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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctctgcgtatttgggtttatttgtttatttattggtttttctttttagaataatataattcatttatttaatagtcgaagtttttcttaaatggctgcagCTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGTGAGAAGGAAATGCTCGCAGCAAAAGAGGCACTCAAGAATAGTGGTGTTG

Basic information

species Physcomitrella patens
transcript PP1S62_94V6.3
intron # 12
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|162156039|gb|FC332206.1|FC332206
EST:     ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAA                         CTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
genomic: ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAAgtaagtttca ... atggctgcagCTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
EST: gi|162163259|gb|FC339377.1|FC339377
EST:     ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAA                         CTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
genomic: ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAAgtaagtttca ... atggctgcagCTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
EST: gi|162155805|gb|FC331834.1|FC331834
EST:     ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAA                         CTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
genomic: ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAAgtaagtttca ... atggctgcagCTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
EST: gi|162268967|gb|FC445459.1|FC445459
EST:     CGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAA                         CTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
genomic: CGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAAgtaagtttca ... atggctgcagCTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
EST: gi|18339879|gb|BJ171906.1|BJ171906
EST:     ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGAGCATCACAGTGAAA                         CTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
genomic: ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAAgtaagtttca ... atggctgcagCTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
EST: gi|208388391|gb|DC949335.1|DC949335
EST:     ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAA                         CTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
genomic: ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAAgtaagtttca ... atggctgcagCTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
EST: gi|162156038|gb|FC332205.1|FC332205
EST:     ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAA                         CTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGC
genomic: ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAAgtaagtttca ... atggctgcagCTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
EST: gi|208362798|gb|DC950598.1|DC950598
EST:     ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAA                         CTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
genomic: ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAAgtaagtttca ... atggctgcagCTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
EST: gi|162172367|gb|FC348308.1|FC348308
EST:     ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAA                         CTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
genomic: ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAAgtaagtttca ... atggctgcagCTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
EST: gi|18336517|gb|BJ168539.1|BJ168539
EST:     ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAA                         CTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
genomic: ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAAgtaagtttca ... atggctgcagCTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
EST: gi|37847380|gb|BJ605388.1|BJ605388
EST:     ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAA                         CTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
genomic: ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAAgtaagtttca ... atggctgcagCTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
EST: gi|162150865|gb|FC327345.1|FC327345
EST:     ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAA                         CTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
genomic: ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAAgtaagtttca ... atggctgcagCTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
EST: gi|67727761|gb|BJ978020.1|BJ978020
EST:     ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAA                         CTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
genomic: ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAAgtaagtttca ... atggctgcagCTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
EST: gi|18334660|gb|BJ166677.1|BJ166677
EST:     ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGAGCATCACAGTGAAA                         CTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
genomic: ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAAgtaagtttca ... atggctgcagCTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
EST: gi|162274343|gb|FC450311.1|FC450311
EST:     ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAA                         CTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
genomic: ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAAgtaagtttca ... atggctgcagCTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
EST: gi|162174294|gb|FC350677.1|FC350677
EST:     GCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAA                         CTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
genomic: GCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAAgtaagtttca ... atggctgcagCTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
EST: gi|162251335|gb|FC427977.1|FC427977
EST:     ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAA                         CTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
genomic: ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAAgtaagtttca ... atggctgcagCTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
EST: gi|18335850|gb|BJ167871.1|BJ167871
EST:     ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAA                         CTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
genomic: ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAAgtaagtttca ... atggctgcagCTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
EST: gi|162153177|gb|FC329583.1|FC329583
EST:     ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAA                         CTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT
genomic: ACACTGCGAGAGTTAAGGACAAAGGTGATCGCGGGACCATCACAGTGAAAgtaagtttca ... atggctgcagCTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagaataatataattcatttatttaatagtcgaagtttttcttaaatggctgcagCTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGTGAGAAGGAAATGCTCGCAGCAAAAGAGGCACTCAAGAATAGTGGTGTTG
                    atttaat  putative branch site (score: 4)
     taatataattcattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctctgcgtatttgggtttatttgtttatttattggtttttctttttagaataatataattcatttatttaatagtcgaagtttttcttaaatggctgcagCTGAAATTCCACCCGTATACCGAGGAGGAGCAGGAGATCGCTATTTTGCGTGAGAAGGAAATGCTCGCAGCAAAAGAGGCACTCAAGAATAGTGGTGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG