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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cggttagtgaacagacagggagtttacagtattcttattttgacttttctcaggttgattggtgacacttttttatgttcacatgtttcttgtggtttagGTACTTGAAACCAGATAGGATAGATCCTGCAAAGGATCCTGAAGATGTGATTAAGCAATTTCTTAATAAG

Basic information

species Physcomitrella patens
transcript PP1S192_39V6.4
intron # 3
splice site 3'
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|18368101|gb|BJ200186.1|BJ200186
EST:     TATGCGAGGTCGAAAATGACTGATGAGGAGCTCCGTGAGAAGCTCCGTGG                         GTACTTGAAACCA
genomic: TATGCGAGGTCGAAAATGACTGATGAGGAGCTCCGTGAGAAGCTCCGTGGgtaagttgtt ... tgtggtttagGTACTTGAAACCA
EST: gi|100373143|gb|BY949230.1|BY949230
EST:     TATGCGAGGTCGANNATGACTGATGAGGAGCTCCGTGAGAAGCTCCGTGG                         GTACTTGAAACCAGATAGGATAGATCCTGCAAAGGATCCTGAAGATGTGAT
genomic: TATGCGAGGTCGAAAATGACTGATGAGGAGCTCCGTGAGAAGCTCCGTGGgtaagttgtt ... tgtggtttagGTACTTGAAACCAGATAGGATAGATCCTGCAAAGGATCCTGAAGATGTGAT
EST: gi|100448078|gb|CJ972377.1|CJ972377
EST:     TATGCGAGGTCGAAAATGACTGATGAGGAGCTCCGTGAGAAGCTCCGTGG                         GTACTTGAAACCAGATAGGATAGATCCTGCAAAGGATCCTGAAGATGTGAT
genomic: TATGCGAGGTCGAAAATGACTGATGAGGAGCTCCGTGAGAAGCTCCGTGGgtaagttgtt ... tgtggtttagGTACTTGAAACCAGATAGGATAGATCCTGCAAAGGATCCTGAAGATGTGAT
EST: gi|208346321|gb|DC905268.1|DC905268
EST:     TATGCGAGGTCGAAAATGACTGATGAGGAGCTCCGTGAGAAGCTCCGTGG                         GTACTTGAAACCAGATAGGATAGATCCTGCAAAGGATCCTGAAGATGTGAT
genomic: TATGCGAGGTCGAAAATGACTGATGAGGAGCTCCGTGAGAAGCTCCGTGGgtaagttgtt ... tgtggtttagGTACTTGAAACCAGATAGGATAGATCCTGCAAAGGATCCTGAAGATGTGAT
EST: gi|18342270|gb|BJ174305.1|BJ174305
EST:     TATGCGAGGTCGAAAATGACTGATGAGGAGCTCCGTGAGAAGCTCCGTGG                         GTACTTGAAACCAGA
genomic: TATGCGAGGTCGAAAATGACTGATGAGGAGCTCCGTGAGAAGCTCCGTGGgtaagttgtt ... tgtggtttagGTACTTGAAACCAGA
EST: gi|18373140|gb|BJ204742.1|BJ204742
EST:     TATGCGAGGTCGAAAATGACTGATGAGGAGCTCCGTGAGAAGCTCCGTGG                         GTACTTGAAACCAGATAGGATAGATCCTGCAAAGGATCCTGAAGATGTGAT
genomic: TATGCGAGGTCGAAAATGACTGATGAGGAGCTCCGTGAGAAGCTCCGTGGgtaagttgtt ... tgtggtttagGTACTTGAAACCAGATAGGATAGATCCTGCAAAGGATCCTGAAGATGTGAT
EST: gi|162279046|gb|FC455073.1|FC455073
EST:     TATGCGAGGTCGAAAATGACTGATGAGGAGCTCCGTGAGAAGCTCCGTGG                         GTACTTGAAACCAGATAGGATAGATCCTGCAAAGGATCCTGAAGATGTGAT
genomic: TATGCGAGGTCGAAAATGACTGATGAGGAGCTCCGTGAGAAGCTCCGTGGgtaagttgtt ... tgtggtttagGTACTTGAAACCAGATAGGATAGATCCTGCAAAGGATCCTGAAGATGTGAT
EST: gi|18369451|gb|BJ201538.1|BJ201538
EST:     TATGCGAGGTCGAAAATGACTGATGAGGAGCTCCGTGAGAAGCTCCGTGG                         GTACTTGAAACCA
genomic: TATGCGAGGTCGAAAATGACTGATGAGGAGCTCCGTGAGAAGCTCCGTGGgtaagttgtt ... tgtggtttagGTACTTGAAACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctcaggttgattggtgacacttttttatgttcacatgtttcttgtggtttagGTACTTGAAACCAGATAGGATAGATCCTGCAAAGGATCCTGAAGATGTGATTAAGCAATTTCTTAATAAG
       ggttgat  putative branch site (score: 5)
                                      tgtttctt  putative PPT
                       ttttttatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cggttagtgaacagacagggagtttacagtattcttattttgacttttctcaggttgattggtgacacttttttatgttcacatgtttcttgtggtttagGTACTTGAAACCAGATAGGATAGATCCTGCAAAGGATCCTGAAGATGTGATTAAGCAATTTCTTAATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA