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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCATTGTTGCTGACAACTACTTCACTGGATCCAAGGATAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATGgtatagtctttcatctttgtttactgtcaactatcaactatcaatgccattaaaattgtcacatgttagatgcactaaagttttttattgatttatcttt...

Basic information

species Glycine max
transcript GLYMA15G04500.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G04500.2 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 5'ss of exon 4
GTCATTGTTGCTGACAACTACTTCACTGGATCCAAGGATAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATGgtatagtctttcatctttgtttactgtcaactatcaactatcaatgccattaaaattgtcacatgttagatgcactaaagttttttattgatttatcttt----
|||||||| || |||||||  |||||||| || || || ||||| || |||||||| || || |||||||||||||| |||||||||||||| |   | |||  |   |   | |     || ||||||   | | ||   | |  | |  | |||     |  ||  |||||  || |   || |      
GTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATGgtattgc--tacattctcagtgcatttagttcatgaactattgttac-atactagtaataaagttttactgctagcaagttttttcgttcaaa-atttgagaaa

upper sequence: GLYMA15G04500.2 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 3
GTCATTGTTGCTGACAACTACTTCACTGGATCCAAGGATAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATGgta--tagtctttcatctttgtttactgtcaactatcaactatcaatgccattaaaattgtcacatgttagatgcactaaagttttttattgatttatcttt
|||||||||||||| ||||  |||||||| || || || ||||| || ||||||||||| || |||||||||||||| |||||||||||||  ||     | | || ||   | | | |  |||      ||  |  | || | |   ||         ||| ||    | |  | | ||||  ||    
GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataactagttagctatgcacatt-taagatattttaagtct-tctctttcagaggatcctgaaagttatgaaccctggatagtcaatgataaataaac

upper sequence: GLYMA15G04500.2 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 4
GTCATTGTTGCTGACAACTACTTCACTGGATCCAAGGATAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATGgta--tagtctttcatctttgtttactgtcaactatcaactatcaatgccattaaaattgtcacatgttagatgca-ctaaagttttttattgatttatcttt
|||||||||||||| ||||  |||||||| || || |||||||| || |||||||| || || |||||||||||||| ||||| |||||||  ||     | |    ||  | ||    ||  |  |    |  | || || | ||  ||         ||||| |     ||    | ||||  ||    
GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataactagttagacatgcatgcttaagacattttaagtcc--tccctttcagatgatcctgaaagttatgcatcctggattagacaatgataaataaa-

upper sequence: GLYMA15G04500.2 (Glycine max), 5'ss of exon 5
lower sequence: AT2G28760.1 (Arabidopsis thaliana), 5'ss of exon 3
------------GTCATTGTTGCTGACAACTACTTCACTGGATCCAAGGATAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATGgtatagtctttcatctttgtttactgtcaactatcaactatcaatgccattaaaattgtcacatgttagatgcactaaagttttttattgatttatcttt
            || || ||||| || || |||||||| ||||| || || || ||||| || |||||||||||||||||||||||||| || |||||||||||||| | |     ||  ||| |   |  ||   | ||   ||   |  ||||   |    |  ||      ||   | |||||   |          
GAAAAGAATGAAGTAATCGTTGCGGATAATTACTTCACAGGATCAAAAGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTAATTCGTCATGgtatagtatct---tcttaattaatcaaacttacttaatactcat-taaccaaaacaatgcattaatactcattcttgtgattttttcag----------

upper sequence: GLYMA15G04500.2 (Glycine max), 5'ss of exon 5
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 5'ss of exon 4
GTCATTGTTGCTGACAACTACTTCACTGGATCCAAGGATAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATGgtatagtctttcatctttgtttactgtcaactatcaactatcaatgccattaaaattgtcacatgttagatgcactaaagtttt--ttattgatttatcttt
|| ||||||||||| ||||| |||||||| || ||||| ||||| || |||||||||||||||||||||||||||||||||||||| ||||| || ||  |  | | |    |||   ||   |  |   ||||  || |    ||||   ||||  || || | |  ||||  || | | |||| |   
GTGATTGTTGCTGATAACTATTTCACTGGTTCAAAGGACAACCTTAAGAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCACGgtatggttttgaaattctctggcttgttg-ctgcta-ttgagaatggaat-attcctgtcttttgttctatccatttatattttggttttgggtttaacag-

upper sequence: GLYMA15G04500.2 (Glycine max), 5'ss of exon 5
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 5'ss of exon 4
GTCATTGTTGCTGACAACTACTTCACTGGATCCAAGGATAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATGgtatagtctttcatctttgtttactgtcaactatcaactatcaatgccattaaaattgtcacatgttagatgcactaaagttttttattgatttatcttt------
|| |||||||| || ||||||||||| || || ||||| || ||||| || ||||||||||||||||||||||||||||| |||||||||| ||| ||| ||||||  ||||  || | | |    |||||        | |   ||||  |||| |         |  |   |   |||  ||| |       
GTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgta-agttttttatcttt--ttac--tccattttattttatca-catatgcatatgcgtcatttgtttggaatttgggatatcccttcagatgaatcctgattggt

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|213611728|gb|DB962965.1|DB962965
EST:     TAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATG                         ATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCAT
genomic: TAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATGgtatagtctt ... cactttttagATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCAT
EST: gi|8827206|gb|BE210936.1|BE210936
EST:     TAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATG                         ATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCAT
genomic: TAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATGgtatagtctt ... cactttttagATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCAT
EST: gi|151412093|gb|EV281905.1|EV281905
EST:     TAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATG                         ATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCAT
genomic: TAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATGgtatagtctt ... cactttttagATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCAT
EST: gi|192316740|gb|FK006443.1|FK006443
EST:     TAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATG                         ATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCAT
genomic: TAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATGgtatagtctt ... cactttttagATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCAT
EST: gi|213591579|gb|DB955787.1|DB955787
EST:     TAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATG                         ATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCAT
genomic: TAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATGgtatagtctt ... cactttttagATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCAT
EST: gi|213592188|gb|DB965979.1|DB965979
EST:     TAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATG                         ATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCAT
genomic: TAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATGgtatagtctt ... cactttttagATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCAT
EST: gi|192316741|gb|FK006444.1|FK006444
EST:     TAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATG                         ATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCAT
genomic: TAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATGgtatagtctt ... cactttttagATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCAT
EST: gi|16279667|gb|BI943554.1|BI943554
EST:     TAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATG                         ATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCAT
genomic: TAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATGgtatagtctt ... cactttttagATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCAT
EST: gi|192317198|gb|FK007909.1|FK007909
EST:     TAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATG                         ATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCAT
genomic: TAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATGgtatagtctt ... cactttttagATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCAT
EST: gi|192296657|gb|FG991225.1|FG991225
EST:     TAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATG                         ATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCAT
genomic: TAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATGgtatagtctt ... cactttttagATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCATTGTTGCTGACAACTACTTCACTGGATCCAAGGATAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATGgtatagtctttcatctttgtttactgtcaactatcaactatcaatgccattaaaattgtcacatgttagatgcactaaagttttttattgatttatcttt

- - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT