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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgattcagctcactctccctgctcttctgattgtggtgcctctttcttttcgaaaattgtcttcatttggcgatgctgtatcttatttcagttgacactgttttgggtgtgttgtatagAAACCAATGGTATGATGCAAAGGGTTTTGGCAAAGACATAAAATGGGCGTACGGACCTTGGCACTTCAATATCGAGGAGCACCTTCTAAATGATGGAATA

Basic information

species Physcomitrella patens
transcript PP1S77_67V6.9
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|162154039|gb|FC330274.1|FC330274
EST:     GTTCGTTCCCTGCAAAAGGTTGACCCAGAACGTTTAAAGTATTACCAAAG                         AAACCAATGGTATGATGCAAAGGGTTTTGGCAAAGACATAAAATGGGCGTA
genomic: GTTCGTTCCCTGCAAAAGGTTGACCCAGAACGTTTAAAGTATTACCAAAGgtaagtgatt ... tgttgtatagAAACCAATGGTATGATGCAAAGGGTTTTGGCAAAGACATAAAATGGGCGTA
EST: gi|162179592|gb|FC355234.1|FC355234
EST:     GTTCGTTCCCTGCAAAAGGTTGACCCAGAACGTTTAAAGTATTACCAAAG                         AAACCAATGGTATGATGCAAAGGGTTTTGGCAAAGACATAAAATGGGCGTA
genomic: GTTCGTTCCCTGCAAAAGGTTGACCCAGAACGTTTAAAGTATTACCAAAGgtaagtgatt ... tgttgtatagAAACCAATGGTATGATGCAAAGGGTTTTGGCAAAGACATAAAATGGGCGTA
EST: gi|162170834|gb|FC347448.1|FC347448
EST:     GTTCGTTCCCTGCAAAAGGTTGACCCAGAACGTTTAAAGTATTACCAAAG                         AAACCAATGGTATGATGCAAAGGGTTTTGGCAAAGACATAAAATGGGCGTA
genomic: GTTCGTTCCCTGCAAAAGGTTGACCCAGAACGTTTAAAGTATTACCAAAGgtaagtgatt ... tgttgtatagAAACCAATGGTATGATGCAAAGGGTTTTGGCAAAGACATAAAATGGGCGTA
EST: gi|162175972|gb|FC352378.1|FC352378
EST:     GTTGACCCAGAACGTTTAAAGTATTACCAAAG                         AAACCAATGGTATGATGCAAAGGGTTTTGGCAAAGACATAAAATGGGCGTA
genomic: GTTGACCCAGAACGTTTAAAGTATTACCAAAGgtaagtgatt ... tgttgtatagAAACCAATGGTATGATGCAAAGGGTTTTGGCAAAGACATAAAATGGGCGTA
EST: gi|162172926|gb|FC348931.1|FC348931
EST:     GTTCGTTCCCTGCAAAAGGTTGACCCAGAACGTTTAAAGTATTACCAAAG                         AAACCAATGGTATGATGCAAAGGGTTTTGGCAAAGACATAAAATGGGCGTA
genomic: GTTCGTTCCCTGCAAAAGGTTGACCCAGAACGTTTAAAGTATTACCAAAGgtaagtgatt ... tgttgtatagAAACCAATGGTATGATGCAAAGGGTTTTGGCAAAGACATAAAATGGGCGTA
EST: gi|208379631|gb|DC927128.1|DC927128
EST:     TCGTTCCCTGCAAAAGGTTGANCCCAGAACGTTTTAAAGTATTACCAAAG                         AAACCAATGGTATGATGCAAAGGGTTTTGGCAAAGACATAAAATGGGCGTA
genomic: TCGTTCCCTGCAAAAGGTTGA-CCCAGAACG-TTTAAAGTATTACCAAAGgtaagtgatt ... tgttgtatagAAACCAATGGTATGATGCAAAGGGTTTTGGCAAAGACATAAAATGGGCGTA
EST: gi|162196272|gb|FC374354.1|FC374354
EST:     GTTCGTTCCCTGCAAAAGGTTGACCCAGAACGTTTAAAGTATTACCAAAG                         AAACCAATGGTATGATGCAAAGGGTTTTGGCAAAGACATAAAATGGGCGTA
genomic: GTTCGTTCCCTGCAAAAGGTTGACCCAGAACGTTTAAAGTATTACCAAAGgtaagtgatt ... tgttgtatagAAACCAATGGTATGATGCAAAGGGTTTTGGCAAAGACATAAAATGGGCGTA
EST: gi|208382425|gb|DC927959.1|DC927959
EST:     TTCGTTCCCTGCAAAAGGNTTGACCCAGAACG-TTAAAGTATTACCAAAG                         AAACCAATGGTATGATGCAAAGGGTTTTGGCAAAGACATAAAATGGGCGTA
genomic: TTCGTTCCCTGCAAAAGG-TTGACCCAGAACGTTTAAAGTATTACCAAAGgtaagtgatt ... tgttgtatagAAACCAATGGTATGATGCAAAGGGTTTTGGCAAAGACATAAAATGGGCGTA
EST: gi|208385455|gb|DC956653.1|DC956653
EST:     TATTACCAANG                         AAACCAATGGTATGATGCAAAGGGTTTTGGCAAAGACATAAAATGGGCGTA
genomic: TATTACCAAAGgtaagtgatt ... tgttgtatagAAACCAATGGTATGATGCAAAGGGTTTTGGCAAAGACATAAAATGGGCGTA
EST: gi|162160009|gb|FC335671.1|FC335671
EST:     GTTCGTTCCCTGCAAAAGGTTGACCCAGAACGTTTAAAGTATTACCAAAG                         AAACCAATGGTATGATGCAAAGGGTTTTGGCAAAGACATAAAATGGGCGTA
genomic: GTTCGTTCCCTGCAAAAGGTTGACCCAGAACGTTTAAAGTATTACCAAAGgtaagtgatt ... tgttgtatagAAACCAATGGTATGATGCAAAGGGTTTTGGCAAAGACATAAAATGGGCGTA
EST: gi|162209829|gb|FC385971.1|FC385971
EST:     GTTCGTTCCCTGCAAAAGGTTGACCCAGAACGTTTAAAGTATTACCAAAG                         AAACCAATGGTATGATGCAAAGGGTTTTGGCAAAGACATAAAATGGGCGTA
genomic: GTTCGTTCCCTGCAAAAGGTTGACCCAGAACGTTTAAAGTATTACCAAAGgtaagtgatt ... tgttgtatagAAACCAATGGTATGATGCAAAGGGTTTTGGCAAAGACATAAAATGGGCGTA
EST: gi|208375875|gb|DC926967.1|DC926967
EST:     GTTCGTTCCCTGCAAAAGGTTGACCCAGAACGTTTAAAGTATTACCAAAG                         AAACCAATGGTATGATGCAAAGGGTTTTGGCAAAGACATAAAATGGGCGTA
genomic: GTTCGTTCCCTGCAAAAGGTTGACCCAGAACGTTTAAAGTATTACCAAAGgtaagtgatt ... tgttgtatagAAACCAATGGTATGATGCAAAGGGTTTTGGCAAAGACATAAAATGGGCGTA
EST: gi|208378525|gb|DC927222.1|DC927222
EST:     GTTCGTTCCCTGCAAAAGGTTGACCCAGAACGTTTAAAGTATNACCAAAG                         AAACCAATGGTATGATGCAAAGGGTTTTGGCAAAGACATAAAATNGGCGTA
genomic: GTTCGTTCCCTGCAAAAGGTTGACCCAGAACGTTTAAAGTATTACCAAAGgtaagtgatt ... tgttgtatagAAACCAATGGTATGATGCAAAGGGTTTTGGCAAAGACATAAAATGGGCGTA
EST: gi|162245636|gb|FC423319.1|FC423319
EST:     CCAGAACGTTTAAAGTATTACCAAAG                         AAACCAATGGTATGATGCAAAGGGTTTTGGCAAAGACATAAAATGGGCGTA
genomic: CCAGAACGTTTAAAGTATTACCAAAGgtaagtgatt ... tgttgtatagAAACCAATGGTATGATGCAAAGGGTTTTGGCAAAGACATAAAATGGGCGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttggcgatgctgtatcttatttcagttgacactgttttgggtgtgttgtatagAAACCAATGGTATGATGCAAAGGGTTTTGGCAAAGACATAAAATGGGCGTACGGACCTTGGCACTTCAATATCGAGGAGCACCTTCTAAATGATGGAATA
                         agttgac  putative branch site (score: 4)
              tatcttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgattcagctcactctccctgctcttctgattgtggtgcctctttcttttcgaaaattgtcttcatttggcgatgctgtatcttatttcagttgacactgttttgggtgtgttgtatagAAACCAATGGTATGATGCAAAGGGTTTTGGCAAAGACATAAAATGGGCGTACGGACCTTGGCACTTCAATATCGAGGAGCACCTTCTAAATGATGGAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA