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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcttttcgtacttgtgaaccttgtgacgttggtattgattgctcgggtttatccttgactgaattcattttgaatttattttatacgttggtcttgcagCTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATTTTGGAGGAAACCATCCGCGGTGGGTTCCCACTCTTGATCATAGCTGAGG

Basic information

species Physcomitrella patens
transcript PP1S15_485V6.2
intron # 5
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|162166112|gb|FC343381.1|FC343381
EST:     ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGG                         CTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
genomic: ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGGgtacgcacta ... ggtcttgcagCTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
EST: gi|162182315|gb|FC357186.1|FC357186
EST:     ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGG                         CTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
genomic: ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGGgtacgcacta ... ggtcttgcagCTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
EST: gi|162250146|gb|FC427871.1|FC427871
EST:     ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGG                         CTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
genomic: ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGGgtacgcacta ... ggtcttgcagCTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
EST: gi|162153515|gb|FC329609.1|FC329609
EST:     ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGG                         CTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
genomic: ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGGgtacgcacta ... ggtcttgcagCTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
EST: gi|162150983|gb|FC327879.1|FC327879
EST:     ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGG                         CTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
genomic: ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGGgtacgcacta ... ggtcttgcagCTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
EST: gi|162173179|gb|FC348726.1|FC348726
EST:     ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGG                         CTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
genomic: ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGGgtacgcacta ... ggtcttgcagCTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
EST: gi|162183969|gb|FC359339.1|FC359339
EST:     ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGG                         CTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
genomic: ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGGgtacgcacta ... ggtcttgcagCTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
EST: gi|162155281|gb|FC331218.1|FC331218
EST:     ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGG                         CTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
genomic: ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGGgtacgcacta ... ggtcttgcagCTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
EST: gi|162166168|gb|FC343411.1|FC343411
EST:     ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGG                         CTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
genomic: ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGGgtacgcacta ... ggtcttgcagCTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
EST: gi|162161164|gb|FC336512.1|FC336512
EST:     ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGG                         CTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
genomic: ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGGgtacgcacta ... ggtcttgcagCTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
EST: gi|162184449|gb|FC359195.1|FC359195
EST:     ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGG                         CTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
genomic: ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGGgtacgcacta ... ggtcttgcagCTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
EST: gi|162186556|gb|FC363320.1|FC363320
EST:     CTGTGGAGTACGACAACTGCAGG                         CTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
genomic: CTGTGGAGTACGACAACTGCAGGgtacgcacta ... ggtcttgcagCTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
EST: gi|162175371|gb|FC352297.1|FC352297
EST:     ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGG                         CTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
genomic: ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGGgtacgcacta ... ggtcttgcagCTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
EST: gi|162161063|gb|FC337048.1|FC337048
EST:     ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGG                         CTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
genomic: ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGGgtacgcacta ... ggtcttgcagCTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
EST: gi|162171512|gb|FC347814.1|FC347814
EST:     ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGG                         CTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
genomic: ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGGgtacgcacta ... ggtcttgcagCTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
EST: gi|162157139|gb|FC333709.1|FC333709
EST:     ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGG                         CTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
genomic: ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGGgtacgcacta ... ggtcttgcagCTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
EST: gi|162180842|gb|FC358343.1|FC358343
EST:     ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGG                         CTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
genomic: ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGGgtacgcacta ... ggtcttgcagCTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
EST: gi|162156893|gb|FC333047.1|FC333047
EST:     ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGG                         CTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
genomic: ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGGgtacgcacta ... ggtcttgcagCTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
EST: gi|162173824|gb|FC349416.1|FC349416
EST:     ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGG                         CTCCTCTTGGTCGAC
genomic: ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGGgtacgcacta ... ggtcttgcagCTCCTCTTGGTCGAC
EST: gi|162179104|gb|FC356505.1|FC356505
EST:     GATGTCTGTGGAGTACGACAACTGCAGG                         CTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
genomic: GATGTCTGTGGAGTACGACAACTGCAGGgtacgcacta ... ggtcttgcagCTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
EST: gi|162154100|gb|FC330543.1|FC330543
EST:     ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGG                         CTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
genomic: ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGGgtacgcacta ... ggtcttgcagCTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
EST: gi|162150359|gb|FC326631.1|FC326631
EST:     ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGG                         CTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
genomic: ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGGgtacgcacta ... ggtcttgcagCTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
EST: gi|162154271|gb|FC330402.1|FC330402
EST:     ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGG                         CTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
genomic: ACTTCGTGACAGACCCCGAGAAGATGTCTGTGGAGTACGACAACTGCAGGgtacgcacta ... ggtcttgcagCTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
EST: gi|162177440|gb|FC352973.1|FC352973
EST:     CTGTGGAGTACGACAACTGCAGG                         CTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT
genomic: CTGTGGAGTACGACAACTGCAGGgtacgcacta ... ggtcttgcagCTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggtttatccttgactgaattcattttgaatttattttatacgttggtcttgcagCTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATTTTGGAGGAAACCATCCGCGGTGGGTTCCCACTCTTGATCATAGCTGAGG
        ccttgac  putative branch site (score: 4)
             actgaattcattttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcttttcgtacttgtgaaccttgtgacgttggtattgattgctcgggtttatccttgactgaattcattttgaatttattttatacgttggtcttgcagCTCCTCTTGGTCGACAAGAAGATCACCACTGCTCGTGATATGATTGGGATTTTGGAGGAAACCATCCGCGGTGGGTTCCCACTCTTGATCATAGCTGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA