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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcagattaactccaacatattattattattattattattattttttctattcaaagcaccgagctcttgatctcttgggcggagaactaattgtacatgagccatgtgttggggtgtttctgcaaagGGTTCTGTACTAGTGAAGTATCCAGCCCTCCTGTCGATGGGGTGCTTGACGGAACTATTTGGGTCCATTCAAGTGGGTATTATTGGAGCCGCAATGAAGG

Basic information

species Physcomitrella patens
transcript PP1S46_43V6.4
intron # 4
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|100399060|gb|BY954179.1|BY954179
EST:     TTTATCTACTATTAAATTGCACCTTGTGGGGGTTGTATCTCATAAATCAG                         GGTTCTGTACTAGTGAAGTATCCAGCCCTCCTGTCGATGGGGTGCTTGACG
genomic: TTTATCTACTATTAAATTGCACCTTGTGGGGGTTGTATCTCATAAATCAGgtgcagatta ... ttctgcaaagGGTTCTGTACTAGTGAAGTATCCAGCCCTCCTGTCGATGGGGTGCTTGACG
EST: gi|37837339|gb|BJ595347.1|BJ595347
EST:     TTTATCTACTATTAAATTGCACCTTGTGGGGGTTGTATCTCATAAATCAG                         GGTTCTGTACTAGTGAAGTATCCAGCCCTCCTGTCGATGGGGTGCTTGACG
genomic: TTTATCTACTATTAAATTGCACCTTGTGGGGGTTGTATCTCATAAATCAGgtgcagatta ... ttctgcaaagGGTTCTGTACTAGTGAAGTATCCAGCCCTCCTGTCGATGGGGTGCTTGACG
EST: gi|100390535|gb|BY952943.1|BY952943
EST:     TTTATCTACTATTAAAATGCACCTTGTGGGGGTTGTATCTCATAAATCAG                         GGTTCTGTACTAG
genomic: TTTATCTACTATTAAATTGCACCTTGTGGGGGTTGTATCTCATAAATCAGgtgcagatta ... ttctgcaaagGGTTCTGTACTAG
EST: gi|208380165|gb|DC927444.1|DC927444
EST:     TTTATCTACTATTAAATTGCACCTTGTGGGGGTTGTATCTCATAAATCAG                         GGTTCTGTACTAGTGAAGTATCCAGCCCTCCTGTCGATGGGGTGCTTGACG
genomic: TTTATCTACTATTAAATTGCACCTTGTGGGGGTTGTATCTCATAAATCAGgtgcagatta ... ttctgcaaagGGTTCTGTACTAGTGAAGTATCCAGCCCTCCTGTCGATGGGGTGCTTGACG
EST: gi|208362740|gb|DC950540.1|DC950540
EST:     TTTATCTACTATTAAATTGCACCTTGTGGGGGTTGTATCTCATAAATCAG                         GGTTCTGTACTAGTGAAGTATCCAGCCCTCCTGTCGATGGGGTGCTTGACG
genomic: TTTATCTACTATTAAATTGCACCTTGTGGGGGTTGTATCTCATAAATCAGgtgcagatta ... ttctgcaaagGGTTCTGTACTAGTGAAGTATCCAGCCCTCCTGTCGATGGGGTGCTTGACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgggcggagaactaattgtacatgagccatgtgttggggtgtttctgcaaagGGTTCTGTACTAGTGAAGTATCCAGCCCTCCTGTCGATGGGGTGCTTGACGGAACTATTTGGGTCCATTCAAGTGGGTATTATTGGAGCCGCAATGAAGG
            aactaat  putative branch site (score: 2)
                                          tgtttct  putative PPT
            aactaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcagattaactccaacatattattattattattattattattttttctattcaaagcaccgagctcttgatctcttgggcggagaactaattgtacatgagccatgtgttggggtgtttctgcaaagGGTTCTGTACTAGTGAAGTATCCAGCCCTCCTGTCGATGGGGTGCTTGACGGAACTATTTGGGTCCATTCAAGTGGGTATTATTGGAGCCGCAATGAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG