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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgcctttatagtatcttataattgcaattttcatgatgttttgttttgttccttatgagtaatgaataataagtgcagAGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTTCGAAAGGCAGATGATGCTGCTAAGGAACTTGAAGCTGCTGGAGGACTTG

Basic information

species Glycine max
transcript GLYMA20G34960.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G34960.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv05s0049g01360.t01 (Vitis vinifera), 3'ss of exon 1
----gtgcgcctttatagt--atcttataattg---caattttcatga--tgttttgtttt----gttccttatgagtaat-gaat---aataagtgcagAGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTTCGAAAGGCAGATGATGCTGCTAAGGAACTTGAAGCTGCTGGAGGACTTG
     |||  || |  |||  |||| |||||      ||||||||||   | || | | ||     ||   | |||  | | || |   ||| |  |||||||||||| ||||| ||||||||||| |||||||||| ||| || |||||||  |||||||||| |||||| || || ||||||||||||||||||  ||
gtagatgcaactctgaagttaatctcataataaacttaattttcatgtgttattctatatttgtaattgtctttgaacacttgagtgcaaatcaacgcagAGTGCTGTGTCTGGTCTAAATAGAGGTCTTGCTGCAATCGAGGATGATCTTCAGAAGGCAGATGCTGCTGCCAAAGAGCTTGAAGCTGCTGGAGGAACTG
















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|20812513|gb|BQ296991.1|BQ296991
EST:     ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTG                         AGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
genomic: ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTGgtgcgccttt ... ataagtgcagAGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
EST: gi|9258212|gb|BE346359.1|BE346359
EST:     ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTG                         AGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
genomic: ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTGgtgcgccttt ... ataagtgcagAGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
EST: gi|120530629|gb|EH258762.1|EH258762
EST:     ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTG                         AGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
genomic: ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTGgtgcgccttt ... ataagtgcagAGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
EST: gi|15813996|gb|BI786271.1|BI786271
EST:     ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTG                         AGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
genomic: ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTGgtgcgccttt ... ataagtgcagAGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
EST: gi|20811656|gb|BQ296134.1|BQ296134
EST:     ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTG                         AGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
genomic: ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTGgtgcgccttt ... ataagtgcagAGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
EST: gi|14008618|gb|BG725222.1|BG725222
EST:     TCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCT-                         ATGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCT
genomic: TCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTGgtgcgccttt ... ataagtgcagA-GTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCT
EST: gi|20498481|gb|BQ273411.1|BQ273411
EST:     ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTG                         AGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
genomic: ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTGgtgcgccttt ... ataagtgcagAGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
EST: gi|23057257|gb|BU577932.1|BU577932
EST:     ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTG                         AGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
genomic: ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTGgtgcgccttt ... ataagtgcagAGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
EST: gi|8669839|gb|BE190946.1|BE190946
EST:     ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTG                         AGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
genomic: ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTGgtgcgccttt ... ataagtgcagAGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
EST: gi|120530496|gb|EH258629.1|EH258629
EST:     ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTG                         AGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
genomic: ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTGgtgcgccttt ... ataagtgcagAGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
EST: gi|33389199|gb|CA852406.1|CA852406
EST:     ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTG                         AGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGTAAGCGAAGACGATCTT
genomic: ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTGgtgcgccttt ... ataagtgcagAGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
EST: gi|7283325|gb|AW595933.1|AW595933
EST:     GATTCCATCTCTTCTTTGAAGCTCAATCTGCTG                         AGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
genomic: GATTCCATCTCTTCTTTGAAGCTCAATCTGCTGgtgcgccttt ... ataagtgcagAGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
EST: gi|20498880|gb|BQ273810.1|BQ273810
EST:     ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTG                         AGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
genomic: ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTGgtgcgccttt ... ataagtgcagAGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
EST: gi|13481231|gb|BG510574.1|BG510574
EST:     ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTG                         AGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
genomic: ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTGgtgcgccttt ... ataagtgcagAGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
EST: gi|26269573|gb|CA820636.1|CA820636
EST:     ACGCTGGGGATACCTCTGATTCCATCNNNNNNNNGAAGCTCAATCTGCTG                         AGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
genomic: ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTGgtgcgccttt ... ataagtgcagAGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
EST: gi|120491718|gb|EH219885.1|EH219885
EST:     ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTG                         AGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
genomic: ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTGgtgcgccttt ... ataagtgcagAGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
EST: gi|12489972|gb|BG043493.1|BG043493
EST:     ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTG                         AGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
genomic: ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTGgtgcgccttt ... ataagtgcagAGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
EST: gi|5760159|gb|AI965522.1|AI965522
EST:     ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTG                         AGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
genomic: ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTGgtgcgccttt ... ataagtgcagAGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
EST: gi|120530540|gb|EH258673.1|EH258673
EST:     ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTG                         AGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
genomic: ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTGgtgcgccttt ... ataagtgcagAGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
EST: gi|151397186|gb|EV267059.1|EV267059
EST:     ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTG                         AGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
genomic: ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTGgtgcgccttt ... ataagtgcagAGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTT
EST: gi|12489934|gb|BG043463.1|BG043463
EST:     ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTG                         AGTGCTGTTTCTGGGCTAAATAAAGGCCTTGCTGCAA
genomic: ACGCTGGGGATACCTCTGATTCCATCTCTTCTTTGAAGCTCAATCTGCTGgtgcgccttt ... ataagtgcagAGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaattttcatgatgttttgttttgttccttatgagtaatgaataataagtgcagAGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTTCGAAAGGCAGATGATGCTGCTAAGGAACTTGAAGCTGCTGGAGGACTTG
                                  agtaatgaataataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgcctttatagtatcttataattgcaattttcatgatgttttgttttgttccttatgagtaatgaataataagtgcagAGTGCTGTTTCTGGGCTAAATAGAGGCCTTGCTGCAAGCGAAGACGATCTTCGAAAGGCAGATGATGCTGCTAAGGAACTTGAAGCTGCTGGAGGACTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA