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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactgtgctggtggtggtagaatatatgcaagaacacaataaatcattgctattgtaccattgatacagtcatggtggctattttactattttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTGGTTGTTGGGATAAGTGGTGATGATGCTGCCTCTCACAAG

Basic information

species Glycine max
transcript GLYMA13G17350.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G17350.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G26060.2 (Arabidopsis thaliana), 3'ss of exon 2
tactgtgctggtggtggtagaatatatgcaagaacacaataaatcattgctattgtaccattgatacagtcatggtggctattttactattttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTGGTTGTTGGGATAAGTGGTGATGATGCTGCCTCTCACAAG
    ||  |        ||   | |   |     | || | | | || ||   | ||   ||  || |   |   |||   |||||||  | ||   |||||||| |||||||| || || |||||||| ||||||||||| || || | |||  |||| || ||||| |||||  |||| |||||||||
----gttgttaaatctttactttctcctccttcccgcattcattgatcgcatatttagtgtttctaaacgta-aatgg---ttttacttgtgtacaacagGCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAAGCTGGTGCAGAGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAG

upper sequence: GLYMA13G17350.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv11s0016g00560.t01 (Vitis vinifera), 3'ss of exon 2
tactgtgctggtggtggtagaatatatgcaagaacacaataaatcattgctatt-gtaccattgatacagtcatgg--tggctattttactatt-------ttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTGGTTGTTGGGATAAGTGGTGATGATGCTGCCTCTCACAAG
          ||  |   |  | ||    || | |  |   ||  |||| |||| | ||| |        ||| ||  |||  |  | || |||          | |||||| || ||||||||||| || |||||||| |||||||||||||||||   |||||| || || |||||||||||  |  | || ||||||
----------gtttttacatgaaatggttaaaacccaatccaagaattggtattagaaccgtcatgggtttcagggaatggaaaactaacaattgatgtggccttggcagGCATGTGCTTTCAGGGACTCTTATGAGAAATTCAAGAAAGCAGGAGCCCAGGTTGTGGGCATTAGTGGTGATGACCCATCATCACACAAG
















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|6481877|gb|AW201148.1|AW201148
EST:     TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAG                         GCTTGCGCTNTCAGGGATTCATATGAGAAGTTCAAGAAAGCATGAGCGGTG
genomic: TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAGgtaaatacac ... tttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
EST: gi|192307069|gb|FK002707.1|FK002707
EST:     TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAG                         GCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
genomic: TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAGgtaaatacac ... tttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
EST: gi|33387642|gb|CA850849.1|CA850849
EST:     TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAG                         GCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
genomic: TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAGgtaaatacac ... tttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
EST: gi|209699189|gb|BW652907.1|BW652907
EST:     TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAG                         GCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCTGTG
genomic: TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAGgtaaatacac ... tttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
EST: gi|26060096|gb|CA803010.1|CA803010
EST:     TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAG                         GCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
genomic: TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAGgtaaatacac ... tttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
EST: gi|31462119|gb|CD404147.1|CD404147
EST:     TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAG                         GCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
genomic: TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAGgtaaatacac ... tttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
EST: gi|298163036|gb|HO011769.1|HO011769
EST:     TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAG                         GCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
genomic: TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAGgtaaatacac ... tttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
EST: gi|9900242|gb|BE609210.1|BE609210
EST:     TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAG                         GCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
genomic: TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAGgtaaatacac ... tttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
EST: gi|10238469|gb|BE807357.1|BE807357
EST:     TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAG                         GCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
genomic: TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAGgtaaatacac ... tttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
EST: gi|20812681|gb|BQ297159.1|BQ297159
EST:     TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAG                         GCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
genomic: TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAGgtaaatacac ... tttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
EST: gi|151405956|gb|EV275771.1|EV275771
EST:     TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAG                         GCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
genomic: TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAGgtaaatacac ... tttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
EST: gi|192307070|gb|FK002708.1|FK002708
EST:     TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAG                         GCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
genomic: TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAGgtaaatacac ... tttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
EST: gi|213600044|gb|DB966504.1|DB966504
EST:     TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAG                         GCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
genomic: TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAGgtaaatacac ... tttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
EST: gi|31460446|gb|CD402414.1|CD402414
EST:     GCTGTACCAAACAG                         GCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
genomic: GCTGTACCAAACAGgtaaatacac ... tttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
EST: gi|31464583|gb|CD406611.1|CD406611
EST:     TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAG                         GCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
genomic: TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAGgtaaatacac ... tttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
EST: gi|31471539|gb|CD413567.1|CD413567
EST:     TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAG                         GCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
genomic: TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAGgtaaatacac ... tttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
EST: gi|209699188|gb|BW652906.1|BW652906
EST:     TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAG                         GCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCTGTG
genomic: TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAGgtaaatacac ... tttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
EST: gi|193411296|gb|FK380671.1|FK380671
EST:     TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAG                         GCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
genomic: TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAGgtaaatacac ... tttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
EST: gi|298166038|gb|HO009009.1|HO009009
EST:     TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAG                         GCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
genomic: TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAGgtaaatacac ... tttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
EST: gi|23064250|gb|BU579023.1|BU579023
EST:     TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAG                         GCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
genomic: TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAGgtaaatacac ... tttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
EST: gi|13789127|gb|BG651718.1|BG651718
EST:     TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAG                         GCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGT-
genomic: TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAGgtaaatacac ... tttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
EST: gi|31474615|gb|CD416643.1|CD416643
EST:     CTGATGAGACCCCTGGCTGTACCAAACAG                         GCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
genomic: CTGATGAGACCCCTGGCTGTACCAAACAGgtaaatacac ... tttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
EST: gi|120533335|gb|EH261468.1|EH261468
EST:     TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAG                         GCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
genomic: TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAGgtaaatacac ... tttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
EST: gi|192293850|gb|FG986059.1|FG986059
EST:     TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAG                         GCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
genomic: TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAGgtaaatacac ... tttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
EST: gi|31457164|gb|CD399192.1|CD399192
EST:     TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAG                         GCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
genomic: TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAGgtaaatacac ... tttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
EST: gi|27426699|gb|CA938219.1|CA938219
EST:     TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAC                         GCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGACAGCAGGAGCGGTG
genomic: TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAGgtaaatacac ... tttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
EST: gi|14991009|gb|BI316682.1|BI316682
EST:     TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAG                         GCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
genomic: TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAGgtaaatacac ... tttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
EST: gi|213606506|gb|DB958988.1|DB958988
EST:     TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAG                         GCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG
genomic: TAGTTGTGTATTTCTACCCTGCTGATGAGACCCCTGGCTGTACCAAACAGgtaaatacac ... tttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgctattgtaccattgatacagtcatggtggctattttactattttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTGGTTGTTGGGATAAGTGGTGATGATGCTGCCTCTCACAAG
             cattgat  putative branch site (score: 4)
                                         ctatttt  putative PPT
                                  tattttactattttat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactgtgctggtggtggtagaatatatgcaagaacacaataaatcattgctattgtaccattgatacagtcatggtggctattttactattttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTGGTTGTTGGGATAAGTGGTGATGATGCTGCCTCTCACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
-actgtgc
- - - - tggtggt
- - - - - - - - - - - - - tgcaaga
- - - - - - - - - - - - - - - - - - - - - - - - gctattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atggtgg