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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATCAAGGAGTCTGATACTGGTTTAGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgtcatatttttgtagattttggtcgaagtgcttttaatattatgggtgttgctaatgatgactgtgtatttaacag

Basic information

species Glycine max
transcript GLYMA19G45140.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G45140.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os06g09290.2 (Oryza sativa), 5'ss of exon 3
GTATCAAGGAGTCTGATACTGGTTTAGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgtcatattt----------ttgtaga--ttttggtcgaagtgcttttaa-----tattatgggtgttgctaatgatgact-gtgtatttaacag-------------------
| || || |||||||| ||||| || ||| |||| ||||||||||| ||||| || ||||| || ||||||||||||||||| || || ||||| ||  ||          |    ||  |||||||   | ||| || ||     || | |   | || |   || |  ||  ||  ||  ||                     
GAATTAAAGAGTCTGACACTGGATTGGCTCCACCTAGCCAGTGGGACCTTGTATCCGATAAGCAGATGATGCAGGAGGAGCAACCCCTGCAGgtaatgcttgacgttcacctaactgactttttggttttattgcattcaaatgcatactgtcaatattccctgtgcttcctcatgccttctactaataagcgtccttctgcaag

upper sequence: GLYMA19G45140.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G181359_T01 (Zea mays), 5'ss of exon 3
GTATCAAGGAGTCTGATACTGGTTTAGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgt------------catatttttgtagattttggtcgaagt-gcttttaatattatgggt-gttgctaatgatgactgtgtatttaacag-----------------------------------------------------------------
|||| |||||||||||||| || || ||| |||| |||||||||||| | ||||| |||||||| |||||||| || || || ||  | || ||            | |  | ||||     || || ||  |  ||||||    | || ||  |  |  |  |||  ||  || ||   ||                                                                 
GTATAAAGGAGTCTGATACAGGGTTGGCTCCACCTAGCCAGTGGGATTTGGTTTCAGATAAACAGATGATGCAAGAAGAACAACCGTTACAAgtatattaaatgaccctgatattgtgttacttcgtagattttacttttacagctttgagttatgacctaccatgcatg-atagttggtagaaatctttttggtttcaattttacatgtgctagtgcattaataacttctctttctctttctgcag

upper sequence: GLYMA19G45140.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 5'ss of exon 3
GTATCAAGGAGTCTGATACTGGTTTAGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgtcatatttttgtagatt-ttggtcgaagtgc----ttttaatattatgggtgttgctaatgatgactgtgtatttaacag---
|||||||||| ||||||||||| |||||||||||||| ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||  | ||| |  |  || |||  | |  |      | ||||||| |||  | |    ||   || ||| || ||  | |    
GTATCAAGGAATCTGATACTGGCTTAGCTGCACCAAGTCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAGGAGCAGCCTCTTCAGgtggtttttcttgattttgttgaacaacatttactgtcttaatataatgtatatc-tgaagagtggctg-gttttggaaactag

upper sequence: GLYMA19G45140.1 (Glycine max), 5'ss of exon 3
lower sequence: EFJ13722 (Selaginella moellendorffii), 5'ss of exon 3
GTATCAAGGAGTCTGATACTGGTTTAGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgtcatatttttgtagattttggtcgaagtgcttttaatattatgggtgttgctaatgatgactgtgtatttaacag
| ||||||||||| || |||||| |||| || || |||||||||||||| || |||||||| ||||||||||| || |||||||| || || || |      || |||||||  ||   |  || ||  | || |   | |  || ||| |     ||  |||   ||
GGATCAAGGAGTCCGACACTGGTCTAGCAGCTCCTAGCCAGTGGGATCTGGTGTCTGATAAGCAAATGATGCAAGAAGAGCAGCCACTGCAAgtaag-----tg-agatttttttcttcgatctcttgcttttcttt-tttctctcatgtt-----tggttttggtag

upper sequence: GLYMA19G45140.1 (Glycine max), 5'ss of exon 3
lower sequence: EFJ29161 (Selaginella moellendorffii), 5'ss of exon 3
GTATCAAGGAGTCTGATACTGGTTTAGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgtcatatttttgtagattttggtcgaagtgcttttaatat-tatgggtgttgctaatgatgactgtgtatttaacag
| ||||||||||| || |||||| |||| || || |||||||||||||| || |||||||| ||||||||||| || |||||||| || || || |      | |   | || |    | |||||||   || | | ||| ||| ||                      
GGATCAAGGAGTCCGACACTGGTCTAGCAGCTCCTAGCCAGTGGGATCTGGTGTCTGATAAGCAAATGATGCAAGAAGAGCAGCCACTGCAAgtaagggagatttttttcttcgatctattgcttttctcatgttttggttttggtag---------------------

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|151411562|gb|EV281373.1|EV281373
EST:     GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAG                         GTAGCAAGGTGCACAAAGATCATAAATCCAAATTCAGAAGATGCCAAATAT
genomic: GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgtcatatttt ... tatttaacagGTAGCAAGGTGCACAAAGATCATAAATCCAAATTCAGAAGATGCCAAATAT
EST: gi|207714809|gb|GD695027.1|GD695027
EST:     GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAG                         GTAGCAAGGTGCACAAAGATCATAAATCCAAATTCAGAAGATGCCAAATAT
genomic: GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgtcatatttt ... tatttaacagGTAGCAAGGTGCACAAAGATCATAAATCCAAATTCAGAAGATGCCAAATAT
EST: gi|254338828|gb|GR847545.1|GR847545
EST:     GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAG                         GTAGCAAGGTGCACAAAGATCATAAATCCAAATTCAGAAGATGCCAAATAT
genomic: GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgtcatatttt ... tatttaacagGTAGCAAGGTGCACAAAGATCATAAATCCAAATTCAGAAGATGCCAAATAT
EST: gi|151410157|gb|EV279965.1|EV279965
EST:     GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAG                         GTAGCAAGGTGCACAAAGATCATAAATCCAAATTCAGAAGATGCCAAATAT
genomic: GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgtcatatttt ... tatttaacagGTAGCAAGGTGCACAAAGATCATAAATCCAAATTCAGAAGATGCCAAATAT
EST: gi|151406841|gb|EV276656.1|EV276656
EST:     GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAG                         GTAGCAAGGTGCACAAAGATCATAAATCCAAATTCAGAAGATGCCAAATAT
genomic: GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgtcatatttt ... tatttaacagGTAGCAAGGTGCACAAAGATCATAAATCCAAATTCAGAAGATGCCAAATAT
EST: gi|254320308|gb|GR831116.1|GR831116
EST:     GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAG                         GTAGCAAGGTGCACAAAGATCATAAATCCAAATTCAGAAGATGCCAAATAT
genomic: GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgtcatatttt ... tatttaacagGTAGCAAGGTGCACAAAGATCATAAATCCAAATTCAGAAGATGCCAAATAT
EST: gi|208225841|gb|GE021038.1|GE021038
EST:     CAAATGATGCAGGAGGAGCAGCCTCTTCAG                         GTAGCAAGGTGCACAAAGATCATAAATCCAAATTCAGAAGATGCCAAATAT
genomic: CAAATGATGCAGGAGGAGCAGCCTCTTCAGgtcatatttt ... tatttaacagGTAGCAAGGTGCACAAAGATCATAAATCCAAATTCAGAAGATGCCAAATAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATCAAGGAGTCTGATACTGGTTTAGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgtcatatttttgtagattttggtcgaagtgcttttaatattatgggtgttgctaatgatgactgtgtatttaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG