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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAGgtagtgcaacactctgtaatatagttgtcatataaacaaaataattgtttgtttttctcatatatatatgctttactgtttccatgaag

Basic information

species Glycine max
transcript GLYMA20G32320.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G32320.1 (Glycine max), 5'ss of exon 6
lower sequence: AT3G54840.1 (Arabidopsis thaliana), 5'ss of exon 6
GAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAGgtagtgcaacactctgtaatatagttgtcatataaacaaaataattgtttgtttttctcatatatatatgctttactgtttccatgaag-----------------------
|| || ||||| ||||||||||| ||||| || ||||| ||||| ||||| ||||||||||| |  || ||  | |||||  ||    ||||        | | ||    |  ||  |||| || |     ||   |  | || || |||  |  ||   | || ||  |||  ||                          
GAACTGCAAAAGCATGGAAGCCCAGATATTGTTATGGCTCTGGTTGGTAACAAAGCTGATCTACATGAAAAAAGAGAAGTACCTACTGAGgtg-------agtttgcgtaaacgtcttcatctagattccgtagc-gcattttgttgtcactttcattgtccttgcttcttcagtggtatcacattttcaatttcttaacag

upper sequence: GLYMA20G32320.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv13s0019g04680.t01 (Vitis vinifera), 5'ss of exon 6
GAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAGgt-agtgcaacact--ctgtaatatagttgtcatataaacaaaataattgtttgtttttctcatatatatatgctttactgtttccatgaag
||  | ||||||||||||||||||||||| || |||||  | || || || |||||||||||||  ||||| || |||||  | || || || ||||  | |||   |||   |  | |      |   | |  || |       | | ||   | |  |    |||| | | | | |||||
GAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAAgtgagtgtcatactatttgtctgaatgcttcagcttttcctatgtattcacaaaatgtgctttaacacgtg---tttattttattcttgaag
















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|19937689|gb|BQ081385.1|BQ081385
EST:     TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAG                         GATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCT
genomic: TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAGgtagtgcaac ... ttccatgaagGATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCT
EST: gi|298188274|gb|HO034967.1|HO034967
EST:     TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAG                         GATGGCACTGACTATGCAGAGAAGAATGATATG
genomic: TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAGgtagtgcaac ... ttccatgaagGATGGCACTGACTATGCAGAGAAGAATGATATG
EST: gi|192303626|gb|FG998636.1|FG998636
EST:     TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAG                         GATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCT
genomic: TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAGgtagtgcaac ... ttccatgaagGATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCT
EST: gi|208166021|gb|GD959081.1|GD959081
EST:     TGGTCGGTAATAAAGCTAATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAG                         GATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCT
genomic: TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAGgtagtgcaac ... ttccatgaagGATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCT
EST: gi|207760676|gb|GD733677.1|GD733677
EST:     TGGTCGGTAATAAAGCTAATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAG                         GATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCT
genomic: TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAGgtagtgcaac ... ttccatgaagGATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCT
EST: gi|8670136|gb|BE191243.1|BE191243
EST:     TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAG                         GATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCT
genomic: TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAGgtagtgcaac ... ttccatgaagGATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCT
EST: gi|213611330|gb|DB983950.1|DB983950
EST:     TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAG                         GATGGCACTGACTATGCAGAGAAGTATGATATGTTTTTCATAGAGACATCT
genomic: TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAGgtagtgcaac ... ttccatgaagGATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCT
EST: gi|151401597|gb|EV271411.1|EV271411
EST:     TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAG                         GATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCT
genomic: TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAGgtagtgcaac ... ttccatgaagGATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCT
EST: gi|31307751|gb|CD392954.1|CD392954
EST:     TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAG                         GATGGCCCTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCT
genomic: TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAGgtagtgcaac ... ttccatgaagGATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCT
EST: gi|33388034|gb|CA851241.1|CA851241
EST:     TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAG                         GATGGCACTGACTATGCA
genomic: TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAGgtagtgcaac ... ttccatgaagGATGGCACTGACTATGCA
EST: gi|8670147|gb|BE191254.1|BE191254
EST:     TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAG                         GATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCT
genomic: TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAGgtagtgcaac ... ttccatgaagGATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCT
EST: gi|120530900|gb|EH259033.1|EH259033
EST:     TGGTCGGTAATACAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAG                         GATGGCACTGACTATGCAGAGAAGAATGATATGTATTTCATAGAGACATCT
genomic: TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAGgtagtgcaac ... ttccatgaagGATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCT
EST: gi|213603351|gb|DB966610.1|DB966610
EST:     TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAG                         GATGGCACTGACTATGC
genomic: TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAGgtagtgcaac ... ttccatgaagGATGGCACTGACTATGC
EST: gi|58017129|gb|CX703871.1|CX703871
EST:     TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAG                         GATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCT
genomic: TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAGgtagtgcaac ... ttccatgaagGATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCT
EST: gi|151399728|gb|EV269599.1|EV269599
EST:     TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAG                         GATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCT
genomic: TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAGgtagtgcaac ... ttccatgaagGATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCT
EST: gi|208308185|gb|GE102837.1|GE102837
EST:     TGGTCGGTAATAAAGCTAATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAG                         GATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCT
genomic: TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAGgtagtgcaac ... ttccatgaagGATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCT
EST: gi|13478097|gb|BG507714.1|BG507714
EST:     TGGTCGGTAATAAAGCTGATCTTCTCCAGAAGCGGGAAGTTGCTGNCCAT                         GATGGCACTGACTATGCANAGAAG
genomic: TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAGgtagtgcaac ... ttccatgaagGATGGCACTGACTATGCAGAGAAG
EST: gi|6665996|gb|AW277455.1|AW277455
EST:     TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAG                         GATGGCACTGACTATGGCAGAGAA-AATGATATGTTTTTCATAGAGACATC
genomic: TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAGgtagtgcaac ... ttccatgaagGATGGCACTGACTATG-CAGAGAAGAATGATATGTTTTTCATAGAGACATC
EST: gi|6667685|gb|AW279136.1|AW279136
EST:     TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAG                         GATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCT
genomic: TGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAGgtagtgcaac ... ttccatgaagGATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCT
EST: gi|7589360|gb|AW705136.1|AW705136
EST:     GCGGGAAGTTGCTGTCCAG                         GATGGCACTGACTATGCAGAGAAGAATGGTATGTTTTTCATAGAGACATCT
genomic: GCGGGAAGTTGCTGTCCAGgtagtgcaac ... ttccatgaagGATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAGgtagtgcaacactctgtaatatagttgtcatataaacaaaataattgtttgtttttctcatatatatatgctttactgtttccatgaag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC