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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTGAGCTCTTGGGTGTGGATACTGCTGATGTTGACATTATGATGGGAACATTCACCAAATCTTTTGGATCCTGTGGAGGTTACATTGCAGGATCGAAGgtacttttgttaaattttagactccaaatttagtgtttaactgaggcagtatgttgctaaaatctgtcagagtaggtgttcagattttctttcctattga...

Basic information

species Glycine max
transcript GLYMA02G07250.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G07250.1 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os01g70370.1 (Oryza sativa), 5'ss of exon 8
TTGTGAGCTCTTGGGTGTGGATACTGCTGATGTTGACATTATGATGGGAACATTCACCAAATCTTTTGGATCCTGTGGAGGTTACATTGCAGGATCGAAGgtacttttgttaaattttagactccaaatttagtgtttaactg-aggcagtatgttgctaaaatctgtcagagtaggtgttcagattttctttcctattga
||||||  |  | || |||||  | || |||||||| ||||||||||||||||| || ||||| |||||||| ||||||||||||||||||| ||| || |||    ||    || |||   | | | ||   ||   ||||  || | |||  ||  | ||||||| |  |     |  ||    ||| |          
TTGTGAATTACTTGGAGTGGACCCAGCGGATGTTGATATTATGATGGGAACATTTACTAAATCATTTGGATCTTGTGGAGGTTACATTGCAGCATCAAAAgta----tgaagcatattaacgtactatttagatgaacaactttagtctgtagatt--ttaaatctgacccatggattactctatgtttatcag-------

upper sequence: GLYMA02G07250.1 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os01g70380.1 (Oryza sativa), 5'ss of exon 8
TTGTGAGCTCTTGGGTGTGGATACTGCTGATGTTGACATTATGATGGGAACATTCACCAAATCTTTTGGATCCTGTGGAGGTTACATTGCAGGATCGAAGgtacttttgttaaattttagactccaaatttagtgtttaactgag-gcagtatgttgctaaaatctgtcagagtaggtgttcagattttctttcctattga
|||||||||  | ||||||||| | |||||||| || ||||||||||||||||| || ||||| |||||||| || |||||||||||||||| ||| || |||      | ||     |   | ||  |    |  ||  |||||  | ||| |||| ||||      ||  |    || |  | || ||           
TTGTGAGCTACTAGGTGTGGATCCAGCTGATGTCGATATTATGATGGGAACATTTACTAAATCATTTGGATCATGCGGAGGTTACATTGCAGCATCAAAAgta------tgaag----aagattcacttgctatacttggctgagcactgta-gttgataaatctgaccatggattatgctgtgtttatcag---------

upper sequence: GLYMA02G07250.1 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os01g70360.1 (Oryza sativa), 5'ss of exon 8
TTGTGAGCTCTTGGGTGTGGATACTGCTGATGTTGACATTATGATGGGAACATTCACCAAATCTTTTGGATCCTGTGGAGGTTACATTGCAGGATCGAAGgtac--ttttgttaaattttagactccaaatttagtgtttaactgaggcagtatgttgctaaaatctgtcagagtaggtgttcagatt-ttctttcctattga----
 ||||||||  | || |||||| | |||||||||||||| |||||||| ||| || | || || ||||||||  |||||||||||||||||| ||| || |||    ||  ||||     ||| ||       |||  ||  |||||     |      |  |   |   | |   | |  |  |||| || |||| | || |    
GTGTGAGCTACTAGGAGTGGATCCGGCTGATGTTGACATCATGATGGGCACACTCTCAAAGTCATTTGGATCGAGTGGAGGTTACATTGCAGCATCAAAAgtatgaattaattaagc---agattcacttaccagttcttgtctgagaagacaaaagagttga---taataaaactgatccttggattattttttcatgtttaccag

upper sequence: GLYMA02G07250.1 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os11g31640.1 (Oryza sativa), 5'ss of exon 8
TTGTGAGCTCTTGGGTGTGGATACTGCTGATGTTGACATTATGATGGGAACATTCACCAAATCTTTTGGATCCTGTGGAGGTTACATTGCAGGATCGAAGgtacttttgttaaa------ttttagactccaaatttagtgtttaactgaggcagtatgttgctaaaatctgtcagagtaggtgttcagattttctttcctattga
|||||||||| | || || ||| | |||||||| ||||| |||||||| || ||||| || || |||||||| ||||| || || ||||||| ||||||||||| | |    |       ||| ||   |   | ||     || |||||  ||     |||||  || || ||||                              
TTGTGAGCTCCTTGGGGTTGATCCAGCTGATGTGGACATAATGATGGGCACTTTCACTAAGTCATTTGGATCATGTGGTGGATATATTGCAGCATCGAAGgtacatcttcagagcacttctttcagttgcttgaattgaaaatttactgattcacc---ttgcttgaa-ctctcag------------------------------

upper sequence: GLYMA02G07250.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G010202_T01 (Zea mays), 5'ss of exon 8
TTGTGAGCTCTTGGGTGTGGATACTGCTGATGTTGACATTATGATGGGAACATTCACCAAATCTTTTGGATCCTGTGGAGGTTACATTGCAGGATCGAAGgtacttttgttaaattttagactccaaatttagtgtttaactgaggcagtatgttgctaaaatctgtcagagtaggtgttcagattttctttcctattga
|||||||||  | || |||||| | ||||||||||||||||||||||| |||||||| ||||| |||||||| ||||||||||||||||||| ||| || |||    |||  | |     |||      ||  ||  | | |        | ||||  ||| |||| |  |  |  ||||||  ||||            
TTGTGAGCTGCTCGGAGTGGATCCAGCTGATGTTGACATTATGATGGGTACATTCACAAAATCATTTGGATCATGTGGAGGTTACATTGCAGCATCAAATgtaagcgtgtatagtc----acttagctgttgttgactgaatacattttgaagttgacaaa-tctgacccaccaaatgttcattttttag----------

upper sequence: GLYMA02G07250.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G142030_T01 (Zea mays), 5'ss of exon 8
TTGTGAGCTCTTGGGTGTGGATACTGCTGATGTTGACATTATGATGGGAACATTCACCAAATCTTTTGGATCCTGTGGAGGTTACATTGCAGGATCGAAGgtacttttgttaaattttagactccaaatttagtgtttaactgaggcagtatgttgctaaaatctgtcagagtaggtgttcagattttctttcctattga--------
|||||| ||| | || || ||  | |||||||| || || |||||||| || |||||||| ||||||||||| ||||| || || ||||| | ||| ||||||| |       | |   ||   | |   || |    |||||  ||| | |||    || | |    |||  || |   | | ||   ||| ||||  |        
TTGTGAACTCCTTGGGGTTGACCCAGCTGATGTAGATATAATGATGGGTACTTTCACCAAGTCTTTTGGATCATGTGGTGGATATATTGCCGCATCAAAGgtacat-------actactgaaagcgatcatattac--aactgtagcactttgt----aagaccgagtaga--agattgaccggttccttttactatataactttcag

upper sequence: GLYMA02G07250.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G067257_T01 (Zea mays), 5'ss of exon 10
-----------------------------------------------------TTGTGAGCTCTTGGGTGTGGATACTGCTGATGTTGACATTATGATGGGAACATTCACCAAATCTTTTGGATCCTGTGGAGGTTACATTGCAGGATCGAAGgtactt-ttgttaaattttagactccaaatttagtgtttaactgaggcagtatgttgctaaaatctgtcagagtaggtgttcagattttctttcctattga
                                                     |||||||||| | || || ||    |||||||| ||||| |||||||| || || ||||| ||||||||||| ||||| || || ||||| | ||| ||||||| |  |  | ||  |  ||||  |  |  | |||   |||  |  ||                                                   
TATCTGGATGAGGCCCATAGCATTGGTGCTGTTGGGCAGTCTGGCCGCGGTGTTTGTGAGCTCCTTGGGGTTGACCTAGCTGATGTAGACATAATGATGGgtacttttaccaagtcttttggatcatgtggtggatatattgctgcatcaaaggtacatactactgaaagt--gactgtat-tacactgtagcacttggtaag---------------------------------------------------

upper sequence: GLYMA02G07250.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G357734_T03 (Zea mays), 5'ss of exon 14
-----------------------------------------------------TTGTGAGCTCTTGGGTGTGGATACTGCTGATGTTGACATTATGATGGGAACATTCACCAAATCTTTTGGATCCTGTGGAGGTTACATTGCAGGATCGAAGgtactt-ttgttaaattttagactccaaatttagtgtttaactgaggcagtatgttgctaaaatctgtcagagtaggtgttcagattttctttcctattga
                                                     |||||||||| | || || ||    |||||||| ||||| |||||||| || || ||||| ||||||||||| ||||| || || ||||| | ||| ||||||| |  |  | ||  |  ||||  |  |  | |||   |||  |  ||                                                   
TATCTGGATGAGGCCCATAGCATTGGTGCTGTTGGGCAGTCTGGCCGCGGTGTTTGTGAGCTCCTTGGGGTTGACCTAGCTGATGTAGACATAATGATGGgtacttttaccaagtcttttggatcatgtggtggatatattgccgcatcaaaggtacatactactgaaagt--gactgtat-tacactgtagcacttggtaag---------------------------------------------------

upper sequence: GLYMA02G07250.1 (Glycine max), 5'ss of exon 8
lower sequence: AT3G48780.1 (Arabidopsis thaliana), 5'ss of exon 8
TTGTGAGCTCTTGGGTGTGGATACTGCTGATGTTGACATTATGATGGGAACATTCACCAAATCTTTTGGATCCTGTGGAGGTTACATTGCAGGATCGAAGgt----acttttgttaaattttagactcca--aatttagtgtttaactgaggcagtatgttgctaaaatctgtcagagtaggtgttcagattttctttcctattga
|||||| ||| | || || || ||| ||||||| ||||| ||||||||||| ||||| ||||||||||| || ||||| || || ||||| ||||| |||||    | |||| |     ||| |  |  |   || |  |||||   |      ||   ||  | || | ||  | |  ||   || |   ||||      |    
TTGTGAACTCCTTGGAGTTGACACTTCTGATGTGGACATAATGATGGGAACTTTCACGAAATCTTTTGGGTCTTGTGGTGGCTATATTGCGGGATCAAAGgttggcaattttatacttcttttgcatttactgatcttttgtttgcattccttggt---ttatttaattttggtaaatcagaatttgaacctttcagaaaaac---

upper sequence: GLYMA02G07250.1 (Glycine max), 5'ss of exon 8
lower sequence: AT5G23670.2 (Arabidopsis thaliana), 5'ss of exon 8
TTGTGAGCTCTTGGGTGTGGATACTGCTGATGTTGACATTATGATGGGAACATTCACCAAATCTTTTGGATCCTGTGGAGGTTACATTGCAGGATCGAAGgtacttttgttaaattttagactccaaatttagtgtttaactgaggcagtatgttgctaaaatctgtcagagtaggtgttcagattttctttcctattga---
|||||| ||| |||| || || || |||||||| ||| | ||||||||||| ||||| ||||||||||| || ||||| || || ||||| ||||| |||||       |   |  || |  |  |  |||| || |      |  |    ||  |      | ||  | |  | || |      |||   |     | |   
TTGTGAACTCCTGGGAGTTGACACAGCTGATGTGGACGTAATGATGGGAACCTTCACAAAATCTTTTGGGTCTTGTGGTGGCTATATTGCTGGATCTAAGgttagaaaatgctacatttgttttta--tttactgatcttgcaaatctcc-tgcagtcttgttttggtaaatcaagtttctgaccttttagtttagctcaaaa

upper sequence: GLYMA02G07250.1 (Glycine max), 5'ss of exon 8
lower sequence: Vv14s0068g01300.t01 (Vitis vinifera), 5'ss of exon 8
TTGTGAGCTCTTGGGTGTGGATACTGCTGATGTTGACATTATGATGGGAACATTCACCAAATCTTTTGGATCCTGTGGAGGTTACATTGCAGGATCGAAGgtacttttgttaaattttagactccaaatt-tagtgtttaactgaggcagtatgttgctaaaatctgtcagagtaggtgttcagattttctttcctattga
|||||||||||| || |||||| |||||||||| || ||  ||||||||||||| || ||||| |||||||| ||||| || || ||||||||||| |||||   ||| |  || |     |     | | |  | | ||  |       ||| |     |  | |||  | ||  ||||  | |    |  |  | |   
TTGTGAGCTCTTAGGAGTGGATCCTGCTGATGTGGATATCCTGATGGGAACATTTACTAAATCATTTGGATCATGTGGTGGCTATATTGCAGGATCAAAGgtttgtttttgcaactgccctcagttgactgtgatatatatatatatatatatat-atatatgtgtgtgtgggtgtgtgtggaaaaaggcaatattctaag

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|21677293|gb|BQ629644.1|BQ629644
EST:     GCAGGATCGAAG                         GACCTTATCCAACACTTGAAGTACGCTTGCCCTGCTCATCTTTATGCAACT
genomic: GCAGGATCGAAGgtacttttgt ... ctactgtcagGACCTTATCCAACACTTGAAGTACGCTTGCCCTGCTCATCTTTATGCAACT
EST: gi|17400406|gb|BM177188.1|BM177188
EST:     CATTCACCAAATCTTTTGGATCCTGTGGAGGTTACATTGCAGGATCGAAG                         GACCCTTATCCA-CACTTGAAGTACGCTTGCCCTGCTCATCTTTATGCAAC
genomic: CATTCACCAAATCTTTTGGATCCTGTGGAGGTTACATTGCAGGATCGAAGgtacttttgt ... ctactgtcagGACC-TTATCCAACACTTGAAGTACGCTTGCCCTGCTCATCTTTATGCAAC
EST: gi|17519162|gb|BM188204.1|BM188204
EST:     CATTCACCAAATCTTTTGGATCCTGTGGAGGTTACATTGCAGGATCGAAG                         GACCTTATCCAACACTTGAAGTACGCTTGCCCTGCTCATCTTTATGCAACT
genomic: CATTCACCAAATCTTTTGGATCCTGTGGAGGTTACATTGCAGGATCGAAGgtacttttgt ... ctactgtcagGACCTTATCCAACACTTGAAGTACGCTTGCCCTGCTCATCTTTATGCAACT
EST: gi|207788288|gb|GD762100.1|GD762100
EST:     CATTCACCAAATCTTTTGGATCCTGTGGAGGTTACATTGCAGGATCGAAG                         GACCTTATCCAACACTTGAAGTACGCTTGCCCTGCTCATCTTTATGCAACT
genomic: CATTCACCAAATCTTTTGGATCCTGTGGAGGTTACATTGCAGGATCGAAGgtacttttgt ... ctactgtcagGACCTTATCCAACACTTGAAGTACGCTTGCCCTGCTCATCTTTATGCAACT
EST: gi|213587414|gb|DB955538.1|DB955538
EST:     CATTCACCAAATCTTTTGGATCCTGTGGAGGTTACATTGCAGGATCGAAG                         GACCTTATCCAACACTTGAAGTACGCTTGCCCTGCTCATCTTTATGCAACT
genomic: CATTCACCAAATCTTTTGGATCCTGTGGAGGTTACATTGCAGGATCGAAGgtacttttgt ... ctactgtcagGACCTTATCCAACACTTGAAGTACGCTTGCCCTGCTCATCTTTATGCAACT
EST: gi|6454129|gb|AW184877.1|AW184877
EST:     CCTGTGGAGGTTACATTGCAGGATCGAAG                         GACCTTATCCAACACTTGAAGTACGCTTGCCCTGCTCATCTTTATGCAACT
genomic: CCTGTGGAGGTTACATTGCAGGATCGAAGgtacttttgt ... ctactgtcagGACCTTATCCAACACTTGAAGTACGCTTGCCCTGCTCATCTTTATGCAACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGTGAGCTCTTGGGTGTGGATACTGCTGATGTTGACATTATGATGGGAACATTCACCAAATCTTTTGGATCCTGTGGAGGTTACATTGCAGGATCGAAGgtacttttgttaaattttagactccaaatttagtgtttaactgaggcagtatgttgctaaaatctgtcagagtaggtgttcagattttctttcctattga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG