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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttatgatctccttgaattttgtttctgtaccaacttgagatttggctattgatcttttatatgttgcattggctatatctgaatttacagGCTATACACTTGATATTCTTGCTCGAGCTCCTTTGTGGAAGTATGGGTTGGATTATCGACATGGTACTGGTCATGGAGTTGGTTCTTACCTTTGTGTTCA

Basic information

species Arabidopsis thaliana
transcript AT4G36760.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G36760.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA11G06900.1 (Glycine max), 3'ss of exon 12
----------------------gtaagttatgatctccttgaattttgtttctgtaccaacttgagatttggctatt-gatcttttatatgttgcattggctatatctgaat-ttacagGCTATACACTTGATATTCTTGCTCGAGCTCCTTTGTGGAAGTATGGGTTGGATTATCGACATGGTACTGGTCATGGAGTTGGTTCTTACCTTTGTGTTCA
                       || ||    |  ||   |||| |  ||   |  | |   |  | ||    ||   || |||   | | ||   ||   | | ||    | ||  |||  || | ||||||||||||||||||  ||||||||||||| ||||  | ||||||||||||||||||||||||||| |||| || ||  |   ||||||
gtataaacaaaataggacaaatttatgtgtcaaattctgcgaatataatt---gagctagtctccgtttcacataaaagaacttggctgttttttcttatttctttcaatttcttttagGGCATTCTCTTGATATTCTTGCTCGAATTCCTTTGTGGAAGGATGGTCTTGATTATCGACATGGTACTGGTCATGGAATTGGGTCCTATTTGAATGTTCA

upper sequence: AT4G36760.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA01G38410.4 (Glycine max), 3'ss of exon 12
---------------------gtaagttatgatctccttgaattttgtttctgtaccaacttgagatttggctattgatcttttatatgttgcattggctatatctgaatt--tacagGCTATACACTTGATATTCTTGCTCGAGCTCCTTTGTGGAAGTATGGGTTGGATTATCGACATGGTACTGGTCATGGAGTTGGTTCTTACCTTTGTGTTCA
                      || ||    |  ||  ||||| |  ||   |  | |   |  | ||    || | | |||   ||| ||    |   |   |   | ||  |  |||  || | |||||||||||||| |||  ||||||||||||| ||||  | ||||||||||||||||||||||||||| |||| || || ||   ||||||
gtataaataaaatagaccggtttatgtgtcaaattctgtgaatataatt---gagctagtatccgtttcacataataa-cttggctatctttttcttatttctttcaatttcttttagGGCATTCTCTTGATATTCTTGCCCGAATTCCTTTGTGGAAGGATGGTCTTGATTATCGACATGGTACTGGTCATGGAATTGGGTCCTATCTGAATGTTCA

upper sequence: AT4G36760.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv04s0023g01300.t01 (Vitis vinifera), 3'ss of exon 12
gtaagttatgatctccttgaattttgtttctgtaccaacttg-agatttggctat---tgatcttttatatgttgcat-tggctatatctgaattt-acagGCTATACACTTGATATTCTTGCTCGAGCTCCTTTGTGGAAGTATGGGTTGGATTATCGACATGGTACTGGTCATGGAGTTGGTTCTTACCTTTGTGTTCA
  || || || |     | | |||  | | | ||   |     |||| ||   |    |||| ||  ||    |   | |   ||||  | | ||| |||||  | |||||||| ||||||||||| |  || ||||||||| ||||  | |||||||||||||| |||||||||||| |||| |||||||||  ||||||
ccaaatt-tgttgcttgtaactttgttctatttaaagatacatagatatgcgcacatatgatgttaaattcactatttatttttataaataatttttacagGACACACACTTGACATTCTTGCTCGTGTCCCATTGTGGAAGGATGGCCTTGATTATCGACATGGAACTGGTCATGGAATTGGATCTTACCTTAATGTTCA

upper sequence: AT4G36760.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S96_73V6.1 (Physcomitrella patens), 3'ss of exon 12
gtaagtta-tgatctccttgaattttgtttctgtacc---aacttga-gatttggctattgatcttttatatgttgcattggctatatctga-atttacagGCTATACACTTGATATTCTTGCTCGAGCTCCTTTGTGGAAGTATGGGTTGGATTATCGACATGGTACTGGTCATGGAGTTGGTTCTTACCTTTGTGTTCA
 ||||  | |||  || || |     ||     ||     |  | ||  ||   | | ||       |  ||  || |||||    || ||  | | | |||  |  | ||||| ||  | ||  ||| ||| || |||||| |||| ||||| ||| ||||||| ||||||||||| |||||||  |||||   ||| ||
-taagaaactgaggtcattaagcgacgtccgcataatttaagatcgataatgaagttgttctagcgattgatagtgaattggtgtgatgtgccaatgatagGTCACGCGCTTGACATCTTGGCAAGAGTTCCCTTATGGAAGGATGGTTTGGACTATAGACATGGAACTGGTCATGGTGTTGGTTGCTACCTAAATGTGCA

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|86064644|gb|DR360401.1|DR360401
EST:     CAAGGGTCATGTTGCACTAGGAAATGCTCGGTTTCCAAAGGGAACAAACG                         GCTATACACTTGATATTCTTGCTCGAGCTCCTTTGTGGAAGTATGGGTTGG
genomic: CAAGGGTCATGTTGCACTAGGAAATGCTCGGTTTCCAAAGGGAACAAACGgtaagttatg ... gaatttacagGCTATACACTTGATATTCTTGCTCGAGCTCCTTTGTGGAAGTATGGGTTGG
EST: gi|116468011|gb|EG510603.1|EG510603
EST:     ATGCTCGGTTTCCAAAGGGAACAAACG                         GCTATACACTTGATATTCTTGCTCGAGCTCCTTTGTGGAAGTATGGGTTGG
genomic: ATGCTCGGTTTCCAAAGGGAACAAACGgtaagttatg ... gaatttacagGCTATACACTTGATATTCTTGCTCGAGCTCCTTTGTGGAAGTATGGGTTGG
EST: gi|116468010|gb|EG510602.1|EG510602
EST:     ATGCTCGGTTTCCAAAGGGAACAAACG                         GCTATACACTTGATATTCTTGCTCGAGCTCCTTTGTGGAAGTATGGGTTGG
genomic: ATGCTCGGTTTCCAAAGGGAACAAACGgtaagttatg ... gaatttacagGCTATACACTTGATATTCTTGCTCGAGCTCCTTTGTGGAAGTATGGGTTGG
EST: gi|125266141|gb|EL280226.1|EL280226
EST:     ACTAGGAAATGCTCGGTTTCCAAAGGGAACAAACG                         GCTATACACTTGATATTCTTGCTCGAGCTCCTTTGTGGAAGTATGGGTTGG
genomic: ACTAGGAAATGCTCGGTTTCCAAAGGGAACAAACGgtaagttatg ... gaatttacagGCTATACACTTGATATTCTTGCTCGAGCTCCTTTGTGGAAGTATGGGTTGG
EST: gi|86064645|gb|DR360402.1|DR360402
EST:     CAAGGGTCATGTTGCACTAGGAAATGCTCGGTTTCCAAAGGGAACAAACG                         GCTATACACTTGATATTCTTGCTCGAGCTCCTTTGTGGAAGTATGGGTTGG
genomic: CAAGGGTCATGTTGCACTAGGAAATGCTCGGTTTCCAAAGGGAACAAACGgtaagttatg ... gaatttacagGCTATACACTTGATATTCTTGCTCGAGCTCCTTTGTGGAAGTATGGGTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagatttggctattgatcttttatatgttgcattggctatatctgaatttacagGCTATACACTTGATATTCTTGCTCGAGCTCCTTTGTGGAAGTATGGGTTGGATTATCGACATGGTACTGGTCATGGAGTTGGTTCTTACCTTTGTGTTCA
           tattgat  putative branch site (score: 3)
           tattgatcttttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttatgatctccttgaattttgtttctgtaccaacttgagatttggctattgatcttttatatgttgcattggctatatctgaatttacagGCTATACACTTGATATTCTTGCTCGAGCTCCTTTGTGGAAGTATGGGTTGGATTATCGACATGGTACTGGTCATGGAGTTGGTTCTTACCTTTGTGTTCA

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