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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaactctgcttctgatacctccattgttctagatataacccagaaaatgttacaaactctttacggtttcctctacagGGTCCTATGGCATTTTACAAGGGTTTCATCCCCAACTTTGGACGCCTTGGCTCATGGAACGTAATCATGTTTTTGACCCTCGAACAG

Basic information

species Arabidopsis thaliana
transcript AT3G54110.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G54110.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S15_443V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------------------------------------------gtaagcaactctgcttctgatacctccattg----ttctagatataacccagaaaatgttacaaactctttacggtttcctctacagGGTCCTATGGCATTTTACAAGGGTTTCATCCCCAACTTTGGACGCCTTGGCTCATGGAACGTAATCATGTTTTTGACCCTCGAACAG
                                                                    ||  |   |||  ||  |   |  | ||||    ||| || |||           ||| |   ||  | |    |||  | |||||||| ||   || ||||||||||| |||   ||||| ||||| || ||||| || |||||||| ||||||||||||||  | || |||
gtccgtgcctccacttccctttttttgtgatgttttcagacccttcgatgttcctagattgccacaaatattcggttctctttgagcagctgcaattgcctattccagttat--tttgtctgctgtgagtgacgttgtg-aatttggtgtacagGGTGCTGGAGCTTTTTACAAGGGGTTCTGGCCCAATTTTGGTCGACTTGGTTCCTGGAACGTTATCATGTTTTTGACTTTGGAGCAG
















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|125071864|gb|EL136757.1|EL136757
EST:     CACCATTGACTGCTTCGTCAAAACTCTGAAGAGCGAC                         GGTCCTATGGCATTTTACAAGGGTTTCATCCCCAACTTTGGACGCCTTGGC
genomic: CACCATTGACTGCTTCGTCAAAACTCTGAAGAGCGACgtaagcaact ... tcctctacagGGTCCTATGGCATTTTACAAGGGTTTCATCCCCAACTTTGGACGCCTTGGC
EST: gi|47832162|gb|CK121846.1|CK121846
EST:     GTGCTTACAAGGGCACCATTGACTGCTTCGTCAAAACTCTGAAGAGCGAC                         GGTCCTATGGCATTTTACAAGGGTTTCATCCCCAACTTTGGACGCCTTGGC
genomic: GTGCTTACAAGGGCACCATTGACTGCTTCGTCAAAACTCTGAAGAGCGACgtaagcaact ... tcctctacagGGTCCTATGGCATTTTACAAGGGTTTCATCCCCAACTTTGGACGCCTTGGC
EST: gi|125103448|gb|EL157852.1|EL157852
EST:     CTTCGTCAAAACTCTGAAGAGCGAC                         GGTCCTATGGCATTTTACAAGGGTTTCATCCCCAACTTTGGACGCCTTGGC
genomic: CTTCGTCAAAACTCTGAAGAGCGACgtaagcaact ... tcctctacagGGTCCTATGGCATTTTACAAGGGTTTCATCCCCAACTTTGGACGCCTTGGC
EST: gi|86087003|gb|DR382762.1|DR382762
EST:     GTGCTTACAAGGGCACCATTGACTGCTTCGTCAAAACTYTGAAGAGCGAC                         GGTCCTATGGCATTTTACAAGGGTTTCATCCCCAACTTTGGACGCCTTGGC
genomic: GTGCTTACAAGGGCACCATTGACTGCTTCGTCAAAACTCTGAAGAGCGACgtaagcaact ... tcctctacagGGTCCTATGGCATTTTACAAGGGTTTCATCCCCAACTTTGGACGCCTTGGC
EST: gi|86081786|gb|DR377545.1|DR377545
EST:     GTGCTTACAAGGGCACCATTGATTGCTTCGTCAAAACTCTGAAGAGCGAC                         GGTCCTATGGCATTTTACAAGGGTTTCATCCCCAACTTTGGACGCCTTGGC
genomic: GTGCTTACAAGGGCACCATTGACTGCTTCGTCAAAACTCTGAAGAGCGACgtaagcaact ... tcctctacagGGTCCTATGGCATTTTACAAGGGTTTCATCCCCAACTTTGGACGCCTTGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttctagatataacccagaaaatgttacaaactctttacggtttcctctacagGGTCCTATGGCATTTTACAAGGGTTTCATCCCCAACTTTGGACGCCTTGGCTCATGGAACGTAATCATGTTTTTGACCCTCGAACAG
         atataac  putative branch site (score: 3)
                                           tttcctctac  putative PPT
      tagatataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcaactctgcttctgatacctccattgttctagatataacccagaaaatgttacaaactctttacggtttcctctacagGGTCCTATGGCATTTTACAAGGGTTTCATCCCCAACTTTGGACGCCTTGGCTCATGGAACGTAATCATGTTTTTGACCCTCGAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA