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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatatattgtgatctagcagagcttttgctttgccccaatatacctattttctaaatttttattcattacatgacattttgtctccatgttgttacatttatttgaatgtgctttctctgatgttctgctgttaatgaattgtgtgattttctttttag

Basic information

species Glycine max
transcript GLYMA07G39380.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G39380.2 (Glycine max), 5'ss of exon 13
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 5'ss of exon 13
GTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatatattgtgatctagcagagcttttgctttgccccaatatacctattttctaaatttttattcattacatgacattttgtctccatgttgttacatttatttgaatgtgctttctctgatgttctgctgttaatgaattgtgtgattttctttttag
||||| ||  |   ||||||||| ||||||||||| ||||||||||||||| | || || |||||||| || |||||||| || ||||  |       |    |||  |  ||| ||||| |    | |     |  |||  |||     ||||| ||  | ||||| |    | ||   | |  || |   ||||| ||                                             
GTTGGCAACCTCGCTGCTCCTGTGGAAGAATGGACCGTTGGTGGAACTGCATTGACATCGTTGATGGATGTTGAGAGGAGGCACGgtaggt-------ttctacagttccgttg-tttgcacttggagattagctagctatgttt-----cattaaatttc-ttttgaccgtttattcaaatacctact---atgtgattaa-------------------------------------------

upper sequence: GLYMA07G39380.2 (Glycine max), 5'ss of exon 13
lower sequence: GRMZM2G143862_T01 (Zea mays), 5'ss of exon 6
GTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatatattgtgatctagcagagcttttgctttgccccaatatacctattttctaaatttttattcattacatgacattttgtctccatgttgttacatttatttgaatgtgctttctctgatgttctgctgttaatgaattgtgtgattttctttttag
||||| ||  |    ||||| |||||||||||||||||||||||||| ||| | || ||| ||||||| || |||||||| || |||| || || |    |  |   | |      |     | |     ||||  ||||       |||| |  | | ||| ||| |   || || |  ||   | | |||                                                     
GTTGGCAACCTTGCGGCTCCAGTAGAAGAATGGACTGTTGGTGGAACAGCATTGACATCACTGATGGATGTTGAGAGGAGGCACGgta-attttcttgcttcactttgttaccaactgatggctactctactatgctctag--cagcattctt--ctttacactttatt--caagtagcaaccaatgtgtga-----------------------------------------------------

upper sequence: GLYMA07G39380.2 (Glycine max), 5'ss of exon 13
lower sequence: GRMZM2G059151_T01 (Zea mays), 5'ss of exon 13
GTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatatattgtgatctagcagagcttttgct-----ttgccccaatatac-cta-------ttttctaaatttttattcat----tacatgacattttgtctccatg---ttgttacatttatttgaa--tgtgctttctctg-atgttctgctgttaatgaattgtgtgattttctttttag-------
||||| ||  |    ||||| || ||||||||||||||||||||||| ||| | || ||| ||||||| || |||||||| || ||||  | |  || |  | |     |    ||      | | | | |||   |||       | ||||  || || |||||     |   ||||||    |     |    || ||   || ||| | |  | | ||||   |  |  || ||| |  | || |   | |||  || || |  |       
GTTGGCAACCTTGCGGCTCCAGTTGAAGAATGGACTGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACGgtaattttcttgcttcacctcgtttccaactgatggctactctactatgttctagttacattcttctcgatgttcattcaaccaatgtgtgacatgccattcttgttccttttttcggttgattagcatttatactttggttataatttgtgccgg-agtgtaacttttgacgttgttctctgcaatcag

upper sequence: GLYMA07G39380.2 (Glycine max), 5'ss of exon 13
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 5'ss of exon 13
GTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatatat-tgtgatctagcagagcttttgctttgccccaatatacctattttctaaatttttattcattacatgacattttgtctccatgttgttacatttatttgaatgtgctttctctgatgttctgctgttaatgaattgtgtgattttctttttag
||||| || ||   ||||||||| |||||||||||||| ||||| ||||| |||||  | |||||||| || ||||||||||| |||| | |  | | |   |  | ||||  | ||  | | || |     |    |||| || || |   || | |    ||||   ||    |                                                                      
GTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACGgtacagaaatataaatcaataaagct--tactaagacacatt----ttgaaatctagatattaaaaaatcagagttgatttcaacttgcag----------------------------------------------------------------------

upper sequence: GLYMA07G39380.2 (Glycine max), 5'ss of exon 13
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 13
GTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatatattgtgatctagcagagcttttgctttgccccaat-atacctattttctaaatttttattcattacatgacattttgtctccatgttgttacatttatttgaatgtgctttctctgatgttctgctgttaatgaattgtgtgattttctttttag
||||| ||| | | |||||| || ||||||||||||||||||||||||||  | |||||||| ||||| ||||||||||||||||||||         |||        | |  ||||||     | || |||||| |  |||  ||  ||  |    ||     |    ||       ||| |                                                              
GTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATGgtatgatagcctctctttttcccatctcactttgcagatgtgattcctattatggaaaacttcttttctcctttggaggctatagtctggcactttatac-------------------------------------------------------------

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|13788196|gb|BG650788.1|BG650788
EST:     TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG                         GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
genomic: TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatatattg ... ttctttttagGTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
EST: gi|254342635|gb|GR858797.1|GR858797
EST:     TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG                         GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
genomic: TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatatattg ... ttctttttagGTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
EST: gi|254342634|gb|GR858796.1|GR858796
EST:     TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG                         GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
genomic: TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatatattg ... ttctttttagGTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
EST: gi|298174798|gb|HO017907.1|HO017907
EST:     TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG                         GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
genomic: TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatatattg ... ttctttttagGTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
EST: gi|151402902|gb|EV272715.1|EV272715
EST:     TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG                         GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
genomic: TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatatattg ... ttctttttagGTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
EST: gi|26058870|gb|CA801784.1|CA801784
EST:     TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG                         GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTG
genomic: TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatatattg ... ttctttttagGTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTG
EST: gi|254318250|gb|GR832418.1|GR832418
EST:     TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG                         GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
genomic: TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatatattg ... ttctttttagGTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
EST: gi|58023377|gb|CX710118.1|CX710118
EST:     TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG                         GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
genomic: TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatatattg ... ttctttttagGTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
EST: gi|151413068|gb|EV282876.1|EV282876
EST:     TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG                         GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
genomic: TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatatattg ... ttctttttagGTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
EST: gi|18712744|gb|BM522681.1|BM522681
EST:     TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG                         GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
genomic: TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatatattg ... ttctttttagGTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatatattgtgatctagcagagcttttgctttgccccaatatacctattttctaaatttttattcattacatgacattttgtctccatgttgttacatttatttgaatgtgctttctctgatgttctgctgttaatgaattgtgtgattttctttttag

- - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA