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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaatgtttttgcttatagatacataaatggttagttacagttaccttatatatttgcctttgacttcgccggagctcataatattaactttatttctagGCACTTTCCACCAAATCAGCTTTTCAGAGGCATAAGCAGTGGCTGCAACATGCTAAAACACGTAGTGCAAGACATAAAATAATGAAG

Basic information

species Glycine max
transcript GLYMA03G37450.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G37450.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os03g22160.1 (Oryza sativa), 3'ss of exon 19
aaaatgtttttgcttatagatacataaatggttagtt-acagttaccttatatatt-tgcctttgac-ttcgccggagctcataatattaactttatttctagGCACTTTCCACCAAATCAGCTTTTCAGAGGCATAAGCAGTGGCTGCAACATGCTAAAACACGTAGTGCAAGACATAAAATAATGAAG
    | | |      | ||     || |    || |  |  |  |     |||||| | ||| |||| | |     | |||||     |    || |||| ||  | | ||  | ||||  || || ||| | ||  |||||||||| |||||||| ||||| || ||||||||||| ||||| ||||| 
--cttttatccatcaagaggattctagagaactattccattggcattgcttatattatacctgtgacatccatttaaactcatctgccttttcttgtttc-agAAATTATCTGCTAAATATGCATTCCAGCGTCACCAGCAGTGGCTTCAACATGCGAAAACTCGCAGTGCAAGACACAAAATTATGAAA

upper sequence: GLYMA03G37450.1 (Glycine max), 3'ss of exon 21
lower sequence: AT4G02260.3 (Arabidopsis thaliana), 3'ss of exon 19
------------------------------aaaatgtttttgcttatagatacataaat--ggttagttacagttaccttatatatttgcctttgacttcgccggagctcataatattaactttatttc-tagGCACTTTCCACCAAATCAGCTTTTCAGAGGCATAAGCAGTGGCTGCAACATGCTAAAACACGTAGTGCAAGACATAAAATAATGAAG
                              ||| |  |     || |   |       |  ||  | ||    || ||||    || | ||   | ||     |    |  || |||||   | |  ||  |||| || || |  ||||| ||||| || || ||||| |||||| |||||||||| |||||| | ||||||||||| || || |||| |
gtttgtacctttttcccttgcttttgttttaaatttctcccttttcttcttgtcctgcttaggaaaattttgattgccttcatcatgttccacgggctctcatg----ttttattattattgtcacatcacagGCCCTCTCAAGTAAATCTGCTTTCCAAAGACATAAACAGTGGTTGCAACATGCCAAAACAAGGAGTGCAAGACACAAGATTATGAGG

upper sequence: GLYMA03G37450.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv07s0005g00770.t01 (Vitis vinifera), 3'ss of exon 19
aaaatgtttttgcttatagatacataaatggttagttacagttaccttatatatttgcctttgacttcgccggagctcataatattaa--ctttattt--ctagGCACTTTCCACCAAATCAGCTTTTCAGAGGCATAAGCAGTGGCTGCAACATGCTAAAACACGTAGTGCAAGACATAAAATAATGAAG
     |||  ||||| |  |  | ||  | | |   |     |   | || | ||| || |   | ||  |  | |   |  |  |    | || |||  | ||||||| || | |||||| ||||| |||||||||||||||||| | |||||||| ||||| ||||||||  | || || || ||||| 
---tggttgctgcttctgaa-gcttactttgctgcatctgcatggatcatctgtttaccatatgcatcttccaatcatttgttgctgggtccttgttttaccagGCACTCTCAAGCAAATCTGCTTTCCAGAGGCATAAGCAGTGGTTACAACATGCAAAAACCCGTAGTGCCCGGCACAAGATCATGAAA

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|151406442|gb|EV276257.1|EV276257
EST:     CCGCTCATGTACTTGCAAATGCAGAAGTTGTGGAGATAATCACATATAAT                         GCACTTTCCACCAAATCAGCTTTTCAGAGGCATAAGCAGTGGCTGCAACAT
genomic: CCGCTCATGTACTTGCAAATGCAGAAGTTGTGGAGATAATCACATATAATgtcagtattg ... ttatttctagGCACTTTCCACCAAATCAGCTTTTCAGAGGCATAAGCAGTGGCTGCAACAT
EST: gi|120496652|gb|EH224819.1|EH224819
EST:     CCGCTCATGTACTTGCAAATGCAGAAGTTGTGGAGATAATCACATATAAT                         GCACTTTCCACCAAATCAGCTTTTCAGAGGCATAAGCAGTGGCTGCAACAT
genomic: CCGCTCATGTACTTGCAAATGCAGAAGTTGTGGAGATAATCACATATAATgtcagtattg ... ttatttctagGCACTTTCCACCAAATCAGCTTTTCAGAGGCATAAGCAGTGGCTGCAACAT
EST: gi|151402145|gb|EV271958.1|EV271958
EST:     CCGCTCATGTACTTGCAAATGCAGAAGTTGTGGAGATAATCACATATAAT                         GCACTTTCCACCAAATCAGCTTTTCAGAGGCATAAGCAGTGGCTGCAACAT
genomic: CCGCTCATGTACTTGCAAATGCAGAAGTTGTGGAGATAATCACATATAATgtcagtattg ... ttatttctagGCACTTTCCACCAAATCAGCTTTTCAGAGGCATAAGCAGTGGCTGCAACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttatatatttgcctttgacttcgccggagctcataatattaactttatttctagGCACTTTCCACCAAATCAGCTTTTCAGAGGCATAAGCAGTGGCTGCAACATGCTAAAACACGTAGTGCAAGACATAAAATAATGAAG
                                     tattaac  putative branch site (score: 1)
                                           ctttatttct  CT-rich tract
                               tcataatattaacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaatgtttttgcttatagatacataaatggttagttacagttaccttatatatttgcctttgacttcgccggagctcataatattaactttatttctagGCACTTTCCACCAAATCAGCTTTTCAGAGGCATAAGCAGTGGCTGCAACATGCTAAAACACGTAGTGCAAGACATAAAATAATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - tgcttat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttcgcc