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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatacctgtcagatccctcttaggcccgttttagagaccatctggtaggatgatgatctcgtgcggttgtgggctctcaaatctaattgttttatttttttgtcgcacgcagCTTGTGACGTGCCAGGAATTCATAGACTATTGCCACAGCCTTGGCGTGAGTGGGAGTTTTTCGAAAACATCTACAAGCTTTCAGGAGTTCCCGTGGTGAC

Basic information

species Physcomitrella patens
transcript PP1S277_10V6.2
intron # 6
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|162192890|gb|FC369884.1|FC369884
EST:     GACAAAGGCAACTGAGAAGCAGATCGTCAAGGCAGATGCATACGTAGCAG                         CTTGTGACGTGCCAGGAATTCATAGACTATTGCCACAGCCTTGGCGTGAGT
genomic: GACAAAGGCAACTGAGAAGCAGATCGTCAAGGCAGATGCATACGTGGCAGgtgaatacct ... tcgcacgcagCTTGTGACGTGCCAGGAATTCATAGACTATTGCCACAGCCTTGGCGTGAGT
EST: gi|162155413|gb|FC332027.1|FC332027
EST:     GACAAAGGCAACTGAGAAGCAGATCGTCAAGGCAGATGCATACGTAGCAG                         CTTGTGACGTGCCAGGAATTCATAGACTATTGCCACAGCCTTGGCGTGAGT
genomic: GACAAAGGCAACTGAGAAGCAGATCGTCAAGGCAGATGCATACGTGGCAGgtgaatacct ... tcgcacgcagCTTGTGACGTGCCAGGAATTCATAGACTATTGCCACAGCCTTGGCGTGAGT
EST: gi|162150291|gb|FC326376.1|FC326376
EST:     GACAAAGGCAACTGAGAAGCAGATCGTCAAGGCAGATGCATACGTAGCAG                         CTTGTGACGTGCCAGGAATTCATAGACTATTGCCACAGCCTTGGCGTGAGT
genomic: GACAAAGGCAACTGAGAAGCAGATCGTCAAGGCAGATGCATACGTGGCAGgtgaatacct ... tcgcacgcagCTTGTGACGTGCCAGGAATTCATAGACTATTGCCACAGCCTTGGCGTGAGT
EST: gi|162174878|gb|FC351670.1|FC351670
EST:     AGATCGTCAAGGCAGATGCATACGTAGCAG                         CTTGTGACGTGCCAGGAATTCATAGACTATTGCCACAGCCTTGGCGTGAGT
genomic: AGATCGTCAAGGCAGATGCATACGTGGCAGgtgaatacct ... tcgcacgcagCTTGTGACGTGCCAGGAATTCATAGACTATTGCCACAGCCTTGGCGTGAGT
EST: gi|162151154|gb|FC327153.1|FC327153
EST:     GACAAAGGCAACTGAGAAGCAGATCGTCAAGGCAGATGCATACGTAGCAG                         CTTGTGACGTGCCAGGAATTCATAGACTATTGCCACAGCCTTGGCGTGAGT
genomic: GACAAAGGCAACTGAGAAGCAGATCGTCAAGGCAGATGCATACGTGGCAGgtgaatacct ... tcgcacgcagCTTGTGACGTGCCAGGAATTCATAGACTATTGCCACAGCCTTGGCGTGAGT
EST: gi|162198693|gb|FC373474.1|FC373474
EST:     GACAAAGGCAACTGAGAAGCAGATCGTCAAGGCAGATGCATACGTAGCAG                         CTTGTGACGTGCCAGGAATTCATAGACTATTGC
genomic: GACAAAGGCAACTGAGAAGCAGATCGTCAAGGCAGATGCATACGTGGCAGgtgaatacct ... tcgcacgcagCTTGTGACGTGCCAGGAATTCATAGACTATTGC
EST: gi|162267925|gb|FC444006.1|FC444006
EST:     CAAGGCAGATGCATACGTGGCAG                         CTTGTGACGTGCCAGGAATTCATAGACTATTGCCACAGCCTTGGCGTGAGT
genomic: CAAGGCAGATGCATACGTGGCAGgtgaatacct ... tcgcacgcagCTTGTGACGTGCCAGGAATTCATAGACTATTGCCACAGCCTTGGCGTGAGT
EST: gi|162225911|gb|FC400955.1|FC400955
EST:     GACAAAGGCAACTGAGAAGCAGATCGTCAAGGCAGATGCATACGTAGCAG                         CTTGTGACGTGCCAGGAATTCATAGACTATTGCCACAGCCTTGGCGTGAGT
genomic: GACAAAGGCAACTGAGAAGCAGATCGTCAAGGCAGATGCATACGTGGCAGgtgaatacct ... tcgcacgcagCTTGTGACGTGCCAGGAATTCATAGACTATTGCCACAGCCTTGGCGTGAGT
EST: gi|162215092|gb|FC391562.1|FC391562
EST:     TGCATACGTAGCAG                         CTTGTGACGTGCCAGGAATTCATAGACTATTGCCACAGCCTTGGCGTGAGT
genomic: TGCATACGTGGCAGgtgaatacct ... tcgcacgcagCTTGTGACGTGCCAGGAATTCATAGACTATTGCCACAGCCTTGGCGTGAGT
EST: gi|162151767|gb|FC328624.1|FC328624
EST:     GACAAAGGCAACTGAGAAGCAGATCGTCAAGGCAGATGCATACGTAGCAG                         CTTGTGACGTGCCAGGAATTCATAGACTATTGCCACAGCCTTGGCGTGAGT
genomic: GACAAAGGCAACTGAGAAGCAGATCGTCAAGGCAGATGCATACGTGGCAGgtgaatacct ... tcgcacgcagCTTGTGACGTGCCAGGAATTCATAGACTATTGCCACAGCCTTGGCGTGAGT
EST: gi|162241669|gb|FC418652.1|FC418652
EST:     CAACTGAGAAGCAGATCGTCAAGGCAGATGCATACGTAGCAG                         CTTGTGACGTGCCAGGAATTCATAGACTATTGCCACAGCCTTGGCGTGAGT
genomic: CAACTGAGAAGCAGATCGTCAAGGCAGATGCATACGTGGCAGgtgaatacct ... tcgcacgcagCTTGTGACGTGCCAGGAATTCATAGACTATTGCCACAGCCTTGGCGTGAGT
EST: gi|100358217|gb|BY965531.1|BY965531
EST:     GACAAAGGCAACTGAGAAGCAGATCGTCAAGGCAGATGCATACGTGGCAG                         CTTGTGACGTGCCAGGAATTCATAGACTATTGCCACAGCCTTGGCGTGAGT
genomic: GACAAAGGCAACTGAGAAGCAGATCGTCAAGGCAGATGCATACGTGGCAGgtgaatacct ... tcgcacgcagCTTGTGACGTGCCAGGAATTCATAGACTATTGCCACAGCCTTGGCGTGAGT
EST: gi|162230035|gb|FC405975.1|FC405975
EST:     GACAAAGGCAACTGAGAAGCAGATCGTCAAGGCAGATGCATACGTAGCAG                         CTTGTGACGTGCCAGGAATTCATAGACTATTGCCACAGCCTTGGCGTGAGT
genomic: GACAAAGGCAACTGAGAAGCAGATCGTCAAGGCAGATGCATACGTGGCAGgtgaatacct ... tcgcacgcagCTTGTGACGTGCCAGGAATTCATAGACTATTGCCACAGCCTTGGCGTGAGT
EST: gi|19789027|gb|BQ041054.1|BQ041054
EST:     GACAAAGGCAACTGAGAAGCAGATCGTCAAGGCAGATGCATACGTGGCAG                         CTTGTGACGTGCCAAGAATTCATAAACTATTGCCACAGACTTGGCGTGAGT
genomic: GACAAAGGCAACTGAGAAGCAGATCGTCAAGGCAGATGCATACGTGGCAGgtgaatacct ... tcgcacgcagCTTGTGACGTGCCAGGAATTCATAGACTATTGCCACAGCCTTGGCGTGAGT
EST: gi|162168664|gb|FC343926.1|FC343926
EST:     GACAAAGGCAACTGAGAAGCAGATCGTCNAGGCAGATGCATACGTAGCAG                         CTTGTGACGTGCCAGGAATTCATAGACT
genomic: GACAAAGGCAACTGAGAAGCAGATCGTCAAGGCAGATGCATACGTGGCAGgtgaatacct ... tcgcacgcagCTTGTGACGTGCCAGGAATTCATAGACT
EST: gi|162188826|gb|FC364840.1|FC364840
EST:     GACAAAGGCAACTGAGAAGCAGATCGTCAAGGCAGATGCATACGTAGCAG                         CTTGTGACGTGCCAGGAATTCATAGACTATTGCCACAGCCTTGGCGTGAGT
genomic: GACAAAGGCAACTGAGAAGCAGATCGTCAAGGCAGATGCATACGTGGCAGgtgaatacct ... tcgcacgcagCTTGTGACGTGCCAGGAATTCATAGACTATTGCCACAGCCTTGGCGTGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcgtgcggttgtgggctctcaaatctaattgttttatttttttgtcgcacgcagCTTGTGACGTGCCAGGAATTCATAGACTATTGCCACAGCCTTGGCGTGAGTGGGAGTTTTTCGAAAACATCTACAAGCTTTCAGGAGTTCCCGTGGTGAC
                       atctaat  putative branch site (score: 3)
                                ttttatttttttgtc  putative PPT
                 tctcaaatctaattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaatacctgtcagatccctcttaggcccgttttagagaccatctggtaggatgatgatctcgtgcggttgtgggctctcaaatctaattgttttatttttttgtcgcacgcagCTTGTGACGTGCCAGGAATTCATAGACTATTGCCACAGCCTTGGCGTGAGTGGGAGTTTTTCGAAAACATCTACAAGCTTTCAGGAGTTCCCGTGGTGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT