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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcataacccaactaccgcctatttcctttcgtttctcttttctcttttccccttttttctttcttggcctgcttgcaatttctctcttgctgtgcccaatttaacctttaagagtgttattcttgtcagTTTTATATGAAGGAGGCCAAGGGAACTGTAGATTACCAAGGGTATATTTTTCCGCGGCGGCGTGGAGGAGATTTG

Basic information

species Physcomitrella patens
transcript PP1S48_255V6.1
intron # 3
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|162168077|gb|FC344391.1|FC344391
EST:     GAGAAGTCAAACGCCGAGGAGAAGTCTCAGGATTCCACAACTGGATTCAG                         TTTNATATGGAGGAGGCCAAGGGAACTGTAGATTACCAAGGGTATATTTTT
genomic: GAGAAGTCAAACGCCGAGGAGAAGTCTCAGGATTCCACAACTGGATTCAGgtgcataacc ... ttcttgtcagTTTTATATGAAGGAGGCCAAGGGAACTGTAGATTACCAAGGGTATATTTTT
EST: gi|162177529|gb|FC353790.1|FC353790
EST:     GAGAAGTCAAACGCCGAGGAGAAGTCTCAGGATTCCACAACTGGATTCAG                         TTTTATATGGAGGAGGCCAAGGGAACTGTAGATTACCAAGGGTATATTTTT
genomic: GAGAAGTCAAACGCCGAGGAGAAGTCTCAGGATTCCACAACTGGATTCAGgtgcataacc ... ttcttgtcagTTTTATATGAAGGAGGCCAAGGGAACTGTAGATTACCAAGGGTATATTTTT
EST: gi|162184972|gb|FC362418.1|FC362418
EST:     GAGAAGTCAAACGCCGAGGAGAAGTCTCAGGATTCCACAACTGGATTCAG                         TTTTATATGGAGGAGGCCAAGGGAACTGTAGATTACCAAGGGTATATTTTT
genomic: GAGAAGTCAAACGCCGAGGAGAAGTCTCAGGATTCCACAACTGGATTCAGgtgcataacc ... ttcttgtcagTTTTATATGAAGGAGGCCAAGGGAACTGTAGATTACCAAGGGTATATTTTT
EST: gi|37830518|gb|BJ588530.1|BJ588530
EST:     GTCTCAGGATTCCACAACTGGATTCCAG                         TTTTATATGAAGGAGGCCAAGGGAACTGTAGATTACCAAGGGTATATTTT
genomic: GTCTCAGGATTCCACAACTGGATT-CAGgtgcataacc ... ttcttgtcagTTTTATATGAAGGAGGCCAAGGGAACTGTAGATTACCAAGGGTATATTTT
EST: gi|162149817|gb|FC325932.1|FC325932
EST:     GAGAAGTCAAACGCCGAGGAGAAGTCTCAGGATTCCACAACTGGATTCAG                         TTTTATATGGAGGAGGCCAAGGGAACTGTAGATTACCAAGGGTATATTTTT
genomic: GAGAAGTCAAACGCCGAGGAGAAGTCTCAGGATTCCACAACTGGATTCAGgtgcataacc ... ttcttgtcagTTTTATATGAAGGAGGCCAAGGGAACTGTAGATTACCAAGGGTATATTTTT
EST: gi|162184334|gb|FC360536.1|FC360536
EST:     GAGAAGTCAAACGCCGAGGAGAAGTCTCAGGATTCCACAACTGGATTCAG                         TTTTATATGGAGGAGGCCAAGGGAACTGTAGATTACCAAGGGTATATTTTT
genomic: GAGAAGTCAAACGCCGAGGAGAAGTCTCAGGATTCCACAACTGGATTCAGgtgcataacc ... ttcttgtcagTTTTATATGAAGGAGGCCAAGGGAACTGTAGATTACCAAGGGTATATTTTT
EST: gi|162164265|gb|FC342080.1|FC342080
EST:     GAGAAGTCAAACGCCGAGGAGAAGTCTCAGGATTCCACAACTGGATTCAG                         TTTTATATGGAGGAGGCCAAGGGAACTGTAGATTACCAAGGGTATATTTTT
genomic: GAGAAGTCAAACGCCGAGGAGAAGTCTCAGGATTCCACAACTGGATTCAGgtgcataacc ... ttcttgtcagTTTTATATGAAGGAGGCCAAGGGAACTGTAGATTACCAAGGGTATATTTTT
EST: gi|208369090|gb|DC955803.1|DC955803
EST:     GAGAAGTCAAACGCCGAGGAGAAGTCTCAGGATTCCACAACTGGATTCAG                         TTTTATATGAAGGAGGCCAAGGGAACTGTAGATTACCAAGGGTATATTTTT
genomic: GAGAAGTCAAACGCCGAGGAGAAGTCTCAGGATTCCACAACTGGATTCAGgtgcataacc ... ttcttgtcagTTTTATATGAAGGAGGCCAAGGGAACTGTAGATTACCAAGGGTATATTTTT
EST: gi|37839957|gb|BJ597965.1|BJ597965
EST:     AGAAGTCAAACGCCCGAGGAGAAGTCTCAGGATTCCACAACTGGATTCAG                         TTTTATATGAAGGAGGCCAAGGGAACTGTAGATTACCAAGGGTATATTTTT
genomic: AGAAGTCAAACG-CCGAGGAGAAGTCTCAGGATTCCACAACTGGATTCAGgtgcataacc ... ttcttgtcagTTTTATATGAAGGAGGCCAAGGGAACTGTAGATTACCAAGGGTATATTTTT
EST: gi|162186348|gb|FC361656.1|FC361656
EST:     GAGAAGTCAAACGCCGAGGAGAAGTCTCAGGATTCCACAACTGGATTCAG                         TTTTATATGGAGGAGGCCAAGGGAACTGTAGATTACCAAGGGTATATTTTT
genomic: GAGAAGTCAAACGCCGAGGAGAAGTCTCAGGATTCCACAACTGGATTCAGgtgcataacc ... ttcttgtcagTTTTATATGAAGGAGGCCAAGGGAACTGTAGATTACCAAGGGTATATTTTT
EST: gi|162278776|gb|FC454619.1|FC454619
EST:     GAGAAGTCAAACGCCGAGGAGAAGTCTCAGGATTCCACAACTGGATTCAG                         TTTTATATGAAGGAGGCCAAGGGAACTGTAGATTACCAAGGGTATATTTTT
genomic: GAGAAGTCAAACGCCGAGGAGAAGTCTCAGGATTCCACAACTGGATTCAGgtgcataacc ... ttcttgtcagTTTTATATGAAGGAGGCCAAGGGAACTGTAGATTACCAAGGGTATATTTTT
EST: gi|162184971|gb|FC362417.1|FC362417
EST:     GAGAAGTCAAACGCCGAGGAGAAGTCTCAGGATTCCACAACTGGATTCAG                         TTTTATATGGAGGAGGCCAAGGGAACTGTAGATTACCAAGGGTATATTTTT
genomic: GAGAAGTCAAACGCCGAGGAGAAGTCTCAGGATTCCACAACTGGATTCAGgtgcataacc ... ttcttgtcagTTTTATATGAAGGAGGCCAAGGGAACTGTAGATTACCAAGGGTATATTTTT
EST: gi|18341097|gb|BJ173130.1|BJ173130
EST:     GAGAAGTCAAACGCCGAGGAGAAGTCTCAGGATTCCACAACTGGATTCAG                         TTTTATATGAAGGAGGCCAAGGGAACTGTAGATTACCAAGGGTATATTTTT
genomic: GAGAAGTCAAACGCCGAGGAGAAGTCTCAGGATTCCACAACTGGATTCAGgtgcataacc ... ttcttgtcagTTTTATATGAAGGAGGCCAAGGGAACTGTAGATTACCAAGGGTATATTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaatttctctcttgctgtgcccaatttaacctttaagagtgttattcttgtcagTTTTATATGAAGGAGGCCAAGGGAACTGTAGATTACCAAGGGTATATTTTTCCGCGGCGGCGTGGAGGAGATTTG
                        atttaac  putative branch site (score: 3)
                                          ttattctt  putative PPT
                       aatttaacctttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcataacccaactaccgcctatttcctttcgtttctcttttctcttttccccttttttctttcttggcctgcttgcaatttctctcttgctgtgcccaatttaacctttaagagtgttattcttgtcagTTTTATATGAAGGAGGCCAAGGGAACTGTAGATTACCAAGGGTATATTTTTCCGCGGCGGCGTGGAGGAGATTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT