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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attggatgtacgaatgtcttcttgtgaggtccttttcattttcctcgaaggtcgtgttgagaaattgacatgctgctgtttttttctctttgttttgcagCGGCTGTTTTCTTCGTCTGCCTTCTAACTACCACAAG

Basic information

species Physcomitrella patens
transcript PP1S96_146V6.2
intron # 31
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|162184004|gb|FC359374.1|FC359374
EST:     ATATCTGGACATAATGAACACTACCGTGGTCAGCCTCTCCTCGGCCTTGG                         CGGCTGTTTTCTTCGTCTGCTTTCTAACTACCACAAG
genomic: ATATCTGGACATAATGAACACTACCGTGGTCAGCCTCTCCTCGGCCTTGGgtaagatgat ... tgttttgcagCGGCTGTTTTCTTCGTCTGCCTTCTAACTACCACAAG
EST: gi|100430637|gb|BY978320.1|BY978320
EST:     ATATCTGGACATAATGAACACTACCGTGGTCAGCCTCTCCTCGGCCTTGG                         CGGCTGTTTTCTTCGTCTGCCTTCTAACTACCACAAG
genomic: ATATCTGGACATAATGAACACTACCGTGGTCAGCCTCTCCTCGGCCTTGGgtaagatgat ... tgttttgcagCGGCTGTTTTCTTCGTCTGCCTTCTAACTACCACAAG
EST: gi|162271360|gb|FC446933.1|FC446933
EST:     ATATCTGGACATAATGAACACTACCGTGGTCAGCCTCTCCTCGGCCTTGG                         CGGCTGTTTTCTTCGTCTGCCTTCTAACTACCACAAG
genomic: ATATCTGGACATAATGAACACTACCGTGGTCAGCCTCTCCTCGGCCTTGGgtaagatgat ... tgttttgcagCGGCTGTTTTCTTCGTCTGCCTTCTAACTACCACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgaaggtcgtgttgagaaattgacatgctgctgtttttttctctttgttttgcagCGGCTGTTTTCTTCGTCTGCCTTCTAACTACCACAAG
                 aattgac  putative branch site (score: 3)
                           ctgctgtttttttctc  putative PPT
                               tgttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attggatgtacgaatgtcttcttgtgaggtccttttcattttcctcgaaggtcgtgttgagaaattgacatgctgctgtttttttctctttgttttgcagCGGCTGTTTTCTTCGTCTGCCTTCTAACTACCACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT