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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgtcatatttttgtagattttgtttgaattgcttttaatatttatggatgttgctaatgatgattttaacag

Basic information

species Glycine max
transcript GLYMA03G42370.4
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G42370.2 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os06g09290.2 (Oryza sativa), 5'ss of exon 3
GTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgtcatatttt-tgtagattttgtttgaat--tgcttttaatatttatggatgt-tgctaatgatgattttaacag--------------------------------------
| || || |||||||| ||||| |||||| |||| ||||||||||| ||||| || ||||| || ||||||||||||||||| || || ||||| ||  ||   ||  |  |   |    |  || ||||| |   |    |||  | ||    ||  |                                              
GAATTAAAGAGTCTGACACTGGATTGGCTCCACCTAGCCAGTGGGACCTTGTATCCGATAAGCAGATGATGCAGGAGGAGCAACCCCTGCAGgtaatgcttgacgttcacctaactgactttttggttttattgcattcaaatgcatactgtcaatattccctgtgcttcctcatgccttctactaataagcgtccttctgcaag

upper sequence: GLYMA03G42370.2 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G181359_T01 (Zea mays), 5'ss of exon 3
GTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgtc---------------atatt-------tttgtagattttgtttgaattgcttttaatatttatggatgttgctaatgatgattttaacag---------------------------------------------------------------
|||| |||||||||||||| || |||||| |||| |||||||||||| | ||||| |||||||| |||||||| || || || ||  | || ||                |||||       || |||||||||  ||  |  ||||| | |  | |   |   |||  |||||  ||   | |                                                                
GTATAAAGGAGTCTGATACAGGGTTGGCTCCACCTAGCCAGTGGGATTTGGTTTCAGATAAACAGATGATGCAAGAAGAACAACCGTTACAAgtatattaaatgaccctgatattgtgttacttcgtagattttacttttacagctttgagttatgacctaccatgc--atgatagttggtagaaatctttttggtttcaattttacatgtgctagtgcattaataacttctctttctctttctgcag

upper sequence: GLYMA03G42370.2 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G110185_T01 (Zea mays), 5'ss of exon 3
GTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgtcatattt-ttgta---gattttgt----ttgaattgctttta-atatttatggatgttgctaatg---atgattttaacag--------------------------------------------------
| || |||||||||||||| ||  ||||| |||| |||||||||||| | ||||| ||||| || |||||||| || || || ||  | || || |||||   || |   ||| ||||     | | ||| ||||| |  |||  | ||| |  | | |   |  || ||    |                                                  
GGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAAgt-atattaactgaacctgatattgtgtcacttagttgtttttacagctttgagcatgatagttaggcacaaaatctttttggtttcagttttacatgtgccagcgcactataacttctctctctttctgcag

upper sequence: GLYMA03G42370.2 (Glycine max), 5'ss of exon 3
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 5'ss of exon 3
GTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgtcatatttttgtagattttgtttgaattgcttttaatatttatggatgttgctaatgatgattttaacag--------------
|||||||||| ||||||||||| || ||||||||||| ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||    ||||| | ||||||||| |||   | |||| | | |    ||  ||   ||    |   |  | |              
GTATCAAGGAATCTGATACTGGCTTAGCTGCACCAAGTCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAGGAGCAGCCTCTTCAGgtgg--tttttcttgattttgtt-gaacaacatttactgtcttaatataatgtatatctgaagagtggctggttttggaaactag

upper sequence: GLYMA03G42370.2 (Glycine max), 5'ss of exon 3
lower sequence: EFJ13722 (Selaginella moellendorffii), 5'ss of exon 3
GTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgtcatatttttgtagattttgtttgaattgcttttaatatttatggatgttgctaatgatgattttaacag
| ||||||||||| || |||||| | || || || |||||||||||||| || |||||||| ||||||||||| || |||||||| || || || |       ||    ||| |||        | |    ||| |   |  |   |    || ||||   ||
GGATCAAGGAGTCCGACACTGGTCTAGCAGCTCCTAGCCAGTGGGATCTGGTGTCTGATAAGCAAATGATGCAAGAAGAGCAGCCACTGCAAgtaa-------gtgagatttttttcttcgatctcttgcttttcttttttctctcatgtttggttttggtag

upper sequence: GLYMA03G42370.2 (Glycine max), 5'ss of exon 3
lower sequence: EFJ29161 (Selaginella moellendorffii), 5'ss of exon 3
GTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgtcatatttttgtagattttgtttgaattgcttttaatatttatggatgttgctaatgatgattttaacag
| ||||||||||| || |||||| | || || || |||||||||||||| || |||||||| ||||||||||| || |||||||| || || || |      | |   | ||   |  |||||||||   || | | | | ||| ||                
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|192301329|gb|FG990219.1|FG990219
EST:     GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAG                         GTAGCAAGGTGCACAAAGATCATAAACCCGAACTCAGAAGATGCCAAATAT
genomic: GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgtcatatttt ... attttaacagGTAGCAAGGTGCACAAAGATCATAAACCCGAACTCAGAAGATGCCAAATAT
EST: gi|213602675|gb|DB956611.1|DB956611
EST:     GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAG                         GTAGCAAGGTGCACAAAGATCATAAACCCGAACTCAGAAGATGCCAAATAT
genomic: GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgtcatatttt ... attttaacagGTAGCAAGGTGCACAAAGATCATAAACCCGAACTCAGAAGATGCCAAATAT
EST: gi|213589227|gb|DB957759.1|DB957759
EST:     GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAG                         GTAGCAAGGTGCACAAAGATCATAAACCCGAACTCAGAAGATGCCAAATAT
genomic: GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgtcatatttt ... attttaacagGTAGCAAGGTGCACAAAGATCATAAACCCGAACTCAGAAGATGCCAAATAT
EST: gi|151405667|gb|EV275481.1|EV275481
EST:     GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAG                         GTAGCAAGGTGCACAAAGATCATAAACCCGAACTCAGAAGATGCCAAATAT
genomic: GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgtcatatttt ... attttaacagGTAGCAAGGTGCACAAAGATCATAAACCCGAACTCAGAAGATGCCAAATAT
EST: gi|209702899|gb|BW667434.1|BW667434
EST:     GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAG                         GTAGCAAGGTGCACAAAGATCATAAACCCGAACTCAGAAGATGCCAAATAT
genomic: GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgtcatatttt ... attttaacagGTAGCAAGGTGCACAAAGATCATAAACCCGAACTCAGAAGATGCCAAATAT
EST: gi|208155594|gb|GD951999.1|GD951999
EST:     GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAG                         GTAGCAAGGTGCACAAAGATCATAAACCCGAACTCAGAAGATGCCAAATAT
genomic: GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgtcatatttt ... attttaacagGTAGCAAGGTGCACAAAGATCATAAACCCGAACTCAGAAGATGCCAAATAT
EST: gi|208228908|gb|GE024272.1|GE024272
EST:     GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAG                         GTAGCAAGGTGCACAAAGATCATAAACCCGAACTCAGAAGATGCCAAATAT
genomic: GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgtcatatttt ... attttaacagGTAGCAAGGTGCACAAAGATCATAAACCCGAACTCAGAAGATGCCAAATAT
EST: gi|208215664|gb|GE008516.1|GE008516
EST:     GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAG                         GTAGCAAGGTGCACAAAGATCATAAACCCGAACTCAGAAGATGCCAAATAT
genomic: GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgtcatatttt ... attttaacagGTAGCAAGGTGCACAAAGATCATAAACCCGAACTCAGAAGATGCCAAATAT
EST: gi|213600299|gb|DB970277.1|DB970277
EST:     GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAG                         GTAGCAAGGTGCACAAAGATCATAAACCCGAACTCAGAAGATGCCAAATAT
genomic: GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgtcatatttt ... attttaacagGTAGCAAGGTGCACAAAGATCATAAACCCGAACTCAGAAGATGCCAAATAT
EST: gi|208196800|gb|GE001032.1|GE001032
EST:     GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAG                         GTAGCAAGGTGCACAA-GATCATAAACCCGAACTCAGAAGATGCCAAATAT
genomic: GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgtcatatttt ... attttaacagGTAGCAAGGTGCACAAAGATCATAAACCCGAACTCAGAAGATGCCAAATAT
EST: gi|213611619|gb|DB969007.1|DB969007
EST:     GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAG                         GTAGCAAGGTGCACAAAGATCATAAACCCGAACTCAGAAGATGCCAAATAT
genomic: GGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgtcatatttt ... attttaacagGTAGCAAGGTGCACAAAGATCATAAACCCGAACTCAGAAGATGCCAAATAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAGgtcatatttttgtagattttgtttgaattgcttttaatatttatggatgttgctaatgatgattttaacag

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