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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAGAGCTTCCAAAATCCGCAAGCTTTTCAACCTGTCTAAGGAGGATGATGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATGgtaaagtgtcttctctctgtaaatgttctatagagatttattttttccttaagaataaattacaagtctaacccatttatacctgtgatcttttctggtg...

Basic information

species Glycine max
transcript GLYMA13G31130.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G31130.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv03s0017g01350.t01 (Vitis vinifera), 5'ss of exon 5
AAGAGAGCTTCCAAAATCCGCAAGCTTTTCAACCTGTCTAAGGAGGATGATGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATGgtaaagtgtcttctctctgtaaatgttctatagagatttattttt-----tccttaagaataaattacaagtc---taacccattt--atacctgtgatcttttctggtg
||||||||||| || || || ||||| |||||||| |||||||||||||||||  |||||||||||||||| ||| |  |||| || ||||| |||  ||||| | |  ||  | |||     | |  | |  | ||||| ||||     |   ||||   |    |||| |    |||   | ||  || |||    |  ||||     
AAGAGAGCTTCTAAGATTCGAAAGCTCTTCAACCTCTCTAAGGAGGATGATGTTCGGAAGTATGTCAACACATATCGTCGAACCTTCACAACAAAATCTGgtacaattcctgatttct-----tatctttttaatatttacttttagaagtttataagtgaagggaacaaattgtataatttaatttaattcctacattgctttc-----

upper sequence: GLYMA13G31130.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv07s0191g00060.t01 (Vitis vinifera), 5'ss of exon 5
AAGAGAGCTTCCAAAATCCGCAAGCTTTTCAACCTGTCTAAGGAGGATGATGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATGgtaaagtgtct--tctctctgtaaatgttctata-gagatttattttttccttaagaataaattacaagtctaacccatttatacctgtgatcttttctggtg
||||| || || || || || |||||||| ||||| || ||||||||||||||  |||||||||| ||||| ||| |  |||| ||||| ||||||  ||||      |||  | ||| | |  |||    ||| || || | |  |  | |||   |  ||  | | || | |    | | || |||||  | |  | |   
AAGAGGGCCTCAAAGATTCGAAAGCTTTTTAACCTCTCGAAGGAGGATGATGTTCGGAAGTATGTGAACACTTATCGCCGAACTTTTACTACTAAATCTGgttggtgttctaatttcttttttgatgggaaatatgatatgtttactgacattatttactaa--agatgtatgattggtct-tatctgtgtgcctggcag---

upper sequence: GLYMA13G31130.1 (Glycine max), 5'ss of exon 6
lower sequence: PP1S3195_1V6.1 (Physcomitrella patens), 5'ss of exon 2
AAGAGAGCTTCCAAAATCCGCAAGCTTTTCAACCTGTCTAAGGAGGATGATGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATGgtaaagtgtcttctctc--tgtaaatgttctatagagatttattttttccttaagaataaattaca---agtctaacccatttatacctgtgatctttt-ctggtg-------------------
||||||||  ||||||| |||||||| ||||| ||  | |||||||||||||||||||| || |||||||||||| |  | |  |||  | |    |  |||| |||     |||    |||   |||  |||   |   |  ||  |       | |     |     ||      |||||  | |  |    | | | |||  |                   
AAGAGAGCCACCAAAATTCGCAAGCTCTTCAATCTCACCAAGGAGGATGATGTGAGGAAATACGTCAACACCTATCGTCGCAGCTTTGTATCGGCCACAGgtacagtcatggctcctgatgtgggtgtcgtattttgccatgcttcctttcgtgcagtcgccgatgtagagcgggggccattgttgcgaggagccctctactgacgtctgcgtgcgtgctttcag

upper sequence: GLYMA13G31130.1 (Glycine max), 5'ss of exon 6
lower sequence: PP1S253_7V6.1 (Physcomitrella patens), 5'ss of exon 5
AAGAGAGCTTCCAAAATCCGCAAGCTTTTCAACCTGTCTAAGGAGGATGATGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATGgtaaagtgtcttctctctg--taaatgttctatagagatttatttt--ttccttaagaataaattacaagtctaacccatttatacctgtgatcttttctggtg----------------------
||||||||| |||||||||| ||||| ||||| ||  | |||||||| ||||||||||| || || ||||| ||| |  | |  |||    ||   |  ||||  || |   ||||     | | |||| |||    || | ||||  ||| || ||       |  |   | |    || |      | |    |  ||  ||                      
AAGAGAGCTACCAAAATCCGAAAGCTCTTCAATCTCACCAAGGAGGACGATGTGAGGAAATACGTAAACACATATCGCCGCAGCTTTGTGTCTGCCACAGgtatggtcttgactcttaaaatgagtgttgtattttaatgtgttttccttcattcagttgctggtttagagccaggggatgtgactgcgaggggctgactactgacggacgcatgcgtgctttcag

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|27424648|gb|CA936168.1|CA936168
EST:     TGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATG                         GGAAAAAGGTGAGCAAAGCTCCGAAGATACAACGACTGGTCACTCCCCTGA
genomic: TGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATGgtaaagtgtc ... ttggttgcagGGAAAAAGGTGAGCAAAGCTCCGAAGATACAACGACTGGTCACTCCCCTGA
EST: gi|19269313|gb|BM885569.1|BM885569
EST:     AGAACATTTACAACTAAAAATG                         GGAAAAAGGTGAGCAAAGCTCCGAAGATACAACGACTGGTCACTCCCCTGA
genomic: AGAACATTTACAACTAAAAATGgtaaagtgtc ... ttggttgcagGGAAAAAGGTGAGCAAAGCTCCGAAGATACAACGACTGGTCACTCCCCTGA
EST: gi|208312736|gb|GE112520.1|GE112520
EST:     TGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATG                         GGAAAAAGGTGAGCAAAGCTCCGAAGATACAACGACTGGTCACTCCCCTGA
genomic: TGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATGgtaaagtgtc ... ttggttgcagGGAAAAAGGTGAGCAAAGCTCCGAAGATACAACGACTGGTCACTCCCCTGA
EST: gi|151407299|gb|EV277114.1|EV277114
EST:     TGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATG                         GGAAAAAGGTGAGCAAAGCTCCGAAGATACAACGACTGGTCACTCCCCTGA
genomic: TGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATGgtaaagtgtc ... ttggttgcagGGAAAAAGGTGAGCAAAGCTCCGAAGATACAACGACTGGTCACTCCCCTGA
EST: gi|11413313|gb|BF425324.1|BF425324
EST:     TGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATG                         GGAANAAAG-TGAGCAAAGCTTCGAAGATACAACGACTGGGCACTCCCCTG
genomic: TGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATGgtaaagtgtc ... ttggttgcagGGAA-AAAGGTGAGCAAAGCTCCGAAGATACAACGACTGGTCACTCCCCTG
EST: gi|151403312|gb|EV273122.1|EV273122
EST:     TGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATG                         GGAAAAAGGTGAGCAAAGCTCCGAAGATACAACGACTGGTCACTCCCCTGA
genomic: TGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATGgtaaagtgtc ... ttggttgcagGGAAAAAGGTGAGCAAAGCTCCGAAGATACAACGACTGGTCACTCCCCTGA
EST: gi|207702799|gb|GD684801.1|GD684801
EST:     TGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATG                         GGAAAAAGGTGAGCAAAGCTCCGAAGATACAACGACTGGTCACTCCCCTGA
genomic: TGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATGgtaaagtgtc ... ttggttgcagGGAAAAAGGTGAGCAAAGCTCCGAAGATACAACGACTGGTCACTCCCCTGA
EST: gi|208249489|gb|GE044594.1|GE044594
EST:     TGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATG                         GGAAAAAGGTGAGCAAAGCTCCGAAGATACAACGACTGGTCACTCCCCTGA
genomic: TGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATGgtaaagtgtc ... ttggttgcagGGAAAAAGGTGAGCAAAGCTCCGAAGATACAACGACTGGTCACTCCCCTGA
EST: gi|208205180|gb|GE008251.1|GE008251
EST:     TGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATG                         GGAAAAAGGTGAGCAAAGCTCCGAAGATACAACGACTGGTCACTCCCCTGA
genomic: TGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATGgtaaagtgtc ... ttggttgcagGGAAAAAGGTGAGCAAAGCTCCGAAGATACAACGACTGGTCACTCCCCTGA
EST: gi|208142669|gb|GD944025.1|GD944025
EST:     TACAACTAAAAATG                         GGAAAAAGGTGAGCAAAGCTCCGAAGATACAACGACTGGTCACTCCCCTGA
genomic: TACAACTAAAAATGgtaaagtgtc ... ttggttgcagGGAAAAAGGTGAGCAAAGCTCCGAAGATACAACGACTGGTCACTCCCCTGA
EST: gi|208312700|gb|GE112162.1|GE112162
EST:     TACAACTAAAAATG                         GGAAAAAGGTGAGCAAAGCTCCGAAGATACAACGACTGGTCACTCCCCTGA
genomic: TACAACTAAAAATGgtaaagtgtc ... ttggttgcagGGAAAAAGGTGAGCAAAGCTCCGAAGATACAACGACTGGTCACTCCCCTGA
EST: gi|26269098|gb|CA820161.1|CA820161
EST:     GAACATTTACAACTAAAAATG                         GGAAAAAGGTGAGCAAAGCTCCGAAGATACAACGACTGGTCACTCCCCTGA
genomic: GAACATTTACAACTAAAAATGgtaaagtgtc ... ttggttgcagGGAAAAAGGTGAGCAAAGCTCCGAAGATACAACGACTGGTCACTCCCCTGA
EST: gi|17519909|gb|BM188951.1|BM188951
EST:     TGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATG                         GGAAAAAGGTGAGCAAAGCTCCGAAG
genomic: TGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATGgtaaagtgtc ... ttggttgcagGGAAAAAGGTGAGCAAAGCTCCGAAG
EST: gi|58017152|gb|CX703894.1|CX703894
EST:     TGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATG                         GGAAAAAGGTGAGCAAAGCTCCGAAGATACAACGACTGGTCACTCCCCTGA
genomic: TGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATGgtaaagtgtc ... ttggttgcagGGAAAAAGGTGAGCAAAGCTCCGAAGATACAACGACTGGTCACTCCCCTGA
EST: gi|18040763|gb|BM309057.1|BM309057
EST:     TGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATG                         GGAAAAAGGTGAGCAAAGCTCCG
genomic: TGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATGgtaaagtgtc ... ttggttgcagGGAAAAAGGTGAGCAAAGCTCCG
EST: gi|151412280|gb|EV282092.1|EV282092
EST:     TGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATG                         GGAAAAAAGGTGTGCAAAGCTCCGAAGACACAACGACTGGTCACTCCCCCT
genomic: TGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATGgtaaagtgtc ... ttggttgcagGGAAAAA-GGTGAGCAAAGCTCCGAAGATACAACGACTGGTCACTCCCC-T
EST: gi|21594126|gb|BQ610061.1|BQ610061
EST:     TGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATG                         GGAAAAAGGTGAGCAAAGCTCCGAAGATACAACGACTGGTCACTCCCCTGA
genomic: TGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATGgtaaagtgtc ... ttggttgcagGGAAAAAGGTGAGCAAAGCTCCGAAGATACAACGACTGGTCACTCCCCTGA
EST: gi|17400921|gb|BM177703.1|BM177703
EST:     TGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATG                         GGAAAAAGGTGAGCAAAGCTCCGAAGATACAACGACTGGTCA
genomic: TGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATGgtaaagtgtc ... ttggttgcagGGAAAAAGGTGAGCAAAGCTCCGAAGATACAACGACTGGTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGAGAGCTTCCAAAATCCGCAAGCTTTTCAACCTGTCTAAGGAGGATGATGTGAGGAAGTATGTCAACACCTATAGGAGAACATTTACAACTAAAAATGgtaaagtgtcttctctctgtaaatgttctatagagatttattttttccttaagaataaattacaagtctaacccatttatacctgtgatcttttctggtg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA