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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatatagtcattctactctaaataaacacgctttgatgaatgaaggatcacgatcatcgaacttcactggaacattattaacagCAAGGGAATACTAGAATCACTGAGAAGAAGAGCAAGGATGATGACTGATGGATTCAACAGCTGCAAAAACGTCGTCTGTAATTTCACAGAAGGTGCTATG

Basic information

species Arabidopsis thaliana
transcript AT1G70580.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G70580.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA02G04320.3 (Glycine max), 3'ss of exon 11
--------------------------------------------------------------------------------------------gtatatatagtcattctactctaaataaac-acgctttgatgaatgaaggatcacgatcatcgaactt-cactggaacattattaacagCAAGGGAATACTAGAATCACTGAGAAGAAGAGCAAGGATGATGACTGATGGATTCAACAGCTGCAAAAACGTCGTCTGTAATTTCACAGAAGGTGCTATG
                                                                                             |   |     ||| |    | ||||     |     | |  ||  | || |||  ||  | ||| |  || |     || | |  |||||  |||||||| |||||||||||||||||||||||||| |||||||||||||||||||| |||| ||| || || |||||||| || ||||        
gtaatcatgccaagactaatttgataaatgccaaatattttgtcaagttaatttgattttctatataggccatgtttgagcatgagaaattcatcatttctcccataccttcccaaatgtttgaaatcataagaaaaaaggggtcattat-gtagaattgacaattacctataacttgcagCACCGGAATACTTGAATCACTGAGAAGAAGAGCAAGGATAATGACTGATGGATTCAACAGTTGCAGAAATGTGGTTTGTAATTTTACTGAAG--------

upper sequence: AT1G70580.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA01G03260.3 (Glycine max), 3'ss of exon 11
------------------------------------------------------------------------------gtatatatagtcattctactctaaataaacacgctt-tgatgaatgaaggatcacgatcatcgaactt-cactggaacattattaacagCAAGGGAATACTAGAATCACTGAGAAGAAGAGCAAGGATGATGACTGATGGATTCAACAGCTGCAAAAACGTCGTCTGTAATTTCACAGAAGGTGCTATG
                                                                               |   |     | | |    | ||||    |   |  | |  ||  | || |||  ||  | ||| |  || |     || | |  |||||  |||||||| |||||||||||||||||||||||| | |||||||||||||||||||| |||| ||| || || |||||||| || ||||        
gtaatcatgctaaggctaatttgataaatgtcaaaatttttgtcaagttaactttgattatttgagcatgagaagttcatcatttctcccgtaccttcccaaatgtctaaaatcataagaaaaaaggggtcattat-gtagaattgacaattaccaataacttgcagCACCGGAATACTTGAATCACTGAGAAGAAGAGCAAGGCTAATGACTGATGGATTCAACAGTTGCAGAAATGTGGTTTGTAATTTTACTGAAG--------
















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|124991853|gb|EL064122.1|EL064122
EST:     ACCAAAGCCTGGAGACATTTCATATGACCAATTCGTTCGTGAGAG                         CAAGGGAATACTAGAATCACTGAGAAGAAGAGCAAGGATGATGA
genomic: ACCAAAGCCTGGAGACATTTCATATGACCAATTCGTTCGTGAGAGgtatatatag ... ttattaacagCAAGGGAATACTAGAATCACTGAGAAGAAGAGCAAGGATGATGA
EST: gi|124784363|gb|EH874109.1|EH874109
EST:     TGACCAATTCGTTCGTGAGAG                         CAAGGGAATACTAGAATCACTGAGAAGAAGAGCAAGGATGATGACTAGATG
genomic: TGACCAATTCGTTCGTGAGAGgtatatatag ... ttattaacagCAAGGGAATACTAGAATCACTGAGAAGAAGAGCAAGGATGATGACT-GATG
EST: gi|125189346|gb|EL204300.1|EL204300
EST:     TATGACCAATTCGTTCGTGAGAG                         CAAGGGAATACTAGAATCACTGAGAAGAAGAGCAAGGATGATGACTGATGG
genomic: TATGACCAATTCGTTCGTGAGAGgtatatatag ... ttattaacagCAAGGGAATACTAGAATCACTGAGAAGAAGAGCAAGGATGATGACTGATGG
EST: gi|124709454|gb|EH800856.1|EH800856
EST:     AGCCCACCAAAGCCTGGAGACATTTCATATGACCAATTCGTTCGTGAGAG                         CAAGGGAATACTAGAATCACTGAGAAGAAGAG
genomic: AGCCCACCAAAGCCTGGAGACATTTCATATGACCAATTCGTTCGTGAGAGgtatatatag ... ttattaacagCAAGGGAATACTAGAATCACTGAGAAGAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttgatgaatgaaggatcacgatcatcgaacttcactggaacattattaacagCAAGGGAATACTAGAATCACTGAGAAGAAGAGCAAGGATGATGACTGATGGATTCAACAGCTGCAAAAACGTCGTCTGTAATTTCACAGAAGGTGCTATG
 ctttgat  putative branch site (score: 5)
                                         aacattattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatatagtcattctactctaaataaacacgctttgatgaatgaaggatcacgatcatcgaacttcactggaacattattaacagCAAGGGAATACTAGAATCACTGAGAAGAAGAGCAAGGATGATGACTGATGGATTCAACAGCTGCAAAAACGTCGTCTGTAATTTCACAGAAGGTGCTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC