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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttaattccttatgttacatgtatgggtgattacttcctgatcttggtgtttcttcacatggaactttctttccaattctctgtcacagGCTAAGGGAATGAATTATCTTCACAATCGCAATCCTCCAATTGTGCATAGAGATCTAAAATCTCCAAACTTATTGGTTGACAAAAAATATACAGTCAAG

Basic information

species Arabidopsis thaliana
transcript AT5G03730.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G03730.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os02g32610.2 (Oryza sativa), 3'ss of exon 11
---------------------------------------------gtatgtttaattccttatgttacatgtatgggtgattacttcctga--------tcttggtgtttcttcacatggaacttt--ctttccaattctctgt-cacagGCTAAGGGAATGAATTATCTTCACAATCGCAATCCTCCAATTGTGCATAGAGATCTAAAATCTCCAAACTTATTGGTTGACAAAAAATATACAGTCAAG
                                             | |||  |       |   ||| ||  |     | ||       ||        | | |||| ||||| | |   | | ||   |||      ||  ||   ||||||||||| |||||||| |||||||| ||||||||||| || || ||  | |||||||| || |||||  | |||||||| ||||| || || || |||
gtaaaatcatatatacttatctcaatacagaatttaggtctaacagaatgactggacatatgctttatataaagtaaaggttgaccgtagaatcaaaattgtaggtgcttctttataaaaatcattgattttgtgtaccttcgtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG

upper sequence: AT5G03730.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA19G37570.2 (Glycine max), 3'ss of exon 11
-------------------------gtatgtttaattccttatgttacatgtatgggt--gattacttcctgatcttggtgtttcttcacatgga--actttctttccaattctctgtcacagGCTAAGGGAATGAATTATCTTCACAATCGCAATCCTCCAATTGTGCATAGAGATCTAAAATCTCCAAACTTATTGGTTGACAAAAAATATACAGTCAAG
                          | | |||  |||  | | ||   || ||   |  ||| | |      || |    ||| | | ||| |   |  |  |||   ||| ||     |||||||||||||||||||||||||| || ||||||||||| ||||| ||||||||||| |||||||||||| |  | |||||||| ||||||||||| |||
gtaaactttcagaaaataaatattattgtttttggttctatttattttttgaattaatatgatcattatgatgtcataacctttgtacccattggttaagtaatttgtcattttcatgtgcagGCTAAGGGAATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG

upper sequence: AT5G03730.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA03G34890.1 (Glycine max), 3'ss of exon 11
--------------------------gtatgtttaattccttatgttacatgtatgggtgattacttcctgatcttggtgtttcttcacatggaactttctttccaattctctgtcacagGCTAAGGGAATGAATTATCTTCACAATCGCAATCCTCCAATTGTGCATAGAGATCTAAAATCTCCAAACTTATTGGTTGACAAAAAATATACAGTCAAG
                           | | || | |||  | | ||   || ||   | || |  || | | ||| ||     ||      | | ||        ||| ||     ||||||||||| |||||||||||||| || ||||||||||| ||||| ||||||||||| |||||||||||| |  | |||||||| ||||||||||| |||
gtaaactttaagaaaataaacatcaattgttttcagttctatttattttttgaattaat-atgatgtcataacctttgtacccattggttaagtatttgtc-----attttcatgtgcagGCTAAGGGGATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG

upper sequence: AT5G03730.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA10G07610.1 (Glycine max), 3'ss of exon 12
-------gtatgtttaattccttatgttac-atgtatgggtgattacttcc-tgatcttggtgtttcttcacatggaactttctttccaattctctgtcacagGCTAAGGGAATGAATTATCTTCACAATCGCAATCCTCCAATTGTGCATAGAGATCTAAAATCTCCAAACTTATTGGTTGACAAAAAATATACAGTCAAG
        | | | |  ||  |  | ||      | ||  |  | |      | ||||| || ||  || |     |||  | | |    || ||  |  ||||| ||||| |||||||||||||| || || ||||| || ||||| ||||||||||| |||||||||||| |  | |||||||| ||||||||||| |||
aactctactgtttctgctttttagtatttttgaatttgtattgtcataaaaataatctttgtattctttgatt---aaccatgtgttattttatcatttgcagGCAAAGGGGATGAATTATCTTCATAAACGTAATCCCCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG

upper sequence: AT5G03730.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA13G21480.1 (Glycine max), 3'ss of exon 10
----------------------gta-tgtttaattccttatgttacatgtatgggtgattacttcctgatcttggtgtttcttcacatggaactttctttccaattctctgtcacagGCTAAGGGAATGAATTATCTTCACAATCGCAATCCTCCAATTGTGCATAGAGATCTAAAATCTCCAAACTTATTGGTTGACAAAAAATATACAGTCAAG
                       || |||||  |   || |  ||  | | ||  | || |  || | ||||| || ||| || |  |  |||  | | |    || ||  |  ||||| ||||| |||||||||||||| || || ||||| || ||||| ||||||||||| |||||||||||| |  | |||||||| ||||||||||| |||
gtatgtatttaaaaaataaactatactgtttcttcttttttagtattttt-tgaattataatgtcataatctttgtatttttttaatt--aaccatgtgttattttatcatttgcagGCAAAGGGGATGAATTATCTTCATAAACGTAATCCCCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG

upper sequence: AT5G03730.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv08s0007g03910.t01 (Vitis vinifera), 3'ss of exon 10
-gtatgtttaat--tccttatgttacatgtatgggtgattacttcctg-atcttggtgtttcttcacatg-gaactttctttccaattctctgtca--cagGCTAAGGGAATGAATTATCTTCACAATCGCAATCCTCCAATTGTGCATAGAGATCTAAAATCTCCAAACTTATTGGTTGACAAAAAATATACAGTCAAG
  | | |||| |  |  |||| ||  ||| |    | |  |  |     | |||| | | |  |||  |  |  |||| |||    || |    ||  ||||| ||||| |||||||||||||| || ||||||||||| ||||| ||| ||||| | || ||||||||| | ||||||||||||||||| || || |||
tatttttttagtgattgttat-ttggatgcaccttttaccagctaaaataacttgttttattatcatttccgtgctttttttttttttttaaaacaaacagGCCAAGGGCATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATCGAGATTTGAAGTCTCCAAACCTTTTGGTTGACAAAAAATACACCGTGAAG

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|116423837|gb|EG466429.1|EG466429
EST:     CAAGGGAGCAATTAGATGAGAGACGTCGCCTGAGTATGGCTTATGATGTG                         GCTAAGGGAATGAATTATCTTCACAATCGCAATCCTCCAATTGTGCATAGA
genomic: CAAGGGAGCAATTAGATGAGAGACGTCGCCTGAGTATGGCTTATGATGTGgtatgtttaa ... tctgtcacagGCTAAGGGAATGAATTATCTTCACAATCGCAATCCTCCAATTGTGCATAGA
EST: gi|116414934|gb|EG457526.1|EG457526
EST:     GTCGCCTGAGTATGGCTTATGATGTG                         GCTAAGGGAATGAATTATCTTCACAATCGCAATCCTCCAATTGTGCATAGA
genomic: GTCGCCTGAGTATGGCTTATGATGTGgtatgtttaa ... tctgtcacagGCTAAGGGAATGAATTATCTTCACAATCGCAATCCTCCAATTGTGCATAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctgatcttggtgtttcttcacatggaactttctttccaattctctgtcacagGCTAAGGGAATGAATTATCTTCACAATCGCAATCCTCCAATTGTGCATAGAGATCTAAAATCTCCAAACTTATTGGTTGACAAAAAATATACAGTCAAG
 tcctgat  putative branch site (score: 3)
                              ctttctttccaattct  putative PPT
                               tttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttaattccttatgttacatgtatgggtgattacttcctgatcttggtgtttcttcacatggaactttctttccaattctctgtcacagGCTAAGGGAATGAATTATCTTCACAATCGCAATCCTCCAATTGTGCATAGAGATCTAAAATCTCCAAACTTATTGGTTGACAAAAAATATACAGTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC