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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgaaattatagtcgtctcgaatctttgccgggttcgtagtgttgtttgtatgtaatctgcttttgtataccttgatggacaatcatcctgtgttgtagGTTTTTGTTGGCATCCTACGTTGCTACACGATAGCCATCGCCATTTTAGTTATACTGGCCGAGACCGAGTGGGAGGCCCTCTTCAATTTCTGGAAG

Basic information

species Physcomitrella patens
transcript PP1S99_180V6.1
intron # 1
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|100388838|gb|BY988714.1|BY988714
EST:     TCTCTCTTTTCCGGTCGTTCGATTACCGCGGCTTCGACTACCGCGTCAGT                         GTTTTTGGTGGCATCCTACGTTGCTACACGATAGCCATCGCC
genomic: TCTCTCTTTTCCGGTCGTTCGATTACCGCGGCTTCGACTACCGCGTCAGTgtatgtcctc ... tgtgttgtagGTTTTTGTTGGCATCCTACGTTGCTACACGATAGCCATCGCC
EST: gi|100358475|gb|BY983924.1|BY983924
EST:     TCTCTCTTTTCCGGTCGTTCGATTACCGCGGCTTCGACTACCGCGTCAGT                         GTTTTTGTTGGCATCC
genomic: TCTCTCTTTTCCGGTCGTTCGATTACCGCGGCTTCGACTACCGCGTCAGTgtatgtcctc ... tgtgttgtagGTTTTTGTTGGCATCC
EST: gi|18356584|gb|BJ188643.1|BJ188643
EST:     TCTCTCTTTTCCGGTCGTTCGATTACCGCGGCTTCGACTACCGCGTCAGT                         GTTTTTGTTGGCATCCTACGTTGCTACACGATAGCCATCGCCATTTTAGTT
genomic: TCTCTCTTTTCCGGTCGTTCGATTACCGCGGCTTCGACTACCGCGTCAGTgtatgtcctc ... tgtgttgtagGTTTTTGTTGGCATCCTACGTTGCTACACGATAGCCATCGCCATTTTAGTT
EST: gi|18351220|gb|BJ183271.1|BJ183271
EST:     TCTCTCTTTTCCGGTCGTTCGATTACCGCGGCTTCGACTACCGCGTCAGT                         GTTTTTGTTGGCATCCTACGTTGCTACACGATAGCCATCGCCATTTTATTT
genomic: TCTCTCTTTTCCGGTCGTTCGATTACCGCGGCTTCGACTACCGCGTCAGTgtatgtcctc ... tgtgttgtagGTTTTTGTTGGCATCCTACGTTGCTACACGATAGCCATCGCCATTTTAGTT
EST: gi|208358918|gb|DC957662.1|DC957662
EST:     TCTCTCTTTTCCGGTCGTTCGATTACCGCGGCTTCGACTACCGCGTCAGT                         GTTTTTGTTGGCATCCTACGTTGCTACACGATAGCCATCGCCATTTTAGTT
genomic: TCTCTCTTTTCCGGTCGTTCGATTACCGCGGCTTCGACTACCGCGTCAGTgtatgtcctc ... tgtgttgtagGTTTTTGTTGGCATCCTACGTTGCTACACGATAGCCATCGCCATTTTAGTT
EST: gi|100392032|gb|BY953188.1|BY953188
EST:     TCTCTCTTTTCCGGTCGTTCGATTACCGCGGCTTCGACTACCGCGTCAGT                         GTTTTTGTTGGCATCCTACGTTGCTACACGATAGCCATCGCCATTTTAGTT
genomic: TCTCTCTTTTCCGGTCGTTCGATTACCGCGGCTTCGACTACCGCGTCAGTgtatgtcctc ... tgtgttgtagGTTTTTGTTGGCATCCTACGTTGCTACACGATAGCCATCGCCATTTTAGTT
EST: gi|208374931|gb|DC956369.1|DC956369
EST:     TCTCTCTTTTCCGGTCGTTCGATTACCGCGGCTTCGACTACCGCGTCAGT                         GTTTTTGTTGGCATCCTACGTTGCTACACGATAGCCATCGCCATTTTAGTT
genomic: TCTCTCTTTTCCGGTCGTTCGATTACCGCGGCTTCGACTACCGCGTCAGTgtatgtcctc ... tgtgttgtagGTTTTTGTTGGCATCCTACGTTGCTACACGATAGCCATCGCCATTTTAGTT
EST: gi|100358426|gb|BY983899.1|BY983899
EST:     TCTCTCTTTTCCGGTCGTTCGATTACCGCGGCTTCGACTACCGCGTCAGT                         GTTTTTGTTGGCATCCTA
genomic: TCTCTCTTTTCCGGTCGTTCGATTACCGCGGCTTCGACTACCGCGTCAGTgtatgtcctc ... tgtgttgtagGTTTTTGTTGGCATCCTA
EST: gi|208389047|gb|DC937380.1|DC937380
EST:     TCTCTCTTTTCCGGTCGTTCGATTACCGCGGCTTCNACTACCGCGTCAGT                         GTTTTTGTTGGCATCCTACGTTGCTACACGATAGCCATCGCCATTTTANTT
genomic: TCTCTCTTTTCCGGTCGTTCGATTACCGCGGCTTCGACTACCGCGTCAGTgtatgtcctc ... tgtgttgtagGTTTTTGTTGGCATCCTACGTTGCTACACGATAGCCATCGCCATTTTAGTT
EST: gi|18354509|gb|BJ186565.1|BJ186565
EST:     TCTCTCTTTTCCGGTCGTTCGATTACCGCGGCTTCGACTACCGCGTCAGT                         GTTTTTGTTGGCATCCTACGTTGCTACA
genomic: TCTCTCTTTTCCGGTCGTTCGATTACCGCGGCTTCGACTACCGCGTCAGTgtatgtcctc ... tgtgttgtagGTTTTTGTTGGCATCCTACGTTGCTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgtatgtaatctgcttttgtataccttgatggacaatcatcctgtgttgtagGTTTTTGTTGGCATCCTACGTTGCTACACGATAGCCATCGCCATTTTAGTTATACTGGCCGAGACCGAGTGGGAGGCCCTCTTCAATTTCTGGAAG
                          ccttgat  putative branch site (score: 5)
                                       tcatcct  putative PPT
                 ttttgtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgaaattatagtcgtctcgaatctttgccgggttcgtagtgttgtttgtatgtaatctgcttttgtataccttgatggacaatcatcctgtgttgtagGTTTTTGTTGGCATCCTACGTTGCTACACGATAGCCATCGCCATTTTAGTTATACTGGCCGAGACCGAGTGGGAGGCCCTCTTCAATTTCTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG