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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgacatgttataaaaaccattagataggagctattttattaggagctacattttctgtctatttcattttagcaactgaaatattattaattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAG

Basic information

species Glycine max
transcript GLYMA20G32320.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G32320.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G54840.2 (Arabidopsis thaliana), 3'ss of exon 5
tatgacatgttataa--aaaccattagataggag-ctattttattaggagctacattttctgtctatttcattttagcaactgaaatatt----attaattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAG
       || ||  |  || ||||| |  |  |  |  |      | ||  |  |  || | |  | |  | |        |  |    |    || ||| |   |||| || ||||| ||||||||||| ||||| || ||||| ||||| ||||| ||||||||||| |  || ||  | |||||  ||    ||
-------tgctaccatgaagccatttggcacaactccgtgcaggaaagatatcaacattatattgaatctagtgctattgttttacccctgcccataaatctaacagGAACTGCAAAAGCATGGAAGCCCAGATATTGTTATGGCTCTGGTTGGTAACAAAGCTGATCTACATGAAAAAAGAGAAGTACCTACTGAG

upper sequence: GLYMA20G32320.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv13s0019g04680.t01 (Vitis vinifera), 3'ss of exon 5
---tatgacatgttataaaaaccattagataggagctatttta-ttaggagctac-attttctgtctatttcattttagcaactgaaatattattaattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAG
   |||    | || |    ||| ||   |      |||| ||  |    | | | || ||   ||| |  | || |||  | | || | || | | ||||  ||||  | ||||||||||||||||||||||| || |||||  | || || || |||||||||||||  ||||| || |||||  | || || 
agatatccttttttgtcttcaccctt---tttaccttattctaacttcctgttgctatgttgaatctttccctttatagtgaattaa-ttttgtca-ttttacagGAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAA
















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:     ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAG                         GAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
genomic: ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagattttc ... aattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
EST: gi|298188274|gb|HO034967.1|HO034967
EST:     ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAG                         GAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
genomic: ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagattttc ... aattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
EST: gi|192303626|gb|FG998636.1|FG998636
EST:     CTTTCAGCAAAGCACAGTACTGGGTTAAG                         GAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
genomic: CTTTCAGCAAAGCACAGTACTGGGTTAAGgtagattttc ... aattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
EST: gi|208166021|gb|GD959081.1|GD959081
EST:     CAAAGCACAGTACTGGGTTAAG                         GAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
genomic: CAAAGCACAGTACTGGGTTAAGgtagattttc ... aattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
EST: gi|207760676|gb|GD733677.1|GD733677
EST:     CAAAGCACAGTACTGGGTTAAG                         GAGCTACAAAAACATGGAAGCCCTGTATTATAGTTGATGGCACTGGTCGGT
genomic: CAAAGCACAGTACTGGGTTAAGgtagattttc ... aattttttagGAGCTACAAAAACATGGAAGCCCTG-A-TATAG-TGATGGCACTGGTCGGT
EST: gi|8670136|gb|BE191243.1|BE191243
EST:     ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAG                         GAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
genomic: ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagattttc ... aattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
EST: gi|213611330|gb|DB983950.1|DB983950
EST:     GCAAAGCACAGTACTGGGTTAAG                         GAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
genomic: GCAAAGCACAGTACTGGGTTAAGgtagattttc ... aattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
EST: gi|151401597|gb|EV271411.1|EV271411
EST:     ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAG                         GAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
genomic: ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagattttc ... aattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
EST: gi|14009240|gb|BG725844.1|BG725844
EST:     ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAG                         GAGCTACAAAAACATGGAAGCCCTGATATA
genomic: ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagattttc ... aattttttagGAGCTACAAAAACATGGAAGCCCTGATATA
EST: gi|33388034|gb|CA851241.1|CA851241
EST:     ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAG                         GAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
genomic: ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagattttc ... aattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
EST: gi|208062999|gb|GD860901.1|GD860901
EST:     ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAG                         GAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
genomic: ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagattttc ... aattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
EST: gi|8670147|gb|BE191254.1|BE191254
EST:     ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAG                         GAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
genomic: ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagattttc ... aattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
EST: gi|120530900|gb|EH259033.1|EH259033
EST:     ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAG                         GAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
genomic: ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagattttc ... aattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
EST: gi|208127836|gb|GD924910.1|GD924910
EST:     ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAG                         GAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
genomic: ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagattttc ... aattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
EST: gi|213603351|gb|DB966610.1|DB966610
EST:     ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAG                         GAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
genomic: ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagattttc ... aattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
EST: gi|58017129|gb|CX703871.1|CX703871
EST:     ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAG                         GAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
genomic: ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagattttc ... aattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
EST: gi|208141217|gb|GD934383.1|GD934383
EST:     ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAG                         GAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
genomic: ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagattttc ... aattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
EST: gi|151399728|gb|EV269599.1|EV269599
EST:     ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAG                         GAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
genomic: ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagattttc ... aattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
EST: gi|208308185|gb|GE102837.1|GE102837
EST:     CAAAGCACAGTACTGGGTTAAG                         GAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
genomic: CAAAGCACAGTACTGGGTTAAGgtagattttc ... aattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
EST: gi|13478097|gb|BG507714.1|BG507714
EST:     ATGATATAACAAGCCCAGAATCTTTCATCAAAGCACAGTACTGGGTTAAG                         GAGCTACAAAAACATGGAAGCCCTGATATATTGATGGCACTGGTCGGTAAT
genomic: ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagattttc ... aattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
EST: gi|19053755|gb|BM732422.1|BM732422
EST:     ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAG                         GAGCTACAAAAACATGGAAGCCC
genomic: ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagattttc ... aattttttagGAGCTACAAAAACATGGAAGCCC
EST: gi|6665996|gb|AW277455.1|AW277455
EST:     ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAG                         GAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
genomic: ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagattttc ... aattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
EST: gi|6667685|gb|AW279136.1|AW279136
EST:     ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAG                         GAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
genomic: ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagattttc ... aattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
EST: gi|6455577|gb|AW186260.1|AW186260
EST:     ATGATATAACAAGCCCAGAATCTTTCAGCANAGCACAGTACTGGGTTAAG                         GAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCA
genomic: ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagattttc ... aattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctacattttctgtctatttcattttagcaactgaaatattattaattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAG
                                         tattaat  putative branch site (score: 2)
                                               tttttt  CT-rich tract
                tatttcattttagcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgacatgttataaaaaccattagataggagctattttattaggagctacattttctgtctatttcattttagcaactgaaatattattaattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- tgacatg
- - - - - -ataaaaa
- - - - - - - - - - - - - - - - - - - - - - -agctaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaactg