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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatattattggaacaagtttaaagttttttttgtttttagtgtttctgtgctgatttttgttctcttcggattttcagTTTTGCAGATTTACAGAAGCCACAAATGGAACTTGATGGGAAGGCTTGTGCTGGTGTTGGGCAGAGCAGTCTCATGGCTTACTATGAGACTATGTTTGAC

Basic information

species Arabidopsis thaliana
transcript AT3G55610.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G55610.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G03830.1 (Glycine max), 3'ss of exon 3
gttatattattggaacaa----gtttaaagttttttttgttttta-----gtgtttctgtgctg---------atttttgttctcttcggattttca--------------gTTTTGCAGATTTACAGAAGCCACAAATGGAACTTGATGGGAAGGCTTGTGCTGGTGTTGGGCAGAGCAGTCTCATGGCTTACTATGAGACTATGTTTGAC
|| |||   ||| ||||     ||||    ||| |||||||| |       ||    ||||  |         ||| |  ||  ||| ||  |||||              | ||||| ||  | |||||||| ||| | ||||||||||| ||||||||||||| |||||| || | ||| || ||||||   |||||   | |||||   
gtaataaagttgtaacacctttgtttttgttttgttttgtttctctcagcatgcacatgtgaggttggttgaaattgtaatttacttgggtctttcatgggacatgtcacagCTTTGCTGACCTTCAGAAGCCGCAAGTTGAACTTGATGGCAAGGCTTGTGCTGCTGTTGGACAAAACAGCCTTATGGCTCTTTATGATGTTTTGTTTAGT
















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|86064871|gb|DR360628.1|DR360628
EST:     GTTGGTCTTGGTCGACAAAGGCTTCGATACAGACAATTAGTCAACAGCAG                         TTTTGCAGATTTACAGAAGCCACAAATGGAACTTGATGGNAAGGCTTGTGC
genomic: GTTGGTCTTGGTCGACAAAGGCTTCGATACAGACAATTAGTCAACAGCAGgttatattat ... ggattttcagTTTTGCAGATTTACAGAAGCCACAAATGGAACTTGATGGGAAGGCTTGTGC
EST: gi|86064874|gb|DR360631.1|DR360631
EST:     GTTGGTCTTGGTCGACAAAGGCTTCGATACAGACAATTAGTCAACAGCAG                         TTTTGCAGATTTACAGAAGCCACAAATGGAACTTGATGGGAAGGCTTGTGC
genomic: GTTGGTCTTGGTCGACAAAGGCTTCGATACAGACAATTAGTCAACAGCAGgttatattat ... ggattttcagTTTTGCAGATTTACAGAAGCCACAAATGGAACTTGATGGGAAGGCTTGTGC
EST: gi|86064868|gb|DR360625.1|DR360625
EST:     GTTGGTCTTGGTCGACAAAGGCTTCGATACAGACAATTAGTCAACAGCAG                         TTTTGCAGATTTACAGAAGCCACAAATGGAACTTGATGGGAAGGCTTGTGC
genomic: GTTGGTCTTGGTCGACAAAGGCTTCGATACAGACAATTAGTCAACAGCAGgttatattat ... ggattttcagTTTTGCAGATTTACAGAAGCCACAAATGGAACTTGATGGGAAGGCTTGTGC
EST: gi|152033743|gb|BP562130.3|BP562130
EST:     GTTGGTCTTGGTCGACAAAGGCTTCGATACAGGCAATTAGTCAACAGCAG                         TTTTGCAGATTTACAGAAGCCACAAATGGAACTTGATGGGAAGGCTTGTGC
genomic: GTTGGTCTTGGTCGACAAAGGCTTCGATACAGACAATTAGTCAACAGCAGgttatattat ... ggattttcagTTTTGCAGATTTACAGAAGCCACAAATGGAACTTGATGGGAAGGCTTGTGC
EST: gi|86064870|gb|DR360627.1|DR360627
EST:     GTTGGTCTTGGTCGACAAAGGCTTCGATACAGACAATTAGTCAACAGCAG                         TTTTGCAGATTTACAGAAGCCACAAATGGAACTTTGATGGGAAGGCTTGTG
genomic: GTTGGTCTTGGTCGACAAAGGCTTCGATACAGACAATTAGTCAACAGCAGgttatattat ... ggattttcagTTTTGCAGATTTACAGAAGCCACAAATGGAACTT-GATGGGAAGGCTTGTG
EST: gi|86064867|gb|DR360624.1|DR360624
EST:     GTTGGTCTTGGTCGACAAAGGCTTCGATACAGACAATTAGTCAACAGCAG                         TTTTGCAGATTTACAGAAGCCACAAATGGAACTTGATGGGAAGGCTTGTGC
genomic: GTTGGTCTTGGTCGACAAAGGCTTCGATACAGACAATTAGTCAACAGCAGgttatattat ... ggattttcagTTTTGCAGATTTACAGAAGCCACAAATGGAACTTGATGGGAAGGCTTGTGC
EST: gi|86064869|gb|DR360626.1|DR360626
EST:     GTTGGTCTTGGNCGACAAAGGCTTCGATACAGACAATTAGTCAACAGCAG                         NTTTGCAGATTTACAGAAGCCACNAATGGAACTTTGATGGGAAGGCTTG
genomic: GTTGGTCTTGGTCGACAAAGGCTTCGATACAGACAATTAGTCAACAGCAGgttatattat ... ggattttcagTTTTGCAGATTTACAGAAGCCACAAATGGAACTT-GATGGGAAGGCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttttttgtttttagtgtttctgtgctgatttttgttctcttcggattttcagTTTTGCAGATTTACAGAAGCCACAAATGGAACTTGATGGGAAGGCTTGTGCTGGTGTTGGGCAGAGCAGTCTCATGGCTTACTATGAGACTATGTTTGAC
                         tgctgat  putative branch site (score: 3)
                               tttttgttctcttcg  CT-rich tract
     ttttgttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatattattggaacaagtttaaagttttttttgtttttagtgtttctgtgctgatttttgttctcttcggattttcagTTTTGCAGATTTACAGAAGCCACAAATGGAACTTGATGGGAAGGCTTGTGCTGGTGTTGGGCAGAGCAGTCTCATGGCTTACTATGAGACTATGTTTGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG