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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGTCTCACATTTTTTGCTCCCAGTGAAGAGAGGCTTGAGTCTGGATTGTACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCTTGGGTGGAAGgtcagtggaacacaacatgcacagttaccttgtttgattttagattttgacatttgctagtcattcattcttatatcaacactactggcctactcttgag...

Basic information

species Glycine max
transcript GLYMA06G02200.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G02200.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os06g51029.1 (Oryza sativa), 5'ss of exon 3
GTGGTCTCACATTTTTTGCTCCCAGTGAAGAGAGGCTTGAGTCTGGATTGTACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCTTGGGTGGAAGgtcagtgg-aacacaacatgcacagttac---cttgtttgattttagattttgacatttgctagtcattcattcttatatcaacactactggcctactcttgag
|||| |||||||| |||||||| || || |||||||||||||||||||||||||| || || ||||| || || || ||||| || ||  | ||||||||||  ||   |    ||  | || |  | |   | |||   ||| | | | |  | | |    |    |     |||| ||       |                
GTGGACTCACATTCTTTGCTCCAAGCGAGGAGAGGCTTGAGTCTGGATTGTACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAGgtgggttttagtgaaatgttcatatctgcgtacatgtgctattgttgttgtgcaaagtcttgaactgtgtgagcttacatggtttgcag---------------

upper sequence: GLYMA06G02200.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G126361_T03 (Zea mays), 5'ss of exon 4
GTGGTCTCACATTTTTTGCTCCCAGTGAAGAGAGGCTTGAGTCTGGATTGTACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCTTGGGTGGAAGgtcagtggaacacaacatgcacagttaccttgtttgattttagattttgacatt-tgc-tagtcattcattcttatatcaacactactggcctactcttgag
|||| |||||||| |||||||| || ||||| ||||| || |||||||||||||| || || || ||||| || || |||||||| ||| | ||||| ||||          |  ||| | | |||   || |      ||   | |||    |  || || | ||  | | | | ||  |  ||  |||  | ||   |  
GTGGACTCACATTCTTTGCTCCAAGCGAAGAAAGGCTAGAATCTGGATTGTACAGCAGGAGCTATCTTGAGAACCAAATGGCTGTAGCCCTTGGTGGCAGgtgctct---ttctgcatactctgttcatttctgcatcattgactgttgctgctgcgcatattgatggactgtgagatgtaatcttatggtttgctgcag--

upper sequence: GLYMA06G02200.1 (Glycine max), 5'ss of exon 3
lower sequence: AT1G50250.1 (Arabidopsis thaliana), 5'ss of exon 3
GTGGTCTCACATTTTTTGCTCCCAGTGAAGAGAGGCTTGAGTCTGGATTGTACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCTTGGGTGGAAGgtcagtggaacacaacatgcaca----gttaccttgtttgattttagattttgacatttgctagtcattcattcttatatcaacactactggcctactcttgag--------
|||| ||||| ||||||||||| || ||||| || ||||||||||||||||||||||| || |||||||| ||||| |||||||||||  | || ||||||| |||     |   | | |||     || ||         | || || | | |||       ||       | ||| | || | |||      |  | |||          
GTGGGCTCACTTTTTTTGCTCCAAGCGAAGAAAGACTTGAGTCTGGATTGTACAGTAGGAGCTACCTTGAGAATCAAATGGCTGTTGCACTTGGCGGAAGgttagttagtaatggcctccacgcctcgtcacaaaagccagtctttgaatat-acagagaagggtttaattatgttaaaccatctctatctctgttgtgttggctatgtcag

upper sequence: GLYMA06G02200.1 (Glycine max), 5'ss of exon 3
lower sequence: AT5G42270.1 (Arabidopsis thaliana), 5'ss of exon 3
GTGGTCTCACATTTTTTGCTCCCAGTGAAGAGAGGCTTGAGTCTGGATTGTACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCTTGGGTGGAAGgtcagtggaacacaacatgcacagttaccttgtttgattttagattttgacatttgctagtcattcattcttatatcaacactactggcctactcttgag
|||| ||||| ||||| ||||| || ||||||||||| ||||| |||||||| || ||||| |||||||| || || |||||||||||  | |||||||||| |||  |  ||   |     | |    ||| || |    ||   |   |   || ||  || |  || || | |   |||   |||            
GTGGGCTCACCTTTTTCGCTCCTAGCGAAGAGAGGCTAGAGTCCGGATTGTATAGCAGAAGCTACCTTGAGAACCAAATGGCTGTTGCACTTGGTGGAAGgt-agtttacaactgaaactgtactggttttgatttacaagagtagtcttcgagtgttaaacaatgtttattgtgttt-cacctatggtag---------

upper sequence: GLYMA06G02200.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv18s0001g00190.t01 (Vitis vinifera), 5'ss of exon 3
GTGGTCTCACATTTTTTGCTCCCAGTGAAGAGAGGCTTGAGTCTGGATTGTACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCTTGGGTGGAAGgtcagtgg---aacacaacatgcacagttacc----ttgtttgattttagattttgacatttgctagtcattcattcttatatcaacactactggcctactcttgag
||||||| || ||||||||||| ||||||||||| || ||||||||| ||||||||||||||||||| || |||||||||||||||||  |||||||||||| ||| |   ||  | |  | ||      |     | |||   || ||| |  |    | |  ||   |  || | || |   ||   ||   ||  |        
GTGGTCTTACCTTTTTTGCTCCAAGTGAAGAGAGACTCGAGTCTGGACTGTACAGTAGAAGTTACCTGGAGAATCAGATGGCTGTTGCACTGGGTGGAAGgttagttgcttaatcccatctccaggaccccacaggtggttgtgttatagttcgtagtgtcttttaagaaggcaattttgtgagaatcatatctgcagat-------

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|193571542|gb|FK532773.1|FK532773
EST:     CTGTGTGCCTTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: CTGT-TGCCTTGGGTGGAAGgtcagtggaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|17962858|gb|BM269614.1|BM269614
EST:     TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCTTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCTTGGGTGGAAGgtcagtggaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|151405829|gb|EV275644.1|EV275644
EST:     TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCTTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCTTGGGTGGAAGgtcagtggaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|192314907|gb|FK010725.1|FK010725
EST:     TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCTTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCTTGGGTGGAAGgtcagtggaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|151393635|gb|EV263510.1|EV263510
EST:     TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCTTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCTTGGGTGGAAGgtcagtggaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|151401015|gb|EV270829.1|EV270829
EST:     TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCTTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCTTGGGTGGAAGgtcagtggaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|20811366|gb|BQ295844.1|BQ295844
EST:     TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCTTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCTTGGGTGGAAGgtcagtggaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|209729428|gb|BW663689.1|BW663689
EST:     TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCTTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCTTGGGTGGAAGgtcagtggaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
EST: gi|209701415|gb|BW667316.1|BW667316
EST:     TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCTTGGGTGGAAG                         GGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC
genomic: TACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCTTGGGTGGAAGgtcagtggaa ... ggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGTCTCACATTTTTTGCTCCCAGTGAAGAGAGGCTTGAGTCTGGATTGTACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCTTGGGTGGAAGgtcagtggaacacaacatgcacagttaccttgtttgattttagattttgacatttgctagtcattcattcttatatcaacactactggcctactcttgag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG