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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatttacttggatattgttcgatattgtgtaaacatgaacctacggtggtttttgctgaagttgggcctaatatgctattcatttcacactgtctccagGTAACGAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTAGCTGCTGTCTCAGCCTCTACATACTCCTACGTCTCACTTTTGAAGTACTTTGCTCCGA

Basic information

species Physcomitrella patens
transcript PP1S29_256V6.2
intron # 7
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|67718262|gb|BJ968521.1|BJ968521
EST:     ACTTCGGCTCCATCGACATCCTGGTGCATTCACTTGCTAATGGGCCTGAA                         GTAACGAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTAGCTGCTGTC
genomic: ACTTCGGCTCCATCGACATCCTGGTGCATTCACTTGCTAATGGGCCTGAAgtaagaactt ... ctgtctccagGTAACGAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTAGCTGCTGTC
EST: gi|18327390|gb|BJ159392.1|BJ159392
EST:     ACTTCGGCTCCATCGACATCCTGGTGCATTCACTTGCTAATGGGCCTGAA                         GTAACGAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTAGCTGCTGTC
genomic: ACTTCGGCTCCATCGACATCCTGGTGCATTCACTTGCTAATGGGCCTGAAgtaagaactt ... ctgtctccagGTAACGAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTAGCTGCTGTC
EST: gi|162182768|gb|FC359515.1|FC359515
EST:     ACTTCGGCTCCATCGACATCCTGGTGCATTCACTTGCTAATGGGCCTGAA                         GTAACGAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTAGCTGCTGTC
genomic: ACTTCGGCTCCATCGACATCCTGGTGCATTCACTTGCTAATGGGCCTGAAgtaagaactt ... ctgtctccagGTAACGAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTAGCTGCTGTC
EST: gi|19777824|gb|BQ039232.1|BQ039232
EST:     ACTTCGGCTCCATCGACATCCTGGTGCATTCACTTGCTAATGGGCCTGAA                         GTAACGAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTAGCTGCTGTC
genomic: ACTTCGGCTCCATCGACATCCTGGTGCATTCACTTGCTAATGGGCCTGAAgtaagaactt ... ctgtctccagGTAACGAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTAGCTGCTGTC
EST: gi|67726751|gb|BJ977010.1|BJ977010
EST:     TGGTGCATTCACTTGCTAATGGGCCTGAA                         GTAACGAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTAGCTGCTGTC
genomic: TGGTGCATTCACTTGCTAATGGGCCTGAAgtaagaactt ... ctgtctccagGTAACGAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTAGCTGCTGTC
EST: gi|162169758|gb|FC345295.1|FC345295
EST:     ACTTCGGCTCCATCGACATCCTGGTGCATTCACTTGCTAATGGGCCTGAA                         GTAACGAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTAGCTGCTGTC
genomic: ACTTCGGCTCCATCGACATCCTGGTGCATTCACTTGCTAATGGGCCTGAAgtaagaactt ... ctgtctccagGTAACGAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTAGCTGCTGTC
EST: gi|162176349|gb|FC353534.1|FC353534
EST:     ACTTCGGCTCCATCGACATCCTGGTGCATTCACTTGCTAATGGGCCTGAA                         GTAACGAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTAGCTGCTGTC
genomic: ACTTCGGCTCCATCGACATCCTGGTGCATTCACTTGCTAATGGGCCTGAAgtaagaactt ... ctgtctccagGTAACGAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTAGCTGCTGTC
EST: gi|100384688|gb|BY950678.1|BY950678
EST:     TTTCG-CTCCATCGACATCCTGGTGCATTCACTTGCTATTGGGGCCTGAA                         GTAACGAAGCCACTTATGAAGACCTCGCGCAAAGGTTACTTA
genomic: TT-CGGCTCCATCGACATCCTGGTGCATTCACTTGCTAATGGG-CCTGAAgtaagaactt ... ctgtctccagGTAACGAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTA
EST: gi|100403476|gb|BY991219.1|BY991219
EST:     ACTTCGGCTCCATCGACATCCTGGTGCATTCACTTGCTAATGGGCCTGAA                         GTAACGAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTAGCTGCTGTC
genomic: ACTTCGGCTCCATCGACATCCTGGTGCATTCACTTGCTAATGGGCCTGAAgtaagaactt ... ctgtctccagGTAACGAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTAGCTGCTGTC
EST: gi|67727852|gb|BJ978111.1|BJ978111
EST:     GGTGCATTCACTTGCTAATGGGGCCTGAA                         GTAACGAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTAGCTGCTGT
genomic: GGTGCATTCACTTGCTAAT-GGGCCTGAAgtaagaactt ... ctgtctccagGTAACGAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTAGCTGCTGT
EST: gi|19789330|gb|BQ041244.1|BQ041244
EST:     ACTTCGGCTCCATCGACATCCTGGTGCATTCACTTGCTAATGGGCCTGAA                         GTAACGAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTAGCTGCTGTC
genomic: ACTTCGGCTCCATCGACATCCTGGTGCATTCACTTGCTAATGGGCCTGAAgtaagaactt ... ctgtctccagGTAACGAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTAGCTGCTGTC
EST: gi|162176594|gb|FC353063.1|FC353063
EST:     ACTTCGGCTCCATCGACATCCTGGTGCATTCACTTGCTAATGGGCCTGAA                         GTAACGAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTAGCTGCTGTC
genomic: ACTTCGGCTCCATCGACATCCTGGTGCATTCACTTGCTAATGGGCCTGAAgtaagaactt ... ctgtctccagGTAACGAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTAGCTGCTGTC
EST: gi|162171618|gb|FC347559.1|FC347559
EST:     ACTTCGGCTCCATCGACATCCTGGTGCATTCACTTGCTAATGGGCCTGAA                         GTAACCAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTAGCTGCTGTC
genomic: ACTTCGGCTCCATCGACATCCTGGTGCATTCACTTGCTAATGGGCCTGAAgtaagaactt ... ctgtctccagGTAACGAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTAGCTGCTGTC
EST: gi|67718833|gb|BJ969092.1|BJ969092
EST:     ACTTCGGCTCCATCGACATCCTGGTGCATTCACTTGCTAATGGGCCTGAA                         GTAACGAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTANCTGCTGTC
genomic: ACTTCGGCTCCATCGACATCCTGGTGCATTCACTTGCTAATGGGCCTGAAgtaagaactt ... ctgtctccagGTAACGAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTAGCTGCTGTC
EST: gi|162241271|gb|FC416902.1|FC416902
EST:     ACTTCGGCTCCATCGACATCCTGGTGCATTCACTTGCTAATGGGCCTGAA                         GTAACGAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTAGCTGCTGTC
genomic: ACTTCGGCTCCATCGACATCCTGGTGCATTCACTTGCTAATGGGCCTGAAgtaagaactt ... ctgtctccagGTAACGAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTAGCTGCTGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtggtttttgctgaagttgggcctaatatgctattcatttcacactgtctccagGTAACGAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTAGCTGCTGTCTCAGCCTCTACATACTCCTACGTCTCACTTTTGAAGTACTTTGCTCCGA
                     gcctaat  putative branch site (score: 3)
                                             ctgtctcc  putative PPT
                                tattcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatttacttggatattgttcgatattgtgtaaacatgaacctacggtggtttttgctgaagttgggcctaatatgctattcatttcacactgtctccagGTAACGAAGCCACTTATGGAGACCTCGCGCAAAGGTTACTTAGCTGCTGTCTCAGCCTCTACATACTCCTACGTCTCACTTTTGAAGTACTTTGCTCCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG