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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattgataacgtgccatttctaaaatagttcctcactttctgtgtttcgttctgggggtttctctgagcgagtttttgtctccaagtaaagtatgtgccctttggttcttccctttctttgcactacacagctgaattggatgtcgttggcagGTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAACCCTGAAATTGGGCAGATGATTGCCGAGGCTATGGGCAAGGTGGGACGCA

Basic information

species Physcomitrella patens
transcript PP1S15_485V6.2
intron # 4
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|162182315|gb|FC357186.1|FC357186
EST:     ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAG                         GTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
genomic: ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAGgtgattgata ... tcgttggcagGTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
EST: gi|162250146|gb|FC427871.1|FC427871
EST:     ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAG                         GTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
genomic: ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAGgtgattgata ... tcgttggcagGTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
EST: gi|162153515|gb|FC329609.1|FC329609
EST:     ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAG                         GTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
genomic: ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAGgtgattgata ... tcgttggcagGTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
EST: gi|162150983|gb|FC327879.1|FC327879
EST:     ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAG                         GTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
genomic: ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAGgtgattgata ... tcgttggcagGTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
EST: gi|162173179|gb|FC348726.1|FC348726
EST:     ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAG                         GTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
genomic: ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAGgtgattgata ... tcgttggcagGTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
EST: gi|162183969|gb|FC359339.1|FC359339
EST:     ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAG                         GTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
genomic: ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAGgtgattgata ... tcgttggcagGTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
EST: gi|162155281|gb|FC331218.1|FC331218
EST:     ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAG                         GTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
genomic: ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAGgtgattgata ... tcgttggcagGTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
EST: gi|162166168|gb|FC343411.1|FC343411
EST:     ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAG                         GTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
genomic: ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAGgtgattgata ... tcgttggcagGTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
EST: gi|162153382|gb|FC329892.1|FC329892
EST:     ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAG                         GTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
genomic: ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAGgtgattgata ... tcgttggcagGTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
EST: gi|162184449|gb|FC359195.1|FC359195
EST:     ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAG                         GTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
genomic: ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAGgtgattgata ... tcgttggcagGTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
EST: gi|162175371|gb|FC352297.1|FC352297
EST:     ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAG                         GTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
genomic: ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAGgtgattgata ... tcgttggcagGTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
EST: gi|162171512|gb|FC347814.1|FC347814
EST:     ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAG                         GTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
genomic: ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAGgtgattgata ... tcgttggcagGTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
EST: gi|162157139|gb|FC333709.1|FC333709
EST:     ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAG                         GTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
genomic: ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAGgtgattgata ... tcgttggcagGTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
EST: gi|162180842|gb|FC358343.1|FC358343
EST:     ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAG                         GTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
genomic: ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAGgtgattgata ... tcgttggcagGTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
EST: gi|162173824|gb|FC349416.1|FC349416
EST:     ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAG                         GTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
genomic: ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAGgtgattgata ... tcgttggcagGTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
EST: gi|162256596|gb|FC432906.1|FC432906
EST:     ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAG                         GTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
genomic: ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAGgtgattgata ... tcgttggcagGTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
EST: gi|67574539|gb|BJ947363.1|BJ947363
EST:     ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAG                         GTAGAAGACAGCGAATTGGCTGACGTTGCTGCT
genomic: ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAGgtgattgata ... tcgttggcagGTAGAAGACAGCGAATTGGCTGACGTTGCTGCT
EST: gi|162154100|gb|FC330543.1|FC330543
EST:     ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAG                         GTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
genomic: ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAGgtgattgata ... tcgttggcagGTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
EST: gi|162150359|gb|FC326631.1|FC326631
EST:     ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAG                         GTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
genomic: ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAGgtgattgata ... tcgttggcagGTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
EST: gi|162255427|gb|FC431841.1|FC431841
EST:     ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAG                         GTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
genomic: ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAGgtgattgata ... tcgttggcagGTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
EST: gi|162154271|gb|FC330402.1|FC330402
EST:     ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAG                         GTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC
genomic: ACAGAACTGTTATTGCCTTGGTGAAGGAGCTGAAGAACATGTCAAAGGAGgtgattgata ... tcgttggcagGTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctttggttcttccctttctttgcactacacagctgaattggatgtcgttggcagGTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAACCCTGAAATTGGGCAGATGATTGCCGAGGCTATGGGCAAGGTGGGACGCA
               tttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattgataacgtgccatttctaaaatagttcctcactttctgtgtttcgttctgggggtttctctgagcgagtttttgtctccaagtaaagtatgtgccctttggttcttccctttctttgcactacacagctgaattggatgtcgttggcagGTAGAAGACAGCGAATTGGCTGACGTTGCTGCTGTTAGTGCCGGCAACAACCCTGAAATTGGGCAGATGATTGCCGAGGCTATGGGCAAGGTGGGACGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG