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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagccaacaatttaccaccatgttgttaattttctctgtgactttttcactgacccagacttattttagGCGGAAAGCATCACAGGTTCAAAAGAGGTTACAAGAATGTCATTGACGAAGCTATTCGCTTG

Basic information

species Arabidopsis thaliana
transcript AT5G17530.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G17530.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G069676_T02 (Zea mays), 3'ss of exon 11
gttagccaacaatttaccaccatgttgttaattttctctgtgactttttcactgacccagacttatttt---agGCGGAAAGCATCACAGGTTCAAAAGAGGTTACAAGAATGTCATTGACGAAGCTATTCGCTTG
||  |   ||  || ||      ||  ||  |||        | |  || ||| | | |   || |||    ||| || ||||||||| | |||||| |||| ||||||||||| || ||||| ||||||||  ||
gtatgt--actgttcacattgtcgtgctttgtttgagtaaataatcatttacttatctatttttttttcttaagGAGGGAAGCATCACCGTTTCAAACGAGGGTACAAGAATGTAATAGACGAGGCTATTCGTCTG

upper sequence: AT5G17530.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA10G35490.2 (Glycine max), 3'ss of exon 11
---------------------------------------------------------------------gttagccaacaa--tttaccaccatgttgtt--------aattttctc----tgtgactttttcactgacccag-------acttattttagGCGGAAAGCATCACAGGTTCAAAAGAGGTTACAAGAATGTCATTGACGAAGCTATTCGCTTG
                                                                     || | | || |    || |    ||    ||        || |||||     || ||   | | | | ||           |  | | ||||| ||||  || ||  ||||||||||||||||||| ||||| ||||| ||||||||||| |||
gtatggaggaatctaaactggcatgatctttagtctacccttctcaccttctttctttaagagttcactgtaaactaaaatcccttgcttttattgaatttgaatggaaaatttcttgaaatgagatagtgttaataacttgctaatgttatatgtcttagGTGGAAGACACCATCGGTTCAAAAGAGGTTACAAAAATGTGATTGATGAAGCTATTCGTTTG

upper sequence: AT5G17530.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA20G32030.1 (Glycine max), 3'ss of exon 11
----------------------------------------------------------------------gttagccaacaatt-taccaccatgttgttaattttctc---tgtgac----tttttcactgacccagact---tattttagGCGGAAAGCATCACAGGTTCAAAAGAGGTTACAAGAATGTCATTGACGAAGCTATTCGCTTG
                                                                      || | | || |    |   |     |||| ||||   |    || ||      |  | |||  || | |||   | | | ||| || |  || ||  ||||||||||||| ||||| ||||| ||||| ||||||||||| |||
gtatggaggaatctaaactggcatgatctttagtctacccttctcacctttttttctttaagagttcactgtaaactaaaatcccttttattgaattgtaaattacttgaaatgagatagtgctaataacttgccaatactgtttgtctcagGTGGCAGACACCATCGGTTCAAAAGAGGCTACAAAAATGTGATTGATGAAGCTATTCGTTTG

upper sequence: AT5G17530.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv13s0019g04370.t01 (Vitis vinifera), 3'ss of exon 12
gttagccaacaatttaccaccatgttgttaattttctctg----tgactttttcactgaccca--gacttattttagGCGGAAAGCATCACAGGTTCAAAAGAGGTTACAAGAATGTCATTGACGAAGCTATTCGCTTG
||  |   | | |  |    |||  |||  || |  | |     ||| ||| |   | || ||  |  |  || |||| |||||||| ||| |||||||||| || || || ||||||||||| |||||||||||||||
gtatgttgaaactgaaatggcataatgtccatatcatataatgatgaatttgttcttaactcaagggttccttatagGAGGAAAGCACCACCGGTTCAAAAGGGGCTATAAAAATGTCATTGATGAAGCTATTCGCTTG

upper sequence: AT5G17530.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: EFJ15375 (Selaginella moellendorffii), 3'ss of exon 10
gttagccaacaatttaccaccatgttgttaattttctctgtgactttttcactgacccagacttattttagGCGGAAAGCATCACAGGTTCAAAAGAGGTTACAAGAATGTCATTGACGAAGCTATTCGCTTG
          |  ||   | ||  |    ||   | |   ||| | |||| |||  ||     | ||  ||| |||||||||||| ||||||| ||||| ||||| ||||| ||||| ||||  || ||||||
--------gtatgttttgatcaaatatgcaacggtgtgattgaatctttc-ctgttcc-----ttttacagGGGGAAAGCATCACCGGTTCAAGAGAGGATACAAAAATGTGATTGATGAAGGCATACGCTTG

upper sequence: AT5G17530.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: EFJ24972 (Selaginella moellendorffii), 3'ss of exon 10
gttagccaacaatttaccaccatgttgttaattttctctgtgactttttcactgacccagacttatttt------agGCGGAAAGCATCACAGGTTCAAAAGAGGTTACAAGAATGTCATTGACGAAGCTATTCGCTTG
                     ||||  || ||    | ||  ||  | | | |||  | | | | ||        ||| |||||||||||| ||||||| ||||| ||||| ||||| ||||| ||||  || ||||||
-------------------gtatgt-attgatcaaatatgcaacggtgtgattgaatctgtcctgttccttttacagGGGGAAAGCATCACCGGTTCAAGAGAGGATACAAAAATGTGATTGATGAAGGCATACGCTTG

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|116424751|gb|EG467343.1|EG467343
EST:     GGATAGTGTCACTTCGGACGGTCTGACCTCATTTATTGAGAAGAAGCTTG                         GCGGAAAGCATCACAGGTTCAAAAGAGGTTACAAGAATGTCATTGACGAAG
genomic: GGATAGTGTCACTTCGGACGGTCTGACCTCATTTATTGAGAAGAAGCTTGgttagccaac ... cttattttagGCGGAAAGCATCACAGGTTCAAAAGAGGTTACAAGAATGTCATTGACGAAG
EST: gi|116424752|gb|EG467344.1|EG467344
EST:     GGATAGTGTCACTTCGGACGGTCTGACCTCATTTATTGAGAAGAAGCTTG                         GCGGAAAGCATCACAGGTTCAAAAGAGGTTACAAGAATGTCATTGACGAAG
genomic: GGATAGTGTCACTTCGGACGGTCTGACCTCATTTATTGAGAAGAAGCTTGgttagccaac ... cttattttagGCGGAAAGCATCACAGGTTCAAAAGAGGTTACAAGAATGTCATTGACGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaccatgttgttaattttctctgtgactttttcactgacccagacttattttagGCGGAAAGCATCACAGGTTCAAAAGAGGTTACAAGAATGTCATTGACGAAGCTATTCGCTTG
                                 cactgac  putative branch site (score: 2)
                                             cttatttt  putative PPT
     atgttgttaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagccaacaatttaccaccatgttgttaattttctctgtgactttttcactgacccagacttattttagGCGGAAAGCATCACAGGTTCAAAAGAGGTTACAAGAATGTCATTGACGAAGCTATTCGCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG