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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACACTTTATGATTCCGTGGTTTGAGAGGCCTGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGTAGTCGTGATCTACAGATGgtaaatacattttgctaagacttacatgtagtcacagagaaatggttttgttatcaaattcgtacaactgaaaaaaaaaaatctgaccttcatattgtat...

Basic information

species Glycine max
transcript GLYMA12G33520.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G33520.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os07g15880.1 (Oryza sativa), 5'ss of exon 2
ACACTTTATGATTCCGTGGTTTGAGAGGCCTGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGTAGTCGTGATCTACAGATGgtaaat--acattttgctaagacttacatgtagtcacagagaaatggttttgttatcaaattcgtacaactgaaaaaaaaaaatctgaccttcatattgtat-
 |||||||||||||| ||||||||||||||  | || |||||||||||||| || ||| |||| || |||||||| ||||| ||  | ||||| |||||||||  |   ||| ||  |||  ||    | |  ||   |  |  ||  | |  |    |  |  |     |  | | |    || |||  | |||  | ||| 
TCACTTTATGATTCCATGGTTTGAGAGGCCAATCATTTATGATGTCCGTGCTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATGgtacgtttgcatctttttaattctatattttcatcgttggaatgtgtgtatacttctcatctaatga---tagatatacttgatttgatttgcatgctctatt

upper sequence: GLYMA12G33520.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os03g62490.1 (Oryza sativa), 5'ss of exon 2
ACACTTTATGATTCCGTGGTTTGAGAGGCCTGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGTAGTCGTGATCTACAGATGgtaaatacattttgctaagacttacatgtagtcacagagaaatggttttgttatca-aattcgtacaactgaaaaaaaaaaatctgaccttcatattgtat
 ||||| ||||| |||||||| ||||||||  | ||||| |||||||| || || ||| | || || ||||| || ||||| || |||||||| ||||||||||| |   | | ||   ||||     |  | ||   |  |||   |||  || |  ||| |||  |   | ||    |  | |    |     |||   
TCACTTCATGATCCCGTGGTTCGAGAGGCCGATCATCTACGATGTCCGAGCCCGCCCCAACCTCGTCGAGAGCACTTCTGGAAGCCGTGATCTCCAGATGgtaaa-attctgtccttgcacttggggtttctgactaggtcatgtcgttgagatgatgatttgtagcatgtagaaggtgatttgttggttgtgatttgcga

upper sequence: GLYMA12G33520.1 (Glycine max), 5'ss of exon 3
lower sequence: AT2G20530.2 (Arabidopsis thaliana), 5'ss of exon 4
ACACTTTATGATTCCGTGGTTTGAGAGGCCTGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGTAGTCGTGATCTACAGATGgta----aatacattttg------ctaagacttacatgtagtcacagagaa-atggttttgttatcaaattcgtacaactgaaaaaaaaaaatctgaccttcatattgtat-
 ||| |||||||||| ||||| || |||||  | |||||||| || ||||||   ||  ||||||||||||| |||||||| || |||||||| |||||||||      | |||||        |||| ||| |   |||    |||      |||||||||  |   |     |  | | |    |     | ||   || | |   |   
TCACCTTATGATTCCATGGTTCGAAAGGCCAATCATCTATGACGTTCGTGCAAAGCCTTATCTAGTTGAGAGCACATCTGGGAGCCGTGATCTCCAGATGgtattccgcttcatttcatcacttctaatactaatgggtataatcaggtcgtgtggttttgtcgtgtgaactacatga-taagcttatgttgtgtggtatttaaacattcag

upper sequence: GLYMA12G33520.1 (Glycine max), 5'ss of exon 3
lower sequence: AT4G28510.1 (Arabidopsis thaliana), 5'ss of exon 3
ACACTTTATGATTCCGTGGTTTGAGAGGCCTGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGTAGTCGTGATCTACAGATGgtaaatacattttgctaagacttacatgtagtcacagagaaatg---gttttgttatca--aattcgtacaactgaaaaaaaaaaatc--tgaccttcatattgtat------------
|||| |||||||||| |||||||| ||||| || |||||||| || ||||| |||||  | || |||||||||||||| || || |||||||| |||||||||      || | ||    |  |  |  |||||    |   ||    ||| || |     || |||| |   | || |  | ||     | |  ||  | | || |            
ACACCTTATGATTCCTTGGTTTGAAAGGCCGGTCATCTATGACGTTCGTGCTCGACCTTACCTTGTTGAGAGTACATCCGGAAGCCGTGATCTTCAGATGgtactctgcttctactcct-cccattttcagtcattttgttttgtgaatttagtgaatgtgaagtcgttcgcttcaacatcataagctcttaagttttttgtggttttaaaactttcag

upper sequence: GLYMA12G33520.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv15s0048g02350.t01 (Vitis vinifera), 5'ss of exon 4
ACACTTTATGATTCCGTGGTTTGAGAGGCCTGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGTAGTCGTGATCTACAGATGgtaaatacattttgctaagacttacatgtagtcacagagaaatggttttgttatcaa--attcgtacaactgaaaaaaaaaaatctgaccttcatattgtat--
 ||| | ||||| || |||||||| ||||| ||||||||||||||||||||||| || ||||| || |||||||| || || || ||||| || |||||||||| ||   ||| |||   |||   | |||  | |  |   ||||| ||||    |  ||  || ||  |||  ||   | |  |  |    |  ||      
TCACCTGATGATCCCATGGTTTGAAAGGCCAGTTATCTATGATGTCCGTGCACGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATGgtaa-tattgttttctagttcttgt-tatag--aaaatgttgtggttatgttgctgatcatgtgttcaggtgatgaagtgagacatagctgcaactttcagact

upper sequence: GLYMA12G33520.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv19s0085g00730.t01 (Vitis vinifera), 5'ss of exon 4
ACACTTTATGATTCCGTGGTTTGAGAGGCCTGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGTAGTCGTGATCTACAGATGgtaaatacattttgctaagacttacatgtagtcacagagaaatggttttgttatcaa--attcgtacaactgaaaaaaaaaaatctgaccttcatattgtat---
 ||| | ||||| || |||||||| ||||| || ||||||||||||||| | || || ||||| || |||||||| || || || | ||| || |||||||||| |   |||| |||   |||   |||||  | |  |   || || |||| |  |  ||  ||     |||  ||   | |  |    | || |||  |    
TCACCTGATGATCCCATGGTTTGATAGGCCAGTCATCTATGATGTCCGTACGCGCCCTCATCTTGTGGAGAGTACTTCAGGGAGCCATGACCTCCAGATGgtaattttgtttt-ctagttcttgt-tgtag--aaaatgttgtgattatgttgttgatcatgtgtttgggtgatgaagtgagacatagt-tgcaaatttcagact

upper sequence: GLYMA12G33520.1 (Glycine max), 5'ss of exon 3
lower sequence: PP1S14_33V6.1 (Physcomitrella patens), 5'ss of exon 2
ACACTTTATGATTCCGTGGTTTGAGAGGCCTGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGTAGTCGTGATCTACAGATGgtaaa-tacattttgctaag--acttacatgtagtcacagagaaatggttttgtt-atcaaattcg--tacaactgaaaaaaaaaaatctgaccttcatattgtat-------------------------------------------------------------------------------------------
 || ||||||||||| |||||||| || ||||| || || |||||||||||||||||| |  | || || || ||||| || ||| | ||||| || |||||||  | | |||||  | |    | |     |||   |    | |  | | | | || |  || |  |   || |||   |   || | |  |||||  |  | |                                                                                           
GCATTTTATGATTCCCTGGTTTGACAGACCTGTGATATACGATGTCCGTGCACGACCCAACATTGTCGAAAGCACATCAGGAAGTAGGGATCTTCAAATGgtaagctgccttttgacatgtggttgaggctgagtggtaatttagtcctctgggtgattacgtttgagtgtgacggaattcatttaagcagttcttcaattcctttagaatttcgctggtagggatcttgccgcaggtgttgtagttgttcttggagttattctaataaagttaatctgcttcttcgttgtttacag

upper sequence: GLYMA12G33520.1 (Glycine max), 5'ss of exon 3
lower sequence: PP1S41_59V6.1 (Physcomitrella patens), 5'ss of exon 2
ACACTTTATGATTCCGTGGTTTGAGAGGCCTGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGTAGTCGTGATCTACAGATGgtaaatacattttgctaagacttacatgtagtcacagagaaatggttttgttatcaaattcgtacaactgaaaaaaaaaaatctgaccttcatattgtat-----------------------------------------------------------------------------------------------------
 || ||||||||||| ||||| || |||||||| || ||||||||||||||||||||  |  | || ||||| || || || ||| | ||||| || ||||||  |  |   |  | | |  ||| ||| |||  |  | |||  |  | | |   | ||  ||    ||| |  || |  |||        || |  ||                                                                                                     
GCATTTTATGATTCCCTGGTTCGACAGGCCTGTGATATATGATGTCCGTGCACGACCTAACATTGTCGAGAGCACGTCGGGGAGTAGGGATCTTCAAATGgtacgttgaa--tagtgatatgtacctgtggtcgaatggcaat--tcctttcagacagtttttatgtttgagatgaatagctctctttcaagtagttcatggaatcgtgtgtttttgttgaaggggtttttgtcggggatggtgttgtttgtttaggaattactgagattacgttttaccctgctgctgcaacgttaacag

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|20449070|gb|BQ253194.1|BQ253194
EST:     CACGACCCCATCTAGTTGAGAGTACATCTGGTAGTCGTGATCTACAGATG                         GTGAAAATTGGACTTCGAGTTCTTACTCGCCCTTTGCCCAACCAATTACCT
genomic: CACGACCCCATCTAGTTGAGAGTACATCTGGTAGTCGTGATCTACAGATGgtaaatacat ... tgttatacagGTGAAAATTGGACTTCGAGTTCTTACTCGCCCTTTGCCCAACCAATTACCT
EST: gi|254329670|gb|GR839223.1|GR839223
EST:     CACGACCCCATCTAGTTGAGAGTACATGTGGTAGTCGTGATCTACAGATG                         GTGAAAATTGGACTTCGAGTTCTTACTCGCCCTTTGCCCAACCAATTACCT
genomic: CACGACCCCATCTAGTTGAGAGTACATCTGGTAGTCGTGATCTACAGATGgtaaatacat ... tgttatacagGTGAAAATTGGACTTCGAGTTCTTACTCGCCCTTTGCCCAACCAATTACCT
EST: gi|192329319|gb|FK020238.1|FK020238
EST:     CACGACCCCATCTAGTTGAGAGTACATCTGGTAGTCGTGATCTACAGATG                         GTGAAAATTGGACTTCGAGTTCTTACTCGCCCTTTGTCCAACCAATTACCT
genomic: CACGACCCCATCTAGTTGAGAGTACATCTGGTAGTCGTGATCTACAGATGgtaaatacat ... tgttatacagGTGAAAATTGGACTTCGAGTTCTTACTCGCCCTTTGCCCAACCAATTACCT
EST: gi|151402542|gb|EV272355.1|EV272355
EST:     CACGACCCCATCTAGTTGAGAGTACATCTGGTAGTCGTGATCTACAGATG                         GTGAAAATTGGACTTCGAGTTCTTACTCGCCCTTTGCCCAACCAATTACCT
genomic: CACGACCCCATCTAGTTGAGAGTACATCTGGTAGTCGTGATCTACAGATGgtaaatacat ... tgttatacagGTGAAAATTGGACTTCGAGTTCTTACTCGCCCTTTGCCCAACCAATTACCT
EST: gi|298192023|gb|HO036105.1|HO036105
EST:     CACGACCCCATCTAGTTGAGAGTACATCTGGTAGTCGTGATCTACAGATG                         GTGAAAATTGGACTTCGAGTTCTTACTCGCCCTTTGCCCAACCAATTACCT
genomic: CACGACCCCATCTAGTTGAGAGTACATCTGGTAGTCGTGATCTACAGATGgtaaatacat ... tgttatacagGTGAAAATTGGACTTCGAGTTCTTACTCGCCCTTTGCCCAACCAATTACCT
EST: gi|192303429|gb|FG997459.1|FG997459
EST:     CACGACCCCATCTAGTTGAGAGTACATCTGGTAGTCGTGATCTACAGATG                         GTGAAAATTGGACTTCGAGTTCTTACTCGCCCTTTGCCCAACCAATTACCT
genomic: CACGACCCCATCTAGTTGAGAGTACATCTGGTAGTCGTGATCTACAGATGgtaaatacat ... tgttatacagGTGAAAATTGGACTTCGAGTTCTTACTCGCCCTTTGCCCAACCAATTACCT
EST: gi|151412668|gb|EV282480.1|EV282480
EST:     CACGACCCCATCTAGTTGAGAGTACATCTGGTAGTCGTGATCTACAGATG                         GTGAAAATTGGACTTCGAGTTCTTACTCGCCCTTTGCCCAACCAATTACCT
genomic: CACGACCCCATCTAGTTGAGAGTACATCTGGTAGTCGTGATCTACAGATGgtaaatacat ... tgttatacagGTGAAAATTGGACTTCGAGTTCTTACTCGCCCTTTGCCCAACCAATTACCT
EST: gi|151413130|gb|EV282938.1|EV282938
EST:     CACGACCCCATCTAGTTGAGAGTACATCTGGTAGTCGTGATCTACAGATG                         GTGAAAATTGGACTTCGAGTTCTTACTCGCCCTTTGCCCAACCAATTACCT
genomic: CACGACCCCATCTAGTTGAGAGTACATCTGGTAGTCGTGATCTACAGATGgtaaatacat ... tgttatacagGTGAAAATTGGACTTCGAGTTCTTACTCGCCCTTTGCCCAACCAATTACCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACACTTTATGATTCCGTGGTTTGAGAGGCCTGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGTAGTCGTGATCTACAGATGgtaaatacattttgctaagacttacatgtagtcacagagaaatggttttgttatcaaattcgtacaactgaaaaaaaaaaatctgaccttcatattgtat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaaaaa