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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCTGTCTGCAAAGACAAAGATTTTCTTTTCCACTGCAGTTTCAATGTGGGACGCTGATTTCTATGTCAAGGTGGATGATGATGTCCATGTCAATTTAGgtacatgctatctcaagatccttgatttctctcttgtttccttcccatttcttcctttaccaccttcctctatcccatttctcacccaaagatgcttaaatattctgacatgtgttgctttttag

Basic information

species Glycine max
transcript GLYMA04G43340.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G43340.2 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os09g27950.1 (Oryza sativa), 5'ss of exon 7
GAGCTGTCTGCAAAGACAAAGATTTTCTTTTCCACTGCAGTTTCAATGTGGGACGCTGATTTCTATGTCAAGGTGGATGATGATGTCCATGTCAATTTAGgtacatgctatctcaagatccttgatttctctcttgtttccttcccatttcttcctttaccaccttcctctatcccatttctcacccaaagatgcttaaatattctgacatgtgttgctttttag
||||| ||||||||||| ||||| |||||||||||||| ||  || | ||||| |||||||||||||||||||||||||||||||| ||||||||  | ||||     |||        | ||||  |   |      |  ||   |||   |  || ||           || |                                                  
GAGCTATCTGCAAAGACCAAGATATTCTTTTCCACTGCTGTGGCATTATGGGATGCTGATTTCTATGTCAAGGTGGATGATGATGTTCATGTCAACCTTGgtaagctttattatttagcctttgaccttgatgagagat--ttgttattcagtaattaactgatgggagtgatgcag------------------------------------------------

upper sequence: GLYMA04G43340.2 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os02g35870.1 (Oryza sativa), 5'ss of exon 7
GAGCTGTCTGCAAAGACAAAGATTTTCTTTTCCACTGCAGTTTCAATGTGGGACGCTGATTTCTATGTCAAGGTGGATGATGATGTCCATGTCAATTTAGgtacatgctatctcaagatccttgatttctctcttgtttccttcccatttcttcctttaccaccttcctctatcccatttctcacccaaagatgcttaaatattctgacatgtgttgctttttag
|| || || || ||||||||||||||||| || || ||||||   || ||||| ||||| || ||||| ||||| ||||||||||| ||||| || ||||||   |    | |     |  || |  |  |  |||    | |    ||     || ||  | |   ||  ||   |   |  | |                                       
GAACTCTCAGCTAAGACAAAGATTTTCTTCTCTACAGCAGTTGGTATTTGGGATGCTGACTTTTATGTGAAGGTTGATGATGATGTGCATGTGAACTTAGgtgggtatattttt----tttttcacgtgccgattgg---ccttatgttgaaatctataataacccacttcatgtgacaacataacag-------------------------------------

upper sequence: GLYMA04G43340.2 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G070708_T02 (Zea mays), 5'ss of exon 7
GAGCTGTCTGCAAAGACAAAGATTTTCTTTTCCACTGCAGTTTCAATGTGGGACGCTGATTTCTATGTCAAGGTGGATGATGATGTCCATGTCAATTTAGgtacatgctatctcaagatccttgatttctctcttgtttccttcccatttcttcctttaccaccttcctctatcccatttctcacccaaagatgcttaaatattctgacatgtgttgctttttag
|| || || || |||||||| || ||||| || ||||| |||   || ||||||||||| ||||| |||||||| ||||||||||| ||||| ||  ||||| | ||     ||     | |||||    |   |  |||||       |  || |||  | |  |  | | | |   | |   | ||    ||   ||| |                       
GAACTCTCAGCTAAGACAAAAATATTCTTCTCTACTGCTGTTGGCATCTGGGACGCTGACTTCTACGTCAAGGTCGATGATGATGTGCATGTAAACCTAGgtgcttggctcttc-----ctttgatg---caagtacttcctcttagaat--tcttttgactcggttttgtttactggtgcatgcaca----tgaccaaacag----------------------

upper sequence: GLYMA04G43340.2 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G133613_T01 (Zea mays), 5'ss of exon 7
GAGCTGTCTGCAAAGACAAAGATTTTCTTTTCCACTGCAGTTTCAATGTGGGACGCTGATTTCTATGTCAAGGTGGATGATGATGTCCATGTCAATTTAGgtacatgctatctcaagatccttgatttctctcttgtttcctt-cccatttcttcctttaccaccttcctctatcccatttctcacccaa---agatgcttaaatattctgacatgtgttgctttttag
 |||||||||| ||||| ||||  ||||| || ||||| ||  |  | |||||||| |||||||||||||||||||| || ||||| ||  | ||  |||||| |  |||  |   | ||| |   | |  ||  ||  |    | ||  ||      | |    ||| | ||    |      | ||     |||  | |  ||    | | |||||  |        
AAGCTGTCTGCGAAGACCAAGACATTCTTCTCAACTGCCGTGGCCTTATGGGACGCGGATTTCTATGTCAAGGTGGACGACGATGTTCACCTGAACCTAGgtaaa--ctacgt---gctcccttgctccgatccggtaacaaaacgcacctccaagagttcagtgttcgtttagagaagacagaaacctgtccagaaaccttcatggcgtaaaatgtgcag--------

upper sequence: GLYMA04G43340.2 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G013079_T01 (Zea mays), 5'ss of exon 7
GAGCTGTCTGCAAAGACAAAGATTTTCTTTTCCACTGCAGTTTCAATGTGGGACGCTGATTTCTATGTCAAGGTGGATGATGATGTCCATGTCAATTTAGgtacatgctatctcaagatccttgatttc-tctcttgtttccttcccatttcttcctttaccaccttcctctatcccatttctcacccaaagatgcttaaatattctgacatgtgttgctttttag
|| || || || |||||||| || ||||| || |||||  ||   || ||||| ||||| ||||| |||||||| ||||||||||| ||||| || |||||| | ||     ||   |  |   ||||    || | ||   || |  |||  |    |    | | | | |  || |                                                
GAACTCTCAGCTAAGACAAAAATATTCTTCTCTACTGCTCTTGGCATCTGGGATGCTGACTTCTACGTCAAGGTTGATGATGATGTGCATGTAAACTTAGgtgcttgtctcttccttagacacaattttacttcctcttgaatttcagttttgtttactggtgcatgcatatgaccaaacag--------------------------------------------

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|23052841|gb|BU577332.1|BU577332
EST:     GGACGCTGATTTCTATGTCAAGGTGGATGATGATGTCCATGTCAATTTAG                         GTGTCTTGGCAACAACCCT
genomic: GGACGCTGATTTCTATGTCAAGGTGGATGATGATGTCCATGTCAATTTAGgtacatgcta ... tgctttttagGTGTCTTGGCAACAACCCT
EST: gi|298180725|gb|HO022164.1|HO022164
EST:     GGACGCTGATTTCTATGTCAAGGTGGATGTTGATGTCCATGTCAATTTAG                         GTGTCTTGCCAACAACCCTTGCTCGTCATCGATCAAAACCCAGGGTCTACA
genomic: GGACGCTGATTTCTATGTCAAGGTGGATGATGATGTCCATGTCAATTTAGgtacatgcta ... tgctttttagGTGTCTTGGCAACAACCCTTGCTCGTCATCGATCAAAACCCAGGGTCTACA
EST: gi|8827480|gb|BE211210.1|BE211210
EST:     GGACGCTGATTTCTATGTCAAGGTGGATGATGATGTCCATGTCAATTTAG                         GTGTCTTGGCAACAACCCTTGCTCGTCATCGATCAAAACCCAGGGTCTACA
genomic: GGACGCTGATTTCTATGTCAAGGTGGATGATGATGTCCATGTCAATTTAGgtacatgcta ... tgctttttagGTGTCTTGGCAACAACCCTTGCTCGTCATCGATCAAAACCCAGGGTCTACA
EST: gi|151395197|gb|EV265068.1|EV265068
EST:     GGACGCTGATTTCTATGTCAAGGTGGATGATGATGTCCATGTCAATTTAC                         GTGTCTTGGCAACAACCCTTGCTCGTCATCGATCAAAACCCAGGGTCTACA
genomic: GGACGCTGATTTCTATGTCAAGGTGGATGATGATGTCCATGTCAATTTAGgtacatgcta ... tgctttttagGTGTCTTGGCAACAACCCTTGCTCGTCATCGATCAAAACCCAGGGTCTACA
EST: gi|51337140|gb|CO981006.1|CO981006
EST:     GATGATGATGTCCATGTCAATTTAG                         GTGTCTTGGCAACAACCCTTGCTCGTCATCGATCAAAACCCAGGGTCTACA
genomic: GATGATGATGTCCATGTCAATTTAGgtacatgcta ... tgctttttagGTGTCTTGGCAACAACCCTTGCTCGTCATCGATCAAAACCCAGGGTCTACA
EST: gi|151412778|gb|EV282590.1|EV282590
EST:     GGACGCTGATTTCTATGTCAAGGTGGATGATGATGTCCATGTCAATTTAG                         GTGTCTTGGCAACAACCCTTGCTCGTCATCGATCAAAACCCAGGGTCTACA
genomic: GGACGCTGATTTCTATGTCAAGGTGGATGATGATGTCCATGTCAATTTAGgtacatgcta ... tgctttttagGTGTCTTGGCAACAACCCTTGCTCGTCATCGATCAAAACCCAGGGTCTACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCTGTCTGCAAAGACAAAGATTTTCTTTTCCACTGCAGTTTCAATGTGGGACGCTGATTTCTATGTCAAGGTGGATGATGATGTCCATGTCAATTTAGgtacatgctatctcaagatccttgatttctctcttgtttccttcccatttcttcctttaccaccttcctctatcccatttctcacccaaagatgcttaaatattctgacatgtgttgctttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA