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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caagagaagtgctaattctttagatattttgacatgcatcacacatgtgaaacgaatgtcattgctaacattctggttaacatgtgcttttaatcagcagGACCAGTGAAGGGGAGAAAGATGAAAGAGGGATGTACAGTAGTTGCACAATCTGGTAACATTTTTCATTAGCATAGAGCTATTCCATATTTAGTCATAAC

Basic information

species Physcomitrella patens
transcript PP1S9_318V6.2
intron # 9
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|37846633|gb|BJ604641.1|BJ604641
EST:     TTGGGTACACTGCTTCATTCCCGAGATTTGTGAACCAAGTATGATT-CAG                         GACCAGTGAAGGGGAGAAAGATGAAAGAGGGATGTACAGTAGTTGCACAAT
genomic: TTGGGTACACTGCTTCATTCCCGAGATTTGTGAACCAAGTATGATTGCAGgtacaacaat ... taatcagcagGACCAGTGAAGGGGAGAAAGATGAAAGAGGGATGTACAGTAGTTGCACAAT
EST: gi|162186213|gb|FC362145.1|FC362145
EST:     TTGGGTACACTGCTTCATTCCCGAGATTTGTGAACCAAGTATGATTGCAG                         GACCAGTGAAGGGGAGAAAGATGAAAGAGGGATGTACAGTAGTTGCACAAT
genomic: TTGGGTACACTGCTTCATTCCCGAGATTTGTGAACCAAGTATGATTGCAGgtacaacaat ... taatcagcagGACCAGTGAAGGGGAGAAAGATGAAAGAGGGATGTACAGTAGTTGCACAAT
EST: gi|37840414|gb|BJ598422.1|BJ598422
EST:     TTGGGTACACTGCTTCATTCCCGAGATTTGTGAACCAAGTATGATT-CAG                         GACCAGTGAAGGGGAGAAAGATGAAAGAGGGATGTACAGTAGTTGCACAAT
genomic: TTGGGTACACTGCTTCATTCCCGAGATTTGTGAACCAAGTATGATTGCAGgtacaacaat ... taatcagcagGACCAGTGAAGGGGAGAAAGATGAAAGAGGGATGTACAGTAGTTGCACAAT
EST: gi|18335610|gb|BJ167630.1|BJ167630
EST:     TTGGGTACACTGCTTCATTCCCGAGATTTGTGAACCAAGTATGATTGCAG                         C
genomic: TTGGGTACACTGCTTCATTCCCGAGATTTGTGAACCAAGTATGATTGCAGgtacaacaat ... taatcagcag-
EST: gi|18335610|gb|BJ167630.1|BJ167630
EST:     TTGGGTACACTGCTTCATTCCCGAGATTTGTGAACCAAGTATGATTGCAG                         C
genomic: TTGGGTACACTGCTTCATTCCCGAGATTTGTGAACCAAGTATGATTGCAGgtacaacaat ... taatcagcag-
EST: gi|18335610|gb|BJ167630.1|BJ167630
EST:     TTGGGTACACTGCTTCATTCCCGAGATTTGTGAACCAAGTATGATTGCAG                         C
genomic: TTGGGTACACTGCTTCATTCCCGAGATTTGTGAACCAAGTATGATTGCAGgtacaacaat ... taatcagcag-
EST: gi|162160286|gb|FC336572.1|FC336572
EST:     TTGGGTACACTGCTTCATTCCCGAGATTTGTGAACCAAGTATGATTGCAG                         GACCAGTGAAGGGGAGAAAGATGAAAGAGGGATGTACAGTAGTTGCACAAT
genomic: TTGGGTACACTGCTTCATTCCCGAGATTTGTGAACCAAGTATGATTGCAGgtacaacaat ... taatcagcagGACCAGTGAAGGGGAGAAAGATGAAAGAGGGATGTACAGTAGTTGCACAAT
EST: gi|208382589|gb|DC919785.1|DC919785
EST:     TTGGGTACACTGCTTCATTCCCGAGATTTGTGAACCAAGTATGATTGCAG                         GACCAGTGAAGGGGAGAAAGATGAAAGAGGGATGTACAGTAGTTGCACAAT
genomic: TTGGGTACACTGCTTCATTCCCGAGATTTGTGAACCAAGTATGATTGCAGgtacaacaat ... taatcagcagGACCAGTGAAGGGGAGAAAGATGAAAGAGGGATGTACAGTAGTTGCACAAT
EST: gi|67699862|gb|BJ960095.1|BJ960095
EST:     TTGGGTACACTGCTTCATTCCCGAGATTTGTGAACCAAGTATGATTGCAG                         GACCAGTGAAGGGGAGAAAGATGAAAGAGGGATGTACAGTAGTTGCACAAT
genomic: TTGGGTACACTGCTTCATTCCCGAGATTTGTGAACCAAGTATGATTGCAGgtacaacaat ... taatcagcagGACCAGTGAAGGGGAGAAAGATGAAAGAGGGATGTACAGTAGTTGCACAAT
EST: gi|18341674|gb|BJ173709.1|BJ173709
EST:     TTGGGTACACTGCTTCATTCCCGAGATTTGTGAACCAAGTATGATTGCAG                         GACCAGTGAAGGGGAGAAAGATGAAAGAGGGATGTACAGTAGTTGCACAAT
genomic: TTGGGTACACTGCTTCATTCCCGAGATTTGTGAACCAAGTATGATTGCAGgtacaacaat ... taatcagcagGACCAGTGAAGGGGAGAAAGATGAAAGAGGGATGTACAGTAGTTGCACAAT
EST: gi|67692207|gb|BJ952440.1|BJ952440
EST:     TTGGGTACACTGCTTCATTCCCGAGATTTGTGAACCAAGTATGATTGCAG                         GACCAGTGAAGGGGAGAAAGATGAAAGAGGGATGTACAGTAGTTGCACAAT
genomic: TTGGGTACACTGCTTCATTCCCGAGATTTGTGAACCAAGTATGATTGCAGgtacaacaat ... taatcagcagGACCAGTGAAGGGGAGAAAGATGAAAGAGGGATGTACAGTAGTTGCACAAT
EST: gi|162237714|gb|FC413329.1|FC413329
EST:     TTGGGTACACTGCTTCATTCCCGAGATTTGTGAACCAAGTATGATTGCAG                         GACCAGTGAAGGGGAGAAAGATGAAAGAGGGATGTACAGTAGTTGCACAAT
genomic: TTGGGTACACTGCTTCATTCCCGAGATTTGTGAACCAAGTATGATTGCAGgtacaacaat ... taatcagcagGACCAGTGAAGGGGAGAAAGATGAAAGAGGGATGTACAGTAGTTGCACAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgaaacgaatgtcattgctaacattctggttaacatgtgcttttaatcagcagGACCAGTGAAGGGGAGAAAGATGAAAGAGGGATGTACAGTAGTTGCACAATCTGGTAACATTTTTCATTAGCATAGAGCTATTCCATATTTAGTCATAAC
                                       tgctttt  CT-rich tract
                                          ttttaatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caagagaagtgctaattctttagatattttgacatgcatcacacatgtgaaacgaatgtcattgctaacattctggttaacatgtgcttttaatcagcagGACCAGTGAAGGGGAGAAAGATGAAAGAGGGATGTACAGTAGTTGCACAATCTGGTAACATTTTTCATTAGCATAGAGCTATTCCATATTTAGTCATAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - gacatgc
- - - - - - - - - - - - - - - - - - - - -cacatgt