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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatatatctcttattgtgttcttttgtcatggtcttaataatgagttaaaatgttgatagtattgtccaccgtcttttgtagGGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGTGTTCTTCAATGGGATCCTGAGTCCTCTGAGCTTATTACAAG

Basic information

species Arabidopsis thaliana
transcript AT4G05420.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os05g51480.1 (Oryza sativa), 3'ss of exon 3
----gtgagtata-tatctcttattgtgttcttttgtcatggtcttaataatgagttaaaatgttgatagtatt-gtccaccgtcttttgtagGGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGTGTTCTTCAATGGGATCCTGAGTCCTCTGAGCTTATTACAAG
    |  | | || | |  ||     ||   || |||  | | | |   | ||  |   ||   | | | ||||  ||   || ||||   ||   ||  | || |||||  | |||||||| ||||| |||||||||||||||||||| || ||||||   ||    || |||||| | || ||
gtcagccaatttactgttcctcgacttgccattctgttgttgccgtg-cactggatggtaaaactaacactatttatcttacgcctttc--agAATGAGACTCAGGACTTCCTTTTCATTGCGACTGAAAGATACAAATTCTGTGTTCTGCAGTGGGATGGAGAAAAATCGGAGCTTCTCACTAG

upper sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os05g51480.2 (Oryza sativa), 3'ss of exon 3
gtgagtatatatctcttattgtgttcttttgtcatggtcttaataatgagttaaaatgttgatagtatt-gtccaccgtcttttgtagGGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGTGTTCTTCAATGGGATCCTGAGTCCTCTGAGCTTATTACAAG
                                                      ||   | | | ||||  ||   || ||||   ||   ||  | || |||||  | |||||||| ||||| |||||||||||||||||||| || ||||||   ||    || |||||| | || ||
----------------------------------------------------gtaaaactaacactatttatcttacgcctttc--agaatgagactcaggacttccttttcattgcgactgaaagatacaaattctgtgttctgcagTGGGATGGAGAAAAATCGGAGCTTCTCACTAG

upper sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G402002_T01 (Zea mays), 3'ss of exon 3
----gtgagtatatatctcttat-tgtgttcttttgtcatggtcttaataatgagttaaaatgttgatagtattgtccaccgtcttttgt----agGGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGTGTTCTTCAATGGGATCCTGAGTCCTCTGAGCTTATTACAAG
    |  | | || |  || |   |  |   |  | |  | || ||  | | |  ||   ||      | | ||       || | || |    ||   ||  | || |||||| | |||||||| || ||||| ||||||||||||||||| ||||||||| | ||    || ||||| || || ||
gtaagctaatttaaagttcatccatccgagatactttatttgtttttgtgaagtatttttataaatggattttttctgtttgtttcttatcctcagAATGAGACTCAGGACTTTCTTTTCATTGCTACGGAGAGGTACAAATTCTGTGTTCTGCAATGGGATGCAGAAAAGTCAGAGCTAATCACCAG

upper sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 3
-------------gtgagtatatatctctta--ttgtgttcttttgtcatggtcttaataatgagttaaa-atgttgatagtattgtccaccgtctttt---gtagGGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGTGTTCTTCAATGGGATCCTGAGTCCTCTGAGCTTATTACAAG
               |  ||  | | | ||   || |  |||  |||  | || ||| |  |   | |   || ||  | || ||||      |  |||     |||| ||||| || || | | | || ||||||||||| |||||||||||||||||||||||||||||| ||||  |  |||||||| ||||| |
gtgagaaaattaaaagcatacgtgttttttgagttattgtctactgttgtagttttattcttccataatgtattttttttgt-ttgtttgttttggtttcaaacagGGTGAAGCACAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGTGTTCTTCAATGGGATTCTGAAACTGCTGAGCTTGTTACACG

upper sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G13680.1 (Glycine max), 3'ss of exon 3
--gtgagtatatatctcttattgtgttcttttgtcatggtcttaataatg-agttaaaatgttgatagtattgtccaccgtcttttgt----------agGGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGTGTTCTTCAATGGGATCCTGAGTCCTCTGAGCTTATTACAAG
  | ||  ||  |    |  |||| || ||  || || |||| |||  || ||||      |  ||| | |  |      | |||| |          |||| |||||||| || | | | || ||||||||||| |||||||||||||||||||||||||||||| | ||| |   ||||||| ||||| |
gtgagaaaattcaagcatccttgt-tttttgagttattgtct-aatgttgtagttttttcttccataatgtaatttttttttttttttggtttcaaccagGGTGAAGCGCAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGTGTTCTTCAATGGGATTCCGAGACTGGTGAGCTTGTTACACG

upper sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 3'ss of exon 3
gtgagtatatatctcttattgtgt-------tcttttgtcatggtcttaataatgagttaaaatgttgatagtattgtccaccgtctt------ttgtagGGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGTGTTCTTCAATGGGATCCTGAGTCCTCTGAGCTTATTACAAG
|| |||||  ||||  |    | |       |   ||   |   |  |||| |||  ||  | || | ||| |||||    | || ||      |   |||||||||| ||||| ||| | ||||| |||||||| |||||||| || |||||||||||||||||| | |||   |||||| ||||||||||
gtaagtat-catcttgtgacatatagaaagcttacttagtagcattataatcatgcttttta-tgctaatactattgcttgctgttttggattctaacagGGCGAAGCACAAGATTTTCTATTCATCGCAACTGAAAGATACAAGTTTTGTGTTCTTCAATGGGATGCAGAGAATTCTGAGGTTATTACAAG

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|116455518|gb|EG498110.1|EG498110
EST:     ACGTTCCTATATATGGAAGAATCGCTACTCTGGAGTTGTTCCGACCCCAT                         GGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGT
genomic: ACGTTCCTATATATGGAAGAATCGCTACTCTGGAGTTGTTCCGACCCCATgtgagtatat ... tcttttgtagGGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGT
EST: gi|116382313|gb|EG424905.1|EG424905
EST:     ACGTTCCTATATATGGAAGAATCGCTACTCTGGAGTTGTTCCGACCCCAT                         GGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGT
genomic: ACGTTCCTATATATGGAAGAATCGCTACTCTGGAGTTGTTCCGACCCCATgtgagtatat ... tcttttgtagGGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGT
EST: gi|116382318|gb|EG424910.1|EG424910
EST:     ACGTTCCTATATATGGAAGAATCGCTACTCTGGAGTTGTTCCGACCCCAT                         GGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGT
genomic: ACGTTCCTATATATGGAAGAATCGCTACTCTGGAGTTGTTCCGACCCCATgtgagtatat ... tcttttgtagGGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGT
EST: gi|116382315|gb|EG424907.1|EG424907
EST:     ACGTTCCTATATATGGAAGAATCGCTACTCTGGAGTTGTTCCGACCCCAT                         GGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGT
genomic: ACGTTCCTATATATGGAAGAATCGCTACTCTGGAGTTGTTCCGACCCCATgtgagtatat ... tcttttgtagGGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catggtcttaataatgagttaaaatgttgatagtattgtccaccgtcttttgtagGGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGTGTTCTTCAATGGGATCCTGAGTCCTCTGAGCTTATTACAAG
                                          ccgtctttt  CT-rich tract
       ttaataatgagttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtatatatctcttattgtgttcttttgtcatggtcttaataatgagttaaaatgttgatagtattgtccaccgtcttttgtagGGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGTGTTCTTCAATGGGATCCTGAGTCCTCTGAGCTTATTACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT