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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttagatagagaaaccatacattctggcaggaaaagcttactccgccttatggaccattgataattcttatctgaaatagaagttgtgatgtgatggcagAACTCGGTTGGGGAAGAATCACATCTGGCTATAGAAACCAGTGGTCATGGAGCTCTAAAGGAAAACCATTGGCTCGACGATGGGGCCTATCTCATG

Basic information

species Arabidopsis thaliana
transcript AT5G17530.3
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 13
lower sequence: GLYMA20G32030.1 (Glycine max), 3'ss of exon 12
-------gttagatagagaaaccatacattctggcaggaaaagcttac-tccgccttatggaccattgataattcttatctgaaatagaagttgtgatgtgatggcagAACTCGGTTGGGGAAGAATCACATCTGGCTATAGAAACCAGTGGTCATGGAGCTCTAAAGGAAAACCATTGGCTCGACGATGGGGCCTATCTCATG
        ||  ||| | | |  ||| || ||  |     ||  | |  |   |   ||| |  | | | |||  ||| ||    | ||||   |  ||   || ||||| ||  |||| || || |||||| |||| || ||||| ||||| ||||||||||| |||||||| |||||||| || ||||| || || || |||
cttgtttcttctatatatatat-atatatacttacttttgaatttcatattttcaccatgta--agtaa-aatatttaacttt--tggaagcaatattgc--tgacagAATTCTATTGGTGAGGAGTCACATTTGGCAATTGAAACTAGTGGACATGGAGCTCTCAAGGAAAATCATTGGCTTGATGATGGCGCATACCTAATG

upper sequence: AT5G17530.3 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA10G35490.2 (Glycine max), 3'ss of exon 12
gttagatagagaaaccatacattctggcaggaaaagcttactccgccttatggaccattgataattcttatctgaaa--tagaagttgtgatgtgatggcagAACTCGGTTGGGGAAGAATCACATCTGGCTATAGAAACCAGTGGTCATGGAGCTCTAAAGGAAAACCATTGGCTCGACGATGGGGCCTATCTCATG
|    ||    || | |   ||      ||   |   ||      | |  |    || |   | | | ||| | |    | ||||   |  ||   || ||||| ||  |||| || || |||||| |||| || ||||| ||||| ||||||||||| |||||||| |||||||| || ||||| || || || |||
gaagcattctaaatcaaattatatatatagtttacttttgaatttcatatttttacaatataagtacatatttaacttttggaagcaatattgc--tgacagAATTCTATTGGCGAGGAGTCACATTTGGCAATTGAAACTAGTGGACATGGAGCTCTCAAGGAAAATCATTGGCTTGATGATGGTGCATACCTAATG

upper sequence: AT5G17530.3 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv13s0019g04370.t01 (Vitis vinifera), 3'ss of exon 13
gttagatagagaaacca-tacattctggcaggaaaagc-ttactccgccttatgga---ccattgataattcttatctgaaatagaagttgtgatgt-gatggcagAACTCGGTTGGGGAAGAATCACATCTGGCTATAGAAACCAGTGGTCATGGAGCTCTAAAGGAAAACCATTGGCTCGACGATGGGGCCTATCTCATG
     ||| | || |   | | || |  ||          || || || || |||    ||| || | |   |  | |  ||  ||||  || |||| | || ||||| || ||||| || || |||||||||||||| || || ||||| ||||||||||| ||||| || || ||||| || ||||| || || ||||||
----tataaacaatcttcttccttgtcacactttggttactattctgcattttgggtttccactgctgagaatatttt--aactgaagcagtaatgttgctgacagAATTCTGTTGGTGAGGAGTCACATCTGGCTATTGAGACTAGTGGCCATGGAGCTCTCAAGGAGAATCACTGGCTTGATGATGGTGCATACCTCATG

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:     ACAGGTTCAAAAGAGGTTACAAGAATGTCATTGACGAAGCTATTCGCTTG                         AACTCGGTTGGGGAAGAATCACATCTGGCTATAGAAACCAGTGGTCATGGA
genomic: ACAGGTTCAAAAGAGGTTACAAGAATGTCATTGACGAAGCTATTCGCTTGgtaataaatg ... gtgatggcagAACTCGGTTGGGGAAGAATCACATCTGGCTATAGAAACCAGTGGTCATGGA
EST: gi|86023635|gb|DR319388.1|DR319388
EST:     CAAGAATGTCATTGACGAAGCTATTCGCTTG                         AACTCGGTTGGGGAAGAATCACATCTGGCTATAGAAACCAGTGGTCATGGA
genomic: CAAGAATGTCATTGACGAAGCTATTCGCTTGgtaataaatg ... gtgatggcagAACTCGGTTGGGGAAGAATCACATCTGGCTATAGAAACCAGTGGTCATGGA
EST: gi|164047369|gb|ES064578.1|ES064578
EST:     GTCATTGACGAAGCTATTCGCTTG                         AACTCGGTTGGGGAAGAATCACATCTGGCTATAGAAACCAGTGGTCATGGA
genomic: GTCATTGACGAAGCTATTCGCTTGgtaataaatg ... gtgatggcagAACTCGGTTGGGGAAGAATCACATCTGGCTATAGAAACCAGTGGTCATGGA
EST: gi|116424752|gb|EG467344.1|EG467344
EST:     ACAGGTTCAAAAGAGGTTACAAGAATGTCATTGACGAAGCTATTCGCTTG                         AACTCGGTTGG
genomic: ACAGGTTCAAAAGAGGTTACAAGAATGTCATTGACGAAGCTATTCGCTTGgtaataaatg ... gtgatggcagAACTCGGTTGG
EST: gi|124724652|gb|EH816054.1|EH816054
EST:     ACAGGTTCAAAAGAGGTTACAAGAATGTCATTGACGAAGCTATTCGCTTG                         AACTCGGTTGGGGAAGAATCACATCTGGCTATAGAAAC
genomic: ACAGGTTCAAAAGAGGTTACAAGAATGTCATTGACGAAGCTATTCGCTTGgtaataaatg ... gtgatggcagAACTCGGTTGGGGAAGAATCACATCTGGCTATAGAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttatggaccattgataattcttatctgaaatagaagttgtgatgtgatggcagAACTCGGTTGGGGAAGAATCACATCTGGCTATAGAAACCAGTGGTCATGGAGCTCTAAAGGAAAACCATTGGCTCGACGATGGGGCCTATCTCATG
          cattgat  putative branch site (score: 4)
           attgataattcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagatagagaaaccatacattctggcaggaaaagcttactccgccttatggaccattgataattcttatctgaaatagaagttgtgatgtgatggcagAACTCGGTTGGGGAAGAATCACATCTGGCTATAGAAACCAGTGGTCATGGAGCTCTAAAGGAAAACCATTGGCTCGACGATGGGGCCTATCTCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - aaccata
- - - - - - - - - - - - - - - gaaaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgaaat