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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTATTGCTAAAAGATCTGGTGATGTCTATATTCCTCGTGGTGTCTCTGTTCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagacaaattatttttctttttactgttaaagttctatatagaaaattagtattacgtggaccatttttttctgatattctatgatattcattggtgacag

Basic information

species Glycine max
transcript GLYMA07G00430.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 5
ACTATTGCTAAAAGATCTGGTGATGTCTATATTCCTCGTGGTGTCTCTGTTCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagacaaattatttttctttttactgttaaagttctatatagaaaattagtattacgtggaccatttttttctgatattctatgatattcattggtgacag--------------------------
||||||||||  | |||||| ||||| || ||||| ||||||||||| ||||| || || ||||||||| |  | ||| | ||| | ||  ||||||     || ||  ||| ||||||    | |||| | |  |         |    |||   ||  ||   || ||||  | |   || |  ||  |  || |  | | |                           
ACTATTGCTATTAAATCTGGAGATGTGTACATTCCGCGTGGTGTCTCAGTTCCTGCCCTTGACAAAGATGCTTTGTGGCATTTTAAGCC--AGAAAA-----ACTAGgtaaagtattttg---tatact-tcaggggggaggggggggggttaccttt-tgttatcctttttcatttagcatgcagtgcaaggcactc-taaaatcatctcctattatcattatgctgcag

upper sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G128877_T02 (Zea mays), 5'ss of exon 5
ACTATTGCTAAAAGATCTGGTGATGTCTATATTCCTCGTGGTGTCTCTGTTCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagacaaattatttttctttttactgttaaagttctatatagaaaattagtattacgtggaccatttttttctgatattctatgatattcattggtgacag
   ||||| |  |  || || ||||| ||||||||||||||||| || ||||| || || ||||||||| || | ||||||||||| || |||||| | ||||       |||    |  |   ||      |  ||  |  |||     ||  | |||  |  |  | || | | |||| |  | | |||||    |       
---ATTGCCATTAAGTCAGGAGATGTGTATATTCCTCGTGGTGTTTCAGTTCCTGCCCTTGACAAAGATGCATTATGGGAATTTCAGCCAAAGAAACTAGGTAgtgacttaatgtagtaccacattgtccaaatggtcttgcatactgtttt--tgttatctcta--agttgtatgtgatttcttgttatatttccag-------

upper sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G128877_T03 (Zea mays), 5'ss of exon 2
ACTATTGCTAAAAGATCTGGTGATGTCTATATTCCTCGTGGTGTCTCTGTTCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagacaaattatttttctttttactgttaaagttctatatagaaaattagtattacgtggaccatttttttctgatattctatgatattcattggtgacag
|| ||||| |  |  || || ||||| ||||||||||||||||| || ||||| || || ||||||||| || | ||||||||||| || |||||| | ||||       |||    |  |   ||      |  ||  |  |||     ||  | |||  |  |  | || | | |||| |  | | |||||    |       
ACCATTGCCATTAAGTCAGGAGATGTGTATATTCCTCGTGGTGTTTCAGTTCCTGCCCTTGACAAAGATGCATTATGGGAATTTCAGCCAAAGAAACTAGgtagtgacttaatgtagtaccacattgtccaaatggtcttgcatactgtttt--tgttatctcta--agttgtatgtgatttcttgttatatttccag-------

upper sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G421857_T01 (Zea mays), 5'ss of exon 5
ACTATTGCTAAAAGATCTGGTGATGTCTATATTCCTCGTGGTGTCTCTGTTCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagacaaat-tatttttctttttactgttaaagttctatatagaaaattagtattacgtggaccattttt---ttctgatattctatg---atattcattggtgacag--------
   || ||||  |  || || ||||| ||||||||||||||||| || ||||| || || |||||||||  | | ||||||||||| || | |||  | ||||       ||  || |       ||  ||  |  ||| |  ||      || ||  |   |      | |||    | ||||  | | |    |  ||   | |||  |         
---ATCGCTATTAAGTCAGGAGATGTGTATATTCCTCGTGGTGTTTCAGTTCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACGAAGCTAGGTAgtgacttaacatagtacctccattgttgaaatggttttgcatgctgtttttgttatctctaagttgtatttgaactttgatgctatctaaataggttttcttgtgctatatttccag

upper sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G421857_T04 (Zea mays), 5'ss of exon 6
ACTATTGCTAAAAGATCTGGTGATGTCTATATTCCTCGTGGTGTCTCTGTTCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagacaaat-tatttttctttttactgttaaagttctatatagaaaattagtattacgtggaccattttt---ttctgatattctatg---atattcattggtgacag--------
|| || ||||  |  || || ||||| ||||||||||||||||| || ||||| || || |||||||||  | | ||||||||||| || | |||  | ||||       ||  || |       ||  ||  |  ||| |  ||      || ||  |   |      | |||    | ||||  | | |    |  ||   | |||  |         
ACCATCGCTATTAAGTCAGGAGATGTGTATATTCCTCGTGGTGTTTCAGTTCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACGAAGCTAGgtagtgacttaacatagtacctccattgttgaaatggttttgcatgctgtttttgttatctctaagttgtatttgaactttgatgctatctaaataggttttcttgtgctatatttccag

upper sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 5
lower sequence: AT1G78900.1 (Arabidopsis thaliana), 5'ss of exon 6
ACTATTGCTAAAAGATCTGGTGATGTCTATATTCCTCGTGGTGTCTCTGTTCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagacaaattatttt-tctttttactgttaaagttctatatagaaaattagtattacgtggaccatttttttctgatattctatgatattcattggtgacag
|||||||| | || ||| |||||||| || |||||||| ||||| ||||||||||| || |||||||||   |||||||| || || || || ||| ||||||  |      ||| |   | |   |     |  |  | |  ||      ||| | ||   ||| | |||   |||   |  | |                    
ACTATTGCAAGAATATCCGGTGATGTGTACATTCCTCGGGGTGTGTCTGTTCCAGCTCTTGACAAAGATTGTCTTTGGGAGTTCCAGCCCAATAAATTTGgta--atgtggtttactccatatgcctgtctatggaagtgttcatttggttttaatcttg-atggtcaattgaattcgttttgtttgcag----------------

upper sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 5
ACTATTGCTAAAAGATCTGGTGATGTCTATATTCCTCGTGGTGTCTCTGTTCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgta-ccagacaaat-tatttttctttttactgttaaagttctatatagaaa--attagtattacgtggaccatttttt--tctgat--attctatgatattcattggtgacag
|| ||||| |||| ||||||||||||||| |||||||||||||| |||||||| ||||| |||||||||| ||| |||||||| || ||||| ||| | ||||  || | |||| |||  || |  | | | |  | ||  | |  | |||  |||| | | |  ||   |  ||  |  ||||||  |  |  |   ||   ||||||  ||
ACCATTGCAAAAATATCTGGTGATGTCTACATTCCTCGTGGTGTATCTGTTCCTGCACTTGACAAAGATATACTCTGGGAATTCCAGCCTAAAAAATTAGgtaatcaaagaaatgtatcattatagtcatt-tggaggtgatttgaaaaaactattattttgatttgagactcttcatactctgattaaaccagtttcatctcttggtggtag

upper sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 5
ACTATTGCTAAAAGATCTGGTGATGTCTATATTCCTCGTGGTGTCTCTGTTCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagacaaattatttttctttttactgttaaagttctatatagaaaattagtattacgtggaccatt--tttttctgatattctatgatattcattggtgacag
||||||||||| |||||||||||||||||||||||||||||||| ||||| ||||| || |||||||||||||| ||||| || || || |||||| | |||||      |||      |  |  ||| || | ||||     | |     |    |||  || | ||||  |  |  | | |||   |     ||| || || |||
ACTATTGCTAAGAGATCTGGTGATGTCTATATTCCTCGTGGTGTTTCTGTCCCAGCCCTTGACAAAGATACACTATGGGAGTTCCAGCCCAAGAAACTAGgtactgcttgaata-----tgctaatac-gtgatagtt--ggtttgtggtctgtccttaactgtatcattgatgctaataaaattgctttcctctcactgttg-cag

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|120532286|gb|EH260419.1|EH260419
EST:     TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTG                         GTGAAGGTGACCTTTTAACTGGTGGAGATTTATATGCT
genomic: TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagaca ... ttggtgacagGTGAAGGTGACCTTTTAACTGGTGGAGATTTATATGCT
EST: gi|209713481|gb|BW679271.1|BW679271
EST:     TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTG                         GTGAAGGTGACCTTTTAACTGGTGGAGATTTATATGCT
genomic: TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagaca ... ttggtgacagGTGAAGGTGACCTTTTAACTGGTGGAGATTTATATGCT
EST: gi|5676817|gb|AI937947.1|AI937947
EST:     TCCAGCACTCGACAAAGATACACTNTGNGAATTTCAACCTAAGAAAATTG                         GTGAAGGTGACCTTTTAACTGGTGGAGATTTATATGCT
genomic: TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagaca ... ttggtgacagGTGAAGGTGACCTTTTAACTGGTGGAGATTTATATGCT
EST: gi|213601517|gb|DB970433.1|DB970433
EST:     TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTG                         GTGAAGGTGACCTTTTAACTGGT
genomic: TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagaca ... ttggtgacagGTGAAGGTGACCTTTTAACTGGT
EST: gi|24136428|gb|BU926938.1|BU926938
EST:     TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTG                         GTGAAGGTGACCTTTTAACTGGTGGAGATTTATATGCT
genomic: TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagaca ... ttggtgacagGTGAAGGTGACCTTTTAACTGGTGGAGATTTATATGCT
EST: gi|209722553|gb|BW682651.1|BW682651
EST:     TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTG                         GTGAAGGTGACCTTTTAACTGGTGGAGATTTATATGCT
genomic: TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagaca ... ttggtgacagGTGAAGGTGACCTTTTAACTGGTGGAGATTTATATGCT
EST: gi|213616520|gb|DB965718.1|DB965718
EST:     TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTG                         GTGAAGGTGACCTTTTAACTGGTGGAGATTTATATGCT
genomic: TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagaca ... ttggtgacagGTGAAGGTGACCTTTTAACTGGTGGAGATTTATATGCT
EST: gi|120530321|gb|EH258454.1|EH258454
EST:     TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTG                         GTGAAGGTGACCTTTTAACTGGTGGAGATTTATATGCT
genomic: TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagaca ... ttggtgacagGTGAAGGTGACCTTTTAACTGGTGGAGATTTATATGCT
EST: gi|192305155|gb|FG993935.1|FG993935
EST:     TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTG                         GTGAAGGTGACCTTTTAACTGGTGGAGATTTATATGCT
genomic: TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagaca ... ttggtgacagGTGAAGGTGACCTTTTAACTGGTGGAGATTTATATGCT
EST: gi|120532224|gb|EH260357.1|EH260357
EST:     TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTG                         GTGAAGGTGACCTTTTAACTGGTGGAGATTTATATGCT
genomic: TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagaca ... ttggtgacagGTGAAGGTGACCTTTTAACTGGTGGAGATTTATATGCT
EST: gi|209728747|gb|BW655427.1|BW655427
EST:     TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTG                         GTGAAGGTGACCTTTTAACTGGTGGAGATTTATATGCT
genomic: TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagaca ... ttggtgacagGTGAAGGTGACCTTTTAACTGGTGGAGATTTATATGCT
EST: gi|213618474|gb|DB967711.1|DB967711
EST:     TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTG                         GTGAAGGTGACCTTTTAACTGGTGGAGATTTATATGCT
genomic: TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagaca ... ttggtgacagGTGAAGGTGACCTTTTAACTGGTGGAGATTTATATGCT
EST: gi|213616575|gb|DB965745.1|DB965745
EST:     TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTG                         GTGAAGGTGACCTTTTAACTGGTGGAGATTTATATGCT
genomic: TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagaca ... ttggtgacagGTGAAGGTGACCTTTTAACTGGTGGAGATTTATATGCT
EST: gi|213607085|gb|DB957061.1|DB957061
EST:     TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTG                         GTGAAGGTGACCTTTTAACTGGTGGAGATTTATATGCT
genomic: TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagaca ... ttggtgacagGTGAAGGTGACCTTTTAACTGGTGGAGATTTATATGCT
EST: gi|213604715|gb|DB960480.1|DB960480
EST:     TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTG                         GTGAAGGTGACCTTTTAACTG
genomic: TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagaca ... ttggtgacagGTGAAGGTGACCTTTTAACTG
EST: gi|209700893|gb|BW683110.1|BW683110
EST:     TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTG                         GTGAAGGTGACCTTTTAACTGGTGGAGATTTATATGCT
genomic: TCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagaca ... ttggtgacagGTGAAGGTGACCTTTTAACTGGTGGAGATTTATATGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTATTGCTAAAAGATCTGGTGATGTCTATATTCCTCGTGGTGTCTCTGTTCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagacaaattatttttctttttactgttaaagttctatatagaaaattagtattacgtggaccatttttttctgatattctatgatattcattggtgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA