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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaatgataaatgtgaccttttcacgaggacacatatcctgacatcttaggtagttacatttgcggcatttactgacactagtctttttatgtcacacagCATTGACTTTGGAGTTTTCTTTCACTGACGGGAAGAACTGGGATGGTCCTTACAAGTTGGTCATGGAAGTACCTCAGAAGTTGAAAGGCTTGCCTCAGAG

Basic information

species Physcomitrella patens
transcript PP1S99_42V6.2
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|100440899|gb|BY962387.1|BY962387
EST:     AAGTCTATGCGAGACCATATATGCCATCAAAATAAACGTGCCCTTACACG                         CATTGACTTTGGAGTTTTCTTTCACTGACGGGAAGAACTGGGATGGTCCTT
genomic: AAGTCTATGCGAGACCATATATGCCATCAAAATAAACGTGCCCTTACACGgtaagcccct ... tgtcacacagCATTGACTTTGGAGTTTTCTTTCACTGACGGGAAGAACTGGGATGGTCCTT
EST: gi|100379974|gb|BY968783.1|BY968783
EST:     AATCTATGCGAGACCATATATGCCATCAAAATAAACGTGCCCCTTACACG                         CATTGACTTTGGAGTTTTCTTTCACTGACCGGGA-GAACTGGGATGGCCCT
genomic: AGTCTATGCGAGACCATATATGCCATCAAAATAAACGTGCCC-TTACACGgtaagcccct ... tgtcacacagCATTGACTTTGGAGTTTTCTTTCACTGAC-GGGAAGAACTGGGATGGTCCT
EST: gi|162195534|gb|FC371835.1|FC371835
EST:     AAGTCTATGCGAGACCATATATGCCATCAAAATAAACGTGCCCTTACACG                         CATTGACTTTGGAGTTTTCTTTCACTGACGGGAAGAACTGGGATGGTCCTT
genomic: AAGTCTATGCGAGACCATATATGCCATCAAAATAAACGTGCCCTTACACGgtaagcccct ... tgtcacacagCATTGACTTTGGAGTTTTCTTTCACTGACGGGAAGAACTGGGATGGTCCTT
EST: gi|208386797|gb|DC937189.1|DC937189
EST:     AAGTCTATGCGAGACCATATATGCCATCAAAATAAACGTGCCCTTACACG                         CATTGACTTTGGAGTTTTCTTTCACTGACGGGAA
genomic: AAGTCTATGCGAGACCATATATGCCATCAAAATAAACGTGCCCTTACACGgtaagcccct ... tgtcacacagCATTGACTTTGGAGTTTTCTTTCACTGACGGGAA
EST: gi|162257183|gb|FC433059.1|FC433059
EST:     AAGTCTATGCGAGACCATATATGCCATCAAAATAAACGTGCCCTTACACG                         CATTGACTTTGGAGTTTTCTTTCACTGACGGGAAGAACTGGGATGGTCCTT
genomic: AAGTCTATGCGAGACCATATATGCCATCAAAATAAACGTGCCCTTACACGgtaagcccct ... tgtcacacagCATTGACTTTGGAGTTTTCTTTCACTGACGGGAAGAACTGGGATGGTCCTT
EST: gi|162226251|gb|FC402959.1|FC402959
EST:     AAGTCTATGCGAGACCATATATGCCATCAAAATAAACGTGCCCTTACACG                         CATTGACTTTGGAGTTTTCTTTCACTGACGGGAAGAACTGGGATGGTCCTT
genomic: AAGTCTATGCGAGACCATATATGCCATCAAAATAAACGTGCCCTTACACGgtaagcccct ... tgtcacacagCATTGACTTTGGAGTTTTCTTTCACTGACGGGAAGAACTGGGATGGTCCTT
EST: gi|162195533|gb|FC371834.1|FC371834
EST:     AGACCATATATGCCATCAAAATAAACGTGCCCTTACACG                         CATTGACTTTGGAGTTTTCTTTCACTGACGGGAAGAACTGGGATGGTCCTT
genomic: AGACCATATATGCCATCAAAATAAACGTGCCCTTACACGgtaagcccct ... tgtcacacagCATTGACTTTGGAGTTTTCTTTCACTGACGGGAAGAACTGGGATGGTCCTT
EST: gi|100427559|gb|BY977558.1|BY977558
EST:     AAGTCTATGCGAGACCATATATGCCATCAAAATAAACGTGCCCTTACACG                         CATTGACTTTGGAGTTTTCTTTCACTGACGGGAAGAACTGGGATGGTCCTT
genomic: AAGTCTATGCGAGACCATATATGCCATCAAAATAAACGTGCCCTTACACGgtaagcccct ... tgtcacacagCATTGACTTTGGAGTTTTCTTTCACTGACGGGAAGAACTGGGATGGTCCTT
EST: gi|100386075|gb|BY970014.1|BY970014
EST:     AAGTCTATGCGAGACCATATATGCCATCAAAATAAACGTGCCCTTACACG                         CATTGACTTTGGGAGTTT-CTTTCACTGACGGGA
genomic: AAGTCTATGCGAGACCATATATGCCATCAAAATAAACGTGCCCTTACACGgtaagcccct ... tgtcacacagCATTGACTTTGG-AGTTTTCTTTCACTGACGGGA
EST: gi|162159901|gb|FC336154.1|FC336154
EST:     AAGTCTATGCGAGACCATATATGCCATCAAAATAAACGTGCCCTTACACG                         CATTGACTTTGGAGTTTTCTTTCACTGACGGGAAGAACTGGGATGGTCCTT
genomic: AAGTCTATGCGAGACCATATATGCCATCAAAATAAACGTGCCCTTACACGgtaagcccct ... tgtcacacagCATTGACTTTGGAGTTTTCTTTCACTGACGGGAAGAACTGGGATGGTCCTT
EST: gi|162227790|gb|FC402705.1|FC402705
EST:     AAGTCTATGCGAGACCATATATGCCATCAAAATAAACGTGCCCTTACACG                         CATTGACTTTGGAGTTTTCTTTCACTGACGGGAAGAACTGGGATGGTCCTT
genomic: AAGTCTATGCGAGACCATATATGCCATCAAAATAAACGTGCCCTTACACGgtaagcccct ... tgtcacacagCATTGACTTTGGAGTTTTCTTTCACTGACGGGAAGAACTGGGATGGTCCTT
EST: gi|67508225|gb|BJ941096.1|BJ941096
EST:     AAGTCTATGCGAGACCATATATGCCATCAAAATAAACGTGCCCTTACACG                         CATTGACTTTGGAGTTTTCTTTCACTGACGGGAAGAACTGGGATGGTCCTT
genomic: AAGTCTATGCGAGACCATATATGCCATCAAAATAAACGTGCCCTTACACGgtaagcccct ... tgtcacacagCATTGACTTTGGAGTTTTCTTTCACTGACGGGAAGAACTGGGATGGTCCTT
EST: gi|100440507|gb|BY962234.1|BY962234
EST:     AAGTCTATGCGAGACCATATATGCCATCAAAATAAACGTGCCCTTACACG                         CATTGACTTTGGAGTTTTCTTTCACTGACGG
genomic: AAGTCTATGCGAGACCATATATGCCATCAAAATAAACGTGCCCTTACACGgtaagcccct ... tgtcacacagCATTGACTTTGGAGTTTTCTTTCACTGACGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaggtagttacatttgcggcatttactgacactagtctttttatgtcacacagCATTGACTTTGGAGTTTTCTTTCACTGACGGGAAGAACTGGGATGGTCCTTACAAGTTGGTCATGGAAGTACCTCAGAAGTTGAAAGGCTTGCCTCAGAG
                         tactgac  putative branch site (score: 1)
                                     tctttttat  putative PPT
                                     tctttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaatgataaatgtgaccttttcacgaggacacatatcctgacatcttaggtagttacatttgcggcatttactgacactagtctttttatgtcacacagCATTGACTTTGGAGTTTTCTTTCACTGACGGGAAGAACTGGGATGGTCCTTACAAGTTGGTCATGGAAGTACCTCAGAAGTTGAAAGGCTTGCCTCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT