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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGAAGCACGGCTTCAATGATGCTATTGCTAAAGTAGGTTTGGTCAAGTTCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatccttctttttgatgcaatagtttaaattttggatgagtttgaagattaccttctacttaaaaaaaggtatttaatggaaaacattacatgtaat...

Basic information

species Glycine max
transcript GLYMA13G24360.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G24360.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv10s0003g00300.t01 (Vitis vinifera), 5'ss of exon 9
GTTGAAGCACGGCTTCAATGATGCTATTGCTAAAGTAGGTTTGGTCAAGTTCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatccttctttttgatgcaatagtttaaattttggatgagtttgaagattaccttctacttaaaaaaaggtatttaatggaaaacattacatg-taat---
| ||||||| ||||| |||||||| ||||||||||| ||| ||  ||||||| ||||||||||||| ||||| || |||||||| || |||||||| |||||| ||  || |||  |  ||   ||||  ||  |    |    |||  |||||     |  | |  |  |    |||       ||  |||  |   |||   
GATGAAGCATGGCTTTAATGATGCAATTGCTAAAGTGGGTCTGACCAAGTTCCTCTCAGATCTCTTTTGGGTGGGAATGTTTTATCACCTCTACAATCAGgtacattatt-tttggggagcttcagttgtaaactaacgt---cttgtggattataaagttatcactatcattctttttcctctcaatgttatttaacaatcaa

upper sequence: GLYMA13G24360.1 (Glycine max), 5'ss of exon 9
lower sequence: PP1S450_22V6.1 (Physcomitrella patens), 5'ss of exon 9
GTTGAAGCACGGCTTCAATGATGCTATTGCTAAAGTAGGTTTGGTCAAGTTCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatccttctttttgatgcaatagtttaaattttggatgagtttgaagattaccttctacttaaaaa--aaggtatttaatggaaaacattacatgtaat-----
  ||||   ||| ||   |  ||  ||||| || || ||  ||   |||||  |||||||  | ||||||||||||||||| || ||||| ||||||||||||           || ||||  ||   | |   ||   | | | |||| || ||  |     | || |  ||| |   |   | |   |  |  ||   ||     
TATGAACGGCGGTTTTGCTTCTGGCATTGCGAAGGTTGGCATGCCTAAGTTTCTCTCAGACTTGTTCTGGGTTGGTATGTTCTATCATCTGTACAACCAGgtatg-------gattcatgccgtacccttatgattcagtaattatgaaaatgacagtactgatgaagattaagctggctttggtatgtcgatttatcggatctata

upper sequence: GLYMA13G24360.1 (Glycine max), 5'ss of exon 9
lower sequence: PP1S450_17V6.1 (Physcomitrella patens), 5'ss of exon 9
GTTGAAGCACGGCTTCAATGATGCTATTGCTAAAGTAGGTTTGGTCAAGTTCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatccttctttttgatgcaatagtttaaattttggatgagtttgaagattaccttctacttaaaaa--aaggtatttaatggaaaacattacatgtaat-----
 |||||   ||||||    ||||| ||| | || || ||  ||   |||||| | |||||  | ||||||||||||||||| || ||||| ||||||||||||           || ||||  ||   | |   ||   | | | |||| || ||  |     | || |  ||| |   |   | |   |  |  ||   ||     
TTTGAACTCCGGCTTTTCGGATGCCATTACAAAGGTTGGCATGCAGAAGTTCTTGTCAGACTTGTTCTGGGTTGGTATGTTCTATCATCTGTACAACCAGgtatg-------gattcatgccgtacccttacgattcagtaattatgaaaatgacagtactgatgaagattaagctggctttggtatgtcgatttatcggatctata

upper sequence: GLYMA13G24360.1 (Glycine max), 5'ss of exon 9
lower sequence: EFJ38162 (Selaginella moellendorffii), 5'ss of exon 8
GTTGAAGCACGGCTTCAATGATGCTATTGCTAAAGTAGGTTTGGTCAAGTTCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatccttctttttgatgcaatagtttaaattt-tggatgagtttgaagattaccttctacttaaaaaaaggtatttaatggaaaacattacatgtaat
 ||| | ||||| ||    ||||| ||||| ||||| ||  |||| |||||  |    ||||||||||||||||| |||||||| ||| | || ||||||||||  | ||  || |  ||||  |        || |  |||   |   ||                                                  
ATTGCAACACGGGTTTGCAGATGCCATTGCCAAAGTTGGAATGGTGAAGTTTCTGAGCGATCTCTTCTGGGTTGGAATGTTTTATCATTTGTATAACCAGgtaagactttagttcttttgcatcaaaggcggcttgtcaatgttctcccag--------------------------------------------------

upper sequence: GLYMA13G24360.1 (Glycine max), 5'ss of exon 9
lower sequence: EFJ15759 (Selaginella moellendorffii), 5'ss of exon 9
GTTGAAGCACGGCTTCAATGATGCTATTGCTAAAGTAGGTTTGGTCAAGTTCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatccttctttttgatgcaatagtttaaattt-tggatgagtttgaagattaccttctacttaaaaaaaggtatttaatggaaaacattacatgtaat
 ||| | ||||| ||    ||||| ||||| ||||| ||  |||| |||||| |    ||||||||||||||||| |||||||| ||||| || ||||||||||  | ||  || |  ||||  |        || |  |||  ||   ||                                                  
ATTGCAACACGGGTTTGCAGATGCCATTGCCAAAGTTGGAATGGTGAAGTTCCTGAGCGATCTCTTCTGGGTTGGAATGTTTTATCATCTGTATAACCAGgtaagactttagttcttttgcatcaaaggcggcttgtcaatgttttcccag--------------------------------------------------

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|5753077|gb|AI960364.1|AI960364
EST:     CGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGG
genomic: CGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTAC-AACCAGgtaaatcctt ... gtcgccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGG
EST: gi|193681309|gb|FK622023.1|FK622023
EST:     CATCTCTACAACCAG                         GT-GCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: CATCTCTACAACCAGgtaaatcctt ... gtcgccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|9903135|gb|BE612103.1|BE612103
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatcctt ... gtcgccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|207835871|gb|GD806554.1|GD806554
EST:     TACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TACCATCTCTACAACCAGgtaaatcctt ... gtcgccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|26269191|gb|CA820254.1|CA820254
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatcctt ... gtcgccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATG
EST: gi|16995981|gb|BM085353.1|BM085353
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatcctt ... gtcgccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|22524864|gb|BU083675.1|BU083675
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACA
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatcctt ... gtcgccatagGTGGCTACCAACACA
EST: gi|6134862|gb|AW133255.1|AW133255
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatcctt ... gtcgccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|207761787|gb|GD732884.1|GD732884
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCA
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatcctt ... gtcgccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCA
EST: gi|9440042|gb|BE440553.1|BE440553
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatcctt ... gtcgccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|105634576|gb|DW247603.1|DW247603
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatcctt ... gtcgccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|22540054|gb|BU089897.1|BU089897
EST:     CGTCTCAGATCTCTTCTGGGTCTG-TATGTTCTACCATCTCTACTTCCAG                         GTGGCTACCAACACACTTGAGAGAGTGGCTCCTCTCACTCATGC
genomic: CGTCTCAGATCTCTTCTGGGT-TGGTATGTTTTACCATCTCTACAACCAGgtaaatcctt ... gtcgccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGC
EST: gi|20812531|gb|BQ297009.1|BQ297009
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatcctt ... gtcgccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|19053945|gb|BM732612.1|BM732612
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTATCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatcctt ... gtcgccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|17519168|gb|BM188210.1|BM188210
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatcctt ... gtcgccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|9903168|gb|BE612136.1|BE612136
EST:     TCGTCTCAAATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatcctt ... gtcgccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|5677127|gb|AI938257.1|AI938257
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatcctt ... gtcgccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|7690957|gb|AW759092.1|AW759092
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatcctt ... gtcgccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|15000011|gb|BI320825.1|BI320825
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatcctt ... gtcgccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|208076403|gb|GD874324.1|GD874324
EST:     ATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: ATGTTTTACCATCTCTACAACCAGgtaaatcctt ... gtcgccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|5753079|gb|AI960366.1|AI960366
EST:     CGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGG
genomic: CGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAA-CCAGgtaaatcctt ... gtcgccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGG
EST: gi|23057431|gb|BU578105.1|BU578105
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatcctt ... gtcgccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|6482509|gb|AW201766.1|AW201766
EST:     CGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: CGTCTCAGATCTCTTCTGGGTTGGTATGTTTTA-CCATCTCTACAACCAGgtaaatcctt ... gtcgccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|26048112|gb|CA784701.1|CA784701
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTC
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatcctt ... gtcgccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTC
EST: gi|151395328|gb|EV265199.1|EV265199
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatcctt ... gtcgccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|193723416|gb|FK660442.1|FK660442
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAAGAGTGGCT
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatcctt ... gtcgccatagGTGGCTACCAACACACTGGAGA-GAGTGGCT
EST: gi|7285024|gb|AW597511.1|AW597511
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTNNTACCATCTCTACAACCAG                         GTGGCTACCAAC
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatcctt ... gtcgccatagGTGGCTACCAAC
EST: gi|7691830|gb|AW759950.1|AW759950
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatcctt ... gtcgccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGAAGCACGGCTTCAATGATGCTATTGCTAAAGTAGGTTTGGTCAAGTTCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatccttctttttgatgcaatagtttaaattttggatgagtttgaagattaccttctacttaaaaaaaggtatttaatggaaaacattacatgtaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaaaaca