgctgcattgatattggaatacggtgtgatattctgattcgtaattgattagctgtaaaagaagtaatttcgaatgttgtgtttctttgcagCGTCTCTGCGCATTGATTACCCAATGTTGTTTGAAGTCCACAACCCTTCAACCTTGCGGACAAGTCATTGTGGCGTGCTGGAGTTTGTGGCAGAGGAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - tgctgca