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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttatctgttattcatgattggtgttttttcttctattattgtcactgctcttgcacctttgtttattcattgtgtcttcattttgagcagGTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATTATTCTGGACCGTAAATCTGCTGGACCG

Basic information

species Arabidopsis thaliana
transcript AT2G20420.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G20420.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 4
-------------gtttgttatctgttattcatgattggtgttttttcttctattattgtcactgctcttgcacctttgtttattcattgtgtcttcattttgagcagGTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATTATTCTGGACCGTAAATCTGCTGGACCG
                 || |    || || ||| |   ||||| | ||   || | ||  | |  ||  | ||     |  |||| |||  | |   |||||| ||||| ||||| ||||||||| ||||||| || ||||||||||||||  |||| |  || ||| | ||  ||||||| |||
tatctttcaaagcaagagtcacacttt-ttaatgctctatgtttctgctcaaatcactgaaaattgtcaagtac-----taaattcgttg-atttgtgttttga-cagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCG

upper sequence: AT2G20420.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 4
gtttgttatctgttattcatgattggtgttttttcttctat-tattgtcactgctcttgcacctttgtttattcattgt----gtcttcattttgagcagGTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATTATTCTGGACCGTAAATCTGCTGGACCG
   |  | | | || ||  || |   | |   | ||| ||| ||  |  |              ||| || ||   |||     | | ||||||   ||||||||||||||||| ||  ||||||| || ||||||||||||||| | || |  ||||| ||||    |||||| || 
tgctactttattttgtttttggtctctttcaatccttttatatagagatatacacaaaaaggggttggttgtttgatgttgaattttccattttttacagGTTTACTTGTGTGAAAAGCTGTCACTTGTAAATGAGATGTACTTTGCTATAACACTGGATCGTACGAGTGCTGGTCCA

upper sequence: AT2G20420.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G18730.1 (Glycine max), 3'ss of exon 4
gtttgttatctgttattcatgattggtgttttttcttctattattgtcactgctcttgcacct-----ttgtttatt---cattgtgtcttca-ttttgagcagGTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATTATTCTGGACCGTAAATCTGCTGGACCG
   || ||  |  | || ||  |  || |  ||   || |||  | |     |     ||        |||||| ||     |||  | |||| ||||   ||||||||||||||||| ||  ||||||| || ||||||||||||||| | || |  ||||| ||||    |||||| || 
---tgctactttgt-tttattttgagtatcattcaatccatttatataggaacatacacaaaaaggggttgtttgttggatgttgaattttcaattttatacagGTTTACTTGTGTGAAAAGCTGTCACTAGTAAATGAGATGTACTTTGCTATAACACTGGATCGTACGAGTGCTGGTCCA

upper sequence: AT2G20420.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv07s0005g03790.t01 (Vitis vinifera), 3'ss of exon 4
---gtttgttatctgttattcatgattggtgttttttcttctattattgtcactgctcttgcacct-ttgtttattcattgtgtcttcattt--tgagcagGTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATTATTCTGGACCGTAAATCTGCTGGACCG
   |||| | |||   |||     |      | ||||    |  || | | |||  | |        ||||||| | ||| | | || ||||  |  |||||||||||||||||| ||  ||||||| |||||||||||||||||| | || | |||||| |||  |||||| || || 
tttgtttataatcaactatcataaagaaacttgtttttaattgatact-tgactattgtgaaggaaattgtttagtgattttttatttatttattatgcagGTTTACTTGTGTGAAAAGATGTCACTTGTCAATGAGATGTACTTTGCTATCACTCTGGATCGTTCATCTGCGGGTCCA

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|116411794|gb|EG454386.1|EG454386
EST:     AAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCAAAGTAGTTAGCAAG                         GTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATT
genomic: AAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCAAAGTAGTTAGCAAGgtttgttatc ... ttttgagcagGTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATT
EST: gi|116476127|gb|EG518719.1|EG518719
EST:     AAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCAAAGTAGTTAGCAAG                         GTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATT
genomic: AAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCAAAGTAGTTAGCAAGgtttgttatc ... ttttgagcagGTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATT
EST: gi|86045986|gb|DR341741.1|DR341741
EST:     AAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCAAAGTAGTTAGCAAG                         GTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATT
genomic: AAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCAAAGTAGTTAGCAAGgtttgttatc ... ttttgagcagGTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATT
EST: gi|86045998|gb|DR341753.1|DR341753
EST:     AAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCAAAGTAGTTAGCAAG                         GTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATT
genomic: AAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCAAAGTAGTTAGCAAGgtttgttatc ... ttttgagcagGTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATT
EST: gi|86046005|gb|DR341760.1|DR341760
EST:     AAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCAAAGTAGTTAGCAAG                         GTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTT
genomic: AAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCAAAGTAGTTAGCAAGgtttgttatc ... ttttgagcagGTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTT
EST: gi|86045999|gb|DR341754.1|DR341754
EST:     AAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCAAAGTAGTTAGCAAG                         GTTTACTTGTGTGAGAAATTGTCAC
genomic: AAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCAAAGTAGTTAGCAAGgtttgttatc ... ttttgagcagGTTTACTTGTGTGAGAAATTGTCAC
EST: gi|86045991|gb|DR341746.1|DR341746
EST:     AAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCAAAGTAGTTAGCAAG                         GTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATT
genomic: AAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCAAAGTAGTTAGCAAGgtttgttatc ... ttttgagcagGTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATT
EST: gi|86045985|gb|DR341740.1|DR341740
EST:     AAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCAAAGTAGTTAGCAAG                         GTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATT
genomic: AAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCAAAGTAGTTAGCAAGgtttgttatc ... ttttgagcagGTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATT
EST: gi|86045989|gb|DR341744.1|DR341744
EST:     AAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCAAAGTAGTTAGCAAG                         GTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATT
genomic: AAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCAAAGTAGTTAGCAAGgtttgttatc ... ttttgagcagGTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATT
EST: gi|86045990|gb|DR341745.1|DR341745
EST:     AAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCAAAGTAGTTAGCAAG                         GTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATT
genomic: AAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCAAAGTAGTTAGCAAGgtttgttatc ... ttttgagcagGTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATT
EST: gi|116485864|gb|EG528456.1|EG528456
EST:     AAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCAAAGTAGTTAGCAAG                         GTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATT
genomic: AAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCAAAGTAGTTAGCAAGgtttgttatc ... ttttgagcagGTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattgtcactgctcttgcacctttgtttattcattgtgtcttcattttgagcagGTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATTATTCTGGACCGTAAATCTGCTGGACCG
                                       tcttcatttt  CT-rich tract
                      tttgtttattcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttatctgttattcatgattggtgttttttcttctattattgtcactgctcttgcacctttgtttattcattgtgtcttcattttgagcagGTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATTATTCTGGACCGTAAATCTGCTGGACCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA