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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgaccaacttcactaatcattcgtcaaccgtttgtcttctaggagactggaatcctcaaattttttgagcgcgggtcttagttgtaacttgtgcatcgtttttgcgcgcagCCACTACATTGTGCCAGAGTTGAGCGGTGAGACAAAGTTTGTTTACTCTTCACGCAAGGCCGTGAGCGAGTACAAGGAGGCTAAGGAG

Basic information

species Physcomitrella patens
transcript PP1S399_19V6.2
intron # 2
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|18347252|gb|BJ179298.1|BJ179298
EST:     AACAAGACGAAGCCCGCCATGGAGATGACCAAGTGGTTCGATACCAACTA                         CCACTACATTGTGCCAGAGTTGAGCGGTGAGACAAAGTTTGTTTACTCTTC
genomic: AACAAGACGAAGCCCGCCATGGAGATGACCAAGTGGTTCGATACCAACTAgtaagtgacc ... ttgcgcgcagCCACTACATTGTGCCAGAGTTGAGCGGTGAGACAAAGTTTGTTTACTCTTC
EST: gi|18344976|gb|BJ177017.1|BJ177017
EST:     AACAAGACGAAGCCCGCCATGGAGATGACCAAGTGGTTCGATACCAACTA                         CCACTACATTGTGCCAGAGTTGAGCGGTGAGACAAAGTTTGTTTACTCTTC
genomic: AACAAGACGAAGCCCGCCATGGAGATGACCAAGTGGTTCGATACCAACTAgtaagtgacc ... ttgcgcgcagCCACTACATTGTGCCAGAGTTGAGCGGTGAGACAAAGTTTGTTTACTCTTC
EST: gi|18368205|gb|BJ200290.1|BJ200290
EST:     AACAAGACGAAGCCCGCCATGGAGATGACCAAGTGGTTCGATACCAACTA                         CCACTACATTGTGCCAGAGTTGAGCGGTGAGACAAAGTTTGTTTACTCTTC
genomic: AACAAGACGAAGCCCGCCATGGAGATGACCAAGTGGTTCGATACCAACTAgtaagtgacc ... ttgcgcgcagCCACTACATTGTGCCAGAGTTGAGCGGTGAGACAAAGTTTGTTTACTCTTC
EST: gi|18331192|gb|BJ163201.1|BJ163201
EST:     AACAAGACGAAGCCCGCCATGGAGATGACCAAGTGGTTCGATACCAACTA                         CCACTACATTGTGCCAGAGTTGAGCGGTGAGA
genomic: AACAAGACGAAGCCCGCCATGGAGATGACCAAGTGGTTCGATACCAACTAgtaagtgacc ... ttgcgcgcagCCACTACATTGTGCCAGAGTTGAGCGGTGAGA
EST: gi|100448742|gb|CJ973041.1|CJ973041
EST:     AACAAGACGAANCCCGCCATGGAGATGACCAAGTGGTTCGATACCAACTA                         CCACTACATTGTGCCAGAGTTGAGCGGTGAGACAAAGTTTGTTTACTCTTC
genomic: AACAAGACGAAGCCCGCCATGGAGATGACCAAGTGGTTCGATACCAACTAgtaagtgacc ... ttgcgcgcagCCACTACATTGTGCCAGAGTTGAGCGGTGAGACAAAGTTTGTTTACTCTTC
EST: gi|100369024|gb|BY984986.1|BY984986
EST:     AACAAGACGAAGCCCGCCATGGAGATGACCAAGTGGTTCGATACCAACTA                         CCACTACATTGTGCCAGAGTTGAGCGGTGAGACAAAGTTTGTTTACTCTTC
genomic: AACAAGACGAAGCCCGCCATGGAGATGACCAAGTGGTTCGATACCAACTAgtaagtgacc ... ttgcgcgcagCCACTACATTGTGCCAGAGTTGAGCGGTGAGACAAAGTTTGTTTACTCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaattttttgagcgcgggtcttagttgtaacttgtgcatcgtttttgcgcgcagCCACTACATTGTGCCAGAGTTGAGCGGTGAGACAAAGTTTGTTTACTCTTCACGCAAGGCCGTGAGCGAGTACAAGGAGGCTAAGGAG
                         ttgtaac  putative branch site (score: 2)
                                       tcgttttt  putative PPT
     tttttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgaccaacttcactaatcattcgtcaaccgtttgtcttctaggagactggaatcctcaaattttttgagcgcgggtcttagttgtaacttgtgcatcgtttttgcgcgcagCCACTACATTGTGCCAGAGTTGAGCGGTGAGACAAAGTTTGTTTACTCTTCACGCAAGGCCGTGAGCGAGTACAAGGAGGCTAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG