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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcccacctggtgatcgccaaaggtagtttcatctttaaatcccttgacctgtccggtctgagggattggctaatttctgatattgttttggcttttgttttcagaggaccacctcgctctgatggagaccgtcccagatttggtgaccgtgatggataccgtggagGCCCACGTGGTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAA

Basic information

species Arabidopsis thaliana
transcript AT4G25740.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G25740.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G02410.3 (Glycine max), 3'ss of exon 3
gcccacctggtgatcgccaaaggtagtttcatctttaaatcccttgacctgtccggtctgagggattggctaatttctgatattgttttggcttttgttttcagaggaccacctcgctctgatggagaccgtcccagatttggtgaccgtgatggataccgtggagGCCCACGTGGTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAA
         || ||    | |       ||||  ||    |  ||   || |    | |  | | ||| | || |  | | ||     ||  | || |   ||| || |||||||||| ||| |||||  |         ||||||||||||||||||||||||||| ||||| ||   || ||   |    || |     | |                     
---------gtaattttaacattcttcctcatggtttttacttttttactatgatttttctgtgtttgaccaaatattcaaatg----tgattgttttcaacagGGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGTGGTGACCGTGATGGATACCGTGGAGGTCCACGCGGACCTGGTGGTGATTTCGGTGACAAGGGT---------------------

upper sequence: AT4G25740.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA01G43110.1 (Glycine max), 3'ss of exon 3
gcccacctggtgatcgccaaaggtagtttcatctttaaatcccttgacc-tgtccggtctgagggattggctaatttctgatatt--gttttggcttttgttttcagaggaccacctcgctctgatggagaccgtcccagatttggtgaccgtgatggataccgtggagGCCCACGTGGTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAA
                      ||| ||| |  || |  |  | | | | | |    | ||| |  |  | |    ||  |||||    | ||  | || |   ||| || |||||||||| ||| |||||  |          |||||||||||||||||||||||||| ||||| ||   ||  |   |    || |     | |                     
----------------------gtaatttaacattcagttttcctcatcgtttttactatgatgtttctgttttgatcaaatattcaaatgtgattgttttgaacagGGGCCCACCTCGCTTTGACGGAGAGAGGAGATTCGGCGGTGACCGTGATGGATACCGTGGAGGTCCACGCGGACCTGGCGGTGATTTCGGTGACAAGGGT---------------------

upper sequence: AT4G25740.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv02s0025g00310.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------------------------------------------------------------------------gcccacctggtgatcgccaaaggtagtttcatctttaaatcccttgacctgtccggtctgagggattggctaatttctgata----ttgttttggcttttg-ttttcagaggaccacctcgctctgatggagaccgtcccagatttggtgaccgtgatggataccgtggagGCCCACGTGGTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAA
                                                                                            |   |     ||||  |  || ||   ||    | |   |   ||| | |||   || |  | | |    | || |   ||     |||||     || || ||||||| || |||||||||| ||| |||||  | || || ||||||||||| ||||| ||||||||||| ||||| ||   |   |   ||  ||| |     | |                     
gtaatgactcaattttgagttgatgttcggtgatttatttatttatttatttatttattattctgttgttaaacaatttggtgcgcattggggttaatggtttgattac--aatgtgaattgggatctgtttggattgccatgttttgtttttgagttcttatgatgtaaaatgggttttgttgaaaattgtgattttcagTGGTCCACCTCGCTTTGAAGGAGATAGACCAAGGTTTGGTGACCGGGATGGGTACCGTGGAGGTCCACGAGGACCTCCAGGTGAGTTTGGTGACAAGGGT---------------------

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|152035849|gb|BP863154.2|BP863154
EST:     CCCTGCTACTTTGAAGAAGTCTGCTAAGCC-GGTGGTCGTCCCTTTGGTG                         GCCCACGTGGTG
genomic: CCCTGCTACTTTGAAGAAGTCTGCTAAGCCCGGTGGTCGTCCCTTTGGTGgcccacctgg ... taccgtggagGCCCACGTGGTG
EST: gi|163973626|gb|ES042710.1|ES042710
EST:     CCCTGCTACTTTGAAGAAGTCTGCTAAGCCCGGTGGTCGTCCCTTTGGTG                         GCCCACCTGGTG
genomic: CCCTGCTACTTTGAAGAAGTCTGCTAAGCCCGGTGGTCGTCCCTTTGGTGgcccacctgg ... taccgtggagGCCCACGTGGTG
EST: gi|86053987|gb|DR349744.1|DR349744
EST:     CCCTGCTACTTTGAAGAAGTCTGCTAAGCCCGGTGGTCGTCCCTTTGGTG                         GCCCACCTGGTG
genomic: CCCTGCTACTTTGAAGAAGTCTGCTAAGCCCGGTGGTCGTCCCTTTGGTGgcccacctgg ... taccgtggagGCCCACGTGGTG
EST: gi|86053948|gb|DR349705.1|DR349705
EST:     NCTGCTACTTTGAAGGAAGTCTGCTAAGCCCGGTGGTCGTCCCTTTGGTG                         GCCCACCTGGTG
genomic: CCTGCTACTTTGAAG-AAGTCTGCTAAGCCCGGTGGTCGTCCCTTTGGTGgcccacctgg ... taccgtggagGCCCACGTGGTG
EST: gi|124936634|gb|EL013503.1|EL013503
EST:     CCTGCTACTTTGAAGAAGTCTGACTAAGCCCGGTGGTCGTCCCTTTGGTG                         GCCCACCTGGT
genomic: CCTGCTACTTTGAAGAAGTCTG-CTAAGCCCGGTGGTCGTCCCTTTGGTGgcccacctgg ... taccgtggagGCCCACGTGGT
EST: gi|86053903|gb|DR349660.1|DR349660
EST:     CCCTGCTACYTTGAAGAAGTCTGCTAAGCCCGGTGGTCGTCCCTTTGGTG                         GCCCACCTGGTG
genomic: CCCTGCTACTTTGAAGAAGTCTGCTAAGCCCGGTGGTCGTCCCTTTGGTGgcccacctgg ... taccgtggagGCCCACGTGGTG
EST: gi|152034625|gb|BP833134.2|BP833134
EST:     CCCTGCTACTTTGAAGAAGTCTGCTAAGCCCGGTGGTCGTCCCTTGGGTG                         GCCCACCTGGTG
genomic: CCCTGCTACTTTGAAGAAGTCTGCTAAGCCCGGTGGTCGTCCCTTTGGTGgcccacctgg ... taccgtggagGCCCACGTGGTG
EST: gi|86053905|gb|DR349662.1|DR349662
EST:     CCCTGCTACTTTGAAGAAGTCTGCTAAGCCCGGTGGTCGTCCCTTTGGTG                         GCCCACCTGGTG
genomic: CCCTGCTACTTTGAAGAAGTCTGCTAAGCCCGGTGGTCGTCCCTTTGGTGgcccacctgg ... taccgtggagGCCCACGTGGTG
EST: gi|152033879|gb|BP818939.2|BP818939
EST:     CCCTGCTACTTTGAAGAAGTCTGCTAAGCCCGGTGGTCGTCCCTTTGGTG                         GCCCACCTGGTG
genomic: CCCTGCTACTTTGAAGAAGTCTGCTAAGCCCGGTGGTCGTCCCTTTGGTGgcccacctgg ... taccgtggagGCCCACGTGGTG
EST: gi|86053953|gb|DR349710.1|DR349710
EST:     CCCTGCTACTTTGAAGAAGTCTGCTAAGCCCGGTGGTCGTCCCTTTGGTG                         GCCCACCTGGTG
genomic: CCCTGCTACTTTGAAGAAGTCTGCTAAGCCCGGTGGTCGTCCCTTTGGTGgcccacctgg ... taccgtggagGCCCACGTGGTG
EST: gi|125039676|gb|EL111945.1|EL111945
EST:     CCCTGCTACTTTGAAGAAGTCTGCTAAGCCCGGTGGTCGTCCCTTTGGTG                         GCCCACCTGGTG
genomic: CCCTGCTACTTTGAAGAAGTCTGCTAAGCCCGGTGGTCGTCCCTTTGGTGgcccacctgg ... taccgtggagGCCCACGTGGTG
EST: gi|86053899|gb|DR349656.1|DR349656
EST:     CCCTGCTACTTTGAAGAAGTCTGCTAAGCCCGGTGGTCGTCCCTTTGGTG                         GCCCACCTGGTG
genomic: CCCTGCTACTTTGAAGAAGTCTGCTAAGCCCGGTGGTCGTCCCTTTGGTGgcccacctgg ... taccgtggagGCCCACGTGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctcgctctgatggagaccgtcccagatttggtgaccgtgatggataccgtggagGCCCACGTGGTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAA
     ctctgat  putative branch site (score: 4)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcccacctggtgatcgccaaaggtagtttcatctttaaatcccttgacctgtccggtctgagggattggctaatttctgatattgttttggcttttgttttcagaggaccacctcgctctgatggagaccgtcccagatttggtgaccgtgatggataccgtggagGCCCACGTGGTGGTGATGAGAAGGGTGGAGCTCCAGCTGATTTCCAGCCGTCTTTCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT