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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataataatattctcacaagtgtgtctctaaaatccaatcatcttattgttttctttgacctctttttcagGGATCAGCCAAACAATATCAAGGAATCGTTGACTGTGTTCAAACAATTGTAAGAGAGGAAGGAGCTCCTGCTCTCTTAAAG

Basic information

species Arabidopsis thaliana
transcript AT4G39460.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G39460.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G15150.1 (Glycine max), 3'ss of exon 10
---------------------------------------------------------------------------------------gtaat--aataatattctcacaagtgtgtc---tctaaa--atccaatcatcttattgttttctttgacctctttttcagGGATCAGCCAAACAATATCAAGGAATCGTTGACTGTGTTCAAACAATTGTAAGAGAGGAAGGAGCTCCTGCTCTCTTAAAG
                                                                                        ||||  |  |        | |||  | |    | | ||  ||| |  ||| | ||   || || |   | || ||  ||||||| || || |||||| | ||||||||||||||||||||||| ||| | |  || |||||| ||| |||  | || |||
gtaagctattatcctgtttcctttttttaatcttgtttttacgacagccatcttcatacatccatacacataaccttatgtatatggataatctagaagctaatcaataagaatattcagtgtgaactatcaagccatttcataagttcctattttc-ctcttcaagGGATCTGCAAACCAATATAAGGGAATCGTTGACTGTGTTCAAACCATTATTAAGGAAGAAGGACCTCGTGCCTTTTTGAAG

upper sequence: AT4G39460.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA05G31870.1 (Glycine max), 3'ss of exon 11
--------------------------------------------------------------------------------------------------------------gtaat--aataatattctcacaagtgtgtc---tctaaa--atccaatcatct-tattgttttctttgacctctttttcagGGATCAGCCAAACAATATCAAGGAATCGTTGACTGTGTTCAAACAATTGTAAGAGAGGAAGGAGCTCCTGCTCTCTTAAAG
                                                                                                               ||||  |  |  |     | |||  | |    | | ||  ||| |  |||   ||  ||  | |||     || ||  ||||||| || || |||||| | ||||||||||||||||||||||| ||| | |  || |||||| ||| |||  | || || 
gtaagcagtaatcctgtttcccttttttaatcttgtttttacaacttagacatctacatacaaccacgcacatacgataccttatgtatatagataccttatgtatatggataatctagaagcaaatcaataagaatattcagtgtgaattatcaagccattcataaggtcctattt---tcctcttcaagGGATCTGCGAACCAATATAAGGGAATCGTTGACTGTGTTCAAACCATTATTAAGGAAGAAGGACCTCGTGCCTTTTTGAAA
















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|124720120|gb|EH811522.1|EH811522
EST:     AGCAGTCACCACTCCGCTTGATGTTAATTAAGACAAGATTAATGGTTCAG                         GGATCAGCCAAA
genomic: AGCAGTCACCACTCCGCTTGATGTTA-TTAAGACAAGATTAATGGTTCAGgtaataataa ... tctttttcagGGATCAGCCAAA
EST: gi|124922748|gb|EL001008.1|EL001008
EST:     ATTAAGACAAGATTAATGGTTCAG                         GGATCAGCCAAACAATATCAAGGAATCGTTGACTGTGTTCAAACAATTGTA
genomic: ATTAAGACAAGATTAATGGTTCAGgtaataataa ... tctttttcagGGATCAGCCAAACAATATCAAGGAATCGTTGACTGTGTTCAAACAATTGTA
EST: gi|86082868|gb|DR378627.1|DR378627
EST:     GAGCAGTCACCACTCCGCTTGATGTTATTAAGACAAGATTAATGGTTCAG                         GGATCAGCCAAACAATATCAAGGAATCGTTGACTGTGTTCAAACAATTGTA
genomic: GAGCAGTCACCACTCCGCTTGATGTTATTAAGACAAGATTAATGGTTCAGgtaataataa ... tctttttcagGGATCAGCCAAACAATATCAAGGAATCGTTGACTGTGTTCAAACAATTGTA
EST: gi|164108520|gb|ES180091.1|ES180091
EST:     GAGCAGTCACCACTCCGCTTGATGTTATTAAGACAAGATTAATGGTTCAG                         GGATCAGCCAAACAATATCAAGGAAT
genomic: GAGCAGTCACCACTCCGCTTGATGTTATTAAGACAAGATTAATGGTTCAGgtaataataa ... tctttttcagGGATCAGCCAAACAATATCAAGGAAT
EST: gi|125083934|gb|EL144328.1|EL144328
EST:     ATTAAGACAAGATTAATGGTTCAG                         GGATCTAGCCAAACAATATCAAGGAATCGTTGACTGTGTTCAAACAATTGT
genomic: ATTAAGACAAGATTAATGGTTCAGgtaataataa ... tctttttcagGGATC-AGCCAAACAATATCAAGGAATCGTTGACTGTGTTCAAACAATTGT
EST: gi|124728087|gb|EH819489.1|EH819489
EST:     GAGCAGTCACCACTCCGCTTGACGTTATTAAGACAAGATTAATGGTTCAG                         GGATCAGCCAAACAATATCAAGGAATCGTTG
genomic: GAGCAGTCACCACTCCGCTTGATGTTATTAAGACAAGATTAATGGTTCAGgtaataataa ... tctttttcagGGATCAGCCAAACAATATCAAGGAATCGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagtgtgtctctaaaatccaatcatcttattgttttctttgacctctttttcagGGATCAGCCAAACAATATCAAGGAATCGTTGACTGTGTTCAAACAATTGTAAGAGAGGAAGGAGCTCCTGCTCTCTTAAAG
                         tcttattgttttcttt  CT-rich tract
                           ttattgttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataataatattctcacaagtgtgtctctaaaatccaatcatcttattgttttctttgacctctttttcagGGATCAGCCAAACAATATCAAGGAATCGTTGACTGTGTTCAAACAATTGTAAGAGAGGAAGGAGCTCCTGCTCTCTTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT