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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGAAGAGACAAGATCATGGAAGAAGTTAATTAATATTGCAGTTTCAGGTGCTGCAGGAATGATTTCTAACCATCTTCTCTTCAAAgtaagttaatcctttaagttactgttttataggataaggttaccaataattggtcttattttatgtatctttggttttccgggtgtgtag

Basic information

species Arabidopsis thaliana
transcript AT5G58330.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G58330.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA20G33380.1 (Glycine max), 5'ss of exon 3
GAAGAAGAGACAAGATCATGGAAGAAGTTAATTAATATTGCAGTTTCAGGTGCTGCAGGAATGATTTCTAACCATCTTCTCTTCAAAgtaagttaatcctttaagttactgttttataggataaggttaccaataattggtcttattttatgtatct-ttggttttccgggtgtgtag---------
||||||||||||||||| |||||||| |||||||| |||||||| ||||||||||| ||||||||| | |||||||| || ||||| || | |  ||  |  |  | | |      |  |  |  |   |  || |   || | |  |||| ||||| ||  |||  |   |   |           
GAAGAAGAGACAAGATCCTGGAAGAAATTAATTAACATTGCAGTCTCAGGTGCTGCTGGAATGATTGCAAACCATCTACTTTTCAAGgtgaatgtattttggatttaaataaaaagtgtgtcagtgaagcacattagaagtttcaacttatctatctcttaatttatctatttccttttattatatc

upper sequence: AT5G58330.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA10G34150.2 (Glycine max), 5'ss of exon 3
GAAGAAGAGACAAGATCATGGAAGAAGTTAATTAATATTGCAGTTTCAGGTGCTGCAGGAATGATTTCTAACCATCTTCTCTTCAAAgtaagttaatcct----ttaagttactgttttataggataaggttaccaataattggtcttattt---tatgtatctttggttttccgggtgtgtag---
||||||||||||||||| |||||||| |||||||| |||||||| ||||||||||| ||||||||| | || ||||| || ||||| || | |  ||  |    |||| | |   || | |  |  |||   |  |  ||||   ||||| |   | |  || | |   |||||   |   |     
GAAGAAGAGACAAGATCCTGGAAGAAATTAATTAACATTGCAGTCTCAGGTGCTGCTGGAATGATTGCAAATCATCTACTTTTCAAGgtgaatgcattttggatttaaataagaattgtgtcagtgaagcacattagaaattcaacttatctatctcttaatttatctatttccaattactttttat

upper sequence: AT5G58330.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv13s0019g05250.t01 (Vitis vinifera), 5'ss of exon 3
GAAGAAGAGACAAGATCATGGAAGAAGTTAATTAATATTGCAGTTTCAGGTGCTGCAGGAATGATTTCTAACCATCTTCTCTTCAAAgtaagttaatcctttaagttactgttttataggataaggttaccaataattggtcttattttatgt-----atct--ttggttttccgggtgtgtag-----
||||| || |||| ||| |||||||| |||||||| |||||||| || |||||||| || ||||| ||||| || || || |||||||||||  ||||  |  | |    |  | | |   |   ||||   ||| ||    || || | | |     ||||  |||  ||| |   | | | |     
GAAGAGGAAACAAAATCCTGGAAGAAATTAATTAACATTGCAGTCTCGGGTGCTGCTGGGATGATATCTAATCACCTGCTTTTCAAAgtaaggaaatc--tcgaatccaaggctcagaatcttctgttatttatatttttgtttcttctttctctgagatctgattgagttttctcttctctggattct

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|124948332|gb|EL024091.1|EL024091
EST:     TGCAGTTTCAGGTGCTGCAGGAATGATTTCTAACCATACTTCTCTTCAAA                         CTTGCTTCAGGGGAAGTAT
genomic: TGCAGTTTCAGGTGCTGCAGGAATGATTTCTAACCAT-CTTCTCTTCAAAgtaagttaat ... gggtgtgtagCTTGCTTCAGGGGAAGTAT
EST: gi|164233905|gb|ES052709.1|ES052709
EST:     CTAACCATCTTCTCTTCAAA                         CTTGCTTCAGGGGAAGTATTTGGTCCAGATCAACCCATTGCATTGAAACTG
genomic: CTAACCATCTTCTCTTCAAAgtaagttaat ... gggtgtgtagCTTGCTTCAGGGGAAGTATTTGGTCCAGATCAACCCATTGCATTGAAACTG
EST: gi|116454058|gb|EG496650.1|EG496650
EST:     TTGCAGTTTCAGGTGCTGCAGGAATGATTTCTAACCATCTTCTCTTCAAA                         CTTGCTTCAGGGGAAGTATTTGGTCCAGATCAACCCATTGCATTGAAACTG
genomic: TTGCAGTTTCAGGTGCTGCAGGAATGATTTCTAACCATCTTCTCTTCAAAgtaagttaat ... gggtgtgtagCTTGCTTCAGGGGAAGTATTTGGTCCAGATCAACCCATTGCATTGAAACTG
EST: gi|116468405|gb|EG510997.1|EG510997
EST:     ACGACGTCGCCTTTTCTCAACTCTTCGTCTCGGCTTCGTCTCTCTTCAAAATTGCACCTTTCAAACCACTTTCGCCATCTTCTTCTTCCACCTCTCCACACAACAACTCCCAACTCCAAAATCTCT
genomic: ACGACGTCGCCTTTTCTCAACTCTTCGTCTCGGCTTCGTCTCTCTTCAAAATTGCACCTTTCAAACCACTTTCGCCATCTTCTTCTTCCACCTCTCCACACAACAACTCCCAACTCCAAAATCTCT
EST: gi|125040866|gb|EL113135.1|EL113135
EST:     ATGATTTCTAACCATCTTCTCTTCAAA                         CTTGCTTCAGGGGAAGTATTTGGTCCAGATCAACCCATTGCATTGAAACTG
genomic: ATGATTTCTAACCATCTTCTCTTCAAAgtaagttaat ... gggtgtgtagCTTGCTTCAGGGGAAGTATTTGGTCCAGATCAACCCATTGCATTGAAACTG
EST: gi|125188852|gb|EL203806.1|EL203806
EST:     TGATTTCTAACCATCTTCTCTTCAAA                         CTTGCTTCAGGGGAAGTATTTGGTCCAGATCAACCCATTG
genomic: TGATTTCTAACCATCTTCTCTTCAAAgtaagttaat ... gggtgtgtagCTTGCTTCAGGGGAAGTATTTGGTCCAGATCAACCCATTG
EST: gi|124919736|gb|EH993474.1|EH993474
EST:     GGTGCTGCAGGAATGATTTCTAACCATCTTCTCTTCAAA                         CTTGCTTCAGGGGAAGTATTTGGTCCAGATCAACCCATTGCATTGAAACTG
genomic: GGTGCTGCAGGAATGATTTCTAACCATCTTCTCTTCAAAgtaagttaat ... gggtgtgtagCTTGCTTCAGGGGAAGTATTTGGTCCAGATCAACCCATTGCATTGAAACTG
EST: gi|116468461|gb|EG511053.1|EG511053
EST:     ACGACGTCGCCTTTTCTCAACTCTTCGTCTCGGCTTCGTCTCTCTTCAAAATTGCACCTTTCAAACCACTTTCGCCATCTTCTTCTTCCACCTCTCCACACAACAACTCCCAACTCCAAAATCTCT
genomic: ACGACGTCGCCTTTTCTCAACTCTTCGTCTCGGCTTCGTCTCTCTTCAAAATTGCACCTTTCAAACCACTTTCGCCATCTTCTTCTTCCACCTCTCCACACAACAACTCCCAACTCCAAAATCTCT
EST: gi|124957772|gb|EL032570.1|EL032570
EST:     TTGCAGTTTCAGGTGCTGCAGGAATGATTTCTAACCATCTTCTCTTCAAA                         CTTGCTTCAGGGGAAGTATTTG
genomic: TTGCAGTTTCAGGTGCTGCAGGAATGATTTCTAACCATCTTCTCTTCAAAgtaagttaat ... gggtgtgtagCTTGCTTCAGGGGAAGTATTTG
EST: gi|164050781|gb|ES006638.1|ES006638
EST:     CTAACCATCTTCTCTTCAAA                         CTTGCTTCAGGGGAAGTATTTGGTCCAGATCTAACCCATTGCATTGAAACT
genomic: CTAACCATCTTCTCTTCAAAgtaagttaat ... gggtgtgtagCTTGCTTCAGGGGAAGTATTTGGTCCAGATC-AACCCATTGCATTGAAACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGAAGAGACAAGATCATGGAAGAAGTTAATTAATATTGCAGTTTCAGGTGCTGCAGGAATGATTTCTAACCATCTTCTCTTCAAAgtaagttaatcctttaagttactgttttataggataaggttaccaataattggtcttattttatgtatctttggttttccgggtgtgtag

- - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG