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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgcgacatgtcaggaacaattttggcgcgaatcatgattatagttgattcatattcttaaaccattttaatcatgagatttgtgagtgttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG

Basic information

species Physcomitrella patens
transcript PP1S99_59V6.2
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|208367480|gb|DC954940.1|DC954940
EST:     CCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAAGAGATACGCTGGATCAGAAAGCATGGACTGTGAAG
genomic: CCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAG-AAGCATGGACTGTGAAG
EST: gi|208362869|gb|DC950819.1|DC950819
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|162157331|gb|FC333459.1|FC333459
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|208372849|gb|DC956250.1|DC956250
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|208363068|gb|DC957995.1|DC957995
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|208369171|gb|DC956046.1|DC956046
EST:     GCTG-TTTCGACA-TCCTGATGA-GTCCCTG-GGAT                         ATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGNAG
genomic: GCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|208390945|gb|DC945934.1|DC945934
EST:     TGATGATGTCCCTGAGGAT                         -TTAAGAATTATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
genomic: TGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|208357946|gb|DC943058.1|DC943058
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|162280155|gb|FC455964.1|FC455964
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|67727485|gb|BJ977744.1|BJ977744
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgattcatattcttaaaccattttaatcatgagatttgtgagtgttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
                     ttttaat  putative branch site (score: 3)
                                           tgttttctcc  putative PPT
       atattcttaaaccatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgcgacatgtcaggaacaattttggcgcgaatcatgattatagttgattcatattcttaaaccattttaatcatgagatttgtgagtgttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA