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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataaatttatggatgttctctatgtgccactaaatgctaaaatttcaggttgtgttaacgttggtatttatttgctatagGAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTGATCATCGTGTTTTTGATGGCAAAGTTGGAG

Basic information

species Glycine max
transcript GLYMA20G33080.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G33080.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv13s0074g00150.t01 (Vitis vinifera), 3'ss of exon 21
-gtataaatttatggatgttctctatg-tgccac-taaatgctaaaatttcaggttgtgttaacgttggtatttatttgctat--agGAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTGATCATCGTGTTTTTGATGGCAAAGTTGGAG
  || | |||  ||  | |   ||||  | |||   |  || |  | ||| || | ||  ||   || | ||||| |||||    |||| ||||||||||  || ||| ||| ||  ||| ||||||||| || ||||||||||||||||||||||||||||||||||
gttagatattgttgcttatatcctattctaccatacacttgatgcatttttagttagttgtatgatttggatttacttgcttctcagGACTTGAGAAGCCTGCAGTTGTCACAAAAATGAACTTAACATTATCCGCTGATCATCGTGTTTTTGATGGCAAAGTTGGAG
















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|27426899|gb|CA938419.1|CA938419
EST:     TGCTGTAGGGAGAGGCAACAAAGTTGTGGAACCAGTAATTGGAACTGATG                         GAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTG
genomic: TGCTGTAGGGAGAGGCAACAAAGTTGTGGAACCAGTAATTGGAACTGATGgtataaattt ... tttgctatagGAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTG
EST: gi|15288026|gb|BI471917.1|BI471917
EST:     GGGAGAGGCAACAAAGTTGTGGAACCAGTAATTGGAACTGATG                         GAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTG
genomic: GGGAGAGGCAACAAAGTTGTGGAACCAGTAATTGGAACTGATGgtataaattt ... tttgctatagGAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTG
EST: gi|8403681|gb|BE059377.1|BE059377
EST:     TGCTGTAGGGAGAGGCAACAAAGTTGTGGAACCAGTAATTGGAACTGATG                         GAATTGCGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTG
genomic: TGCTGTAGGGAGAGGCAACAAAGTTGTGGAACCAGTAATTGGAACTGATGgtataaattt ... tttgctatagGAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTG
EST: gi|6964563|gb|AW433256.1|AW433256
EST:     TGCTGTAGGGAGAGGCAACAAAGTTGTGGAACCAGTAATTGGAACTGATG                         GAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTG
genomic: TGCTGTAGGGAGAGGCAACAAAGTTGTGGAACCAGTAATTGGAACTGATGgtataaattt ... tttgctatagGAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTG
EST: gi|6227678|gb|AW156277.1|AW156277
EST:     TGCTGTAGGGAGAGGCAACAAAGTTGTGGAACCAGTAATTGGAACTGATG                         GAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTG
genomic: TGCTGTAGGGAGAGGCAACAAAGTTGTGGAACCAGTAATTGGAACTGATGgtataaattt ... tttgctatagGAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTG
EST: gi|51336348|gb|CO980214.1|CO980214
EST:     TGCTGTAGGGAGAGGCAACAAAGTTGTGGAACCAGTAATTGGAACTGATG                         GAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTG
genomic: TGCTGTAGGGAGAGGCAACAAAGTTGTGGAACCAGTAATTGGAACTGATGgtataaattt ... tttgctatagGAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTG
EST: gi|13311756|gb|BG405407.1|BG405407
EST:     GTTGTGGAACCAGTAATTGGAACTGATG                         GAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTG
genomic: GTTGTGGAACCAGTAATTGGAACTGATGgtataaattt ... tttgctatagGAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTG
EST: gi|192310210|gb|FK000690.1|FK000690
EST:     TGCTGTAGGGAGAGGCAAC-AATTTGTGGAACCAGTAATTGGAACTGATG                         GAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTG
genomic: TGCTGTAGGGAGAGGCAACAAAGTTGTGGAACCAGTAATTGGAACTGATGgtataaattt ... tttgctatagGAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTG
EST: gi|21256352|gb|BQ453240.1|BQ453240
EST:     TGCTGTAGGGAGAGGCAACAAAGTTGTGGAACCAGTAATTGGAACTGATG                         GAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTG
genomic: TGCTGTAGGGAGAGGCAACAAAGTTGTGGAACCAGTAATTGGAACTGATGgtataaattt ... tttgctatagGAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTG
EST: gi|51344360|gb|CO985093.1|CO985093
EST:     TGCTGTAGGGAGAGGCAACAAAGTTGTGGAACCAGTAATTGGAACTGATG                         GAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTG
genomic: TGCTGTAGGGAGAGGCAACAAAGTTGTGGAACCAGTAATTGGAACTGATGgtataaattt ... tttgctatagGAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTG
EST: gi|57575389|gb|CX548364.1|CX548364
EST:     TGCTGTAGGGAGAGGCAACAAAGTTGTGGAACCAGTAATTGGAACTGATG                         GAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTG
genomic: TGCTGTAGGGAGAGGCAACAAAGTTGTGGAACCAGTAATTGGAACTGATGgtataaattt ... tttgctatagGAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTG
EST: gi|209716666|gb|BW654299.1|BW654299
EST:     TGCTGTAGGGAGAGGCAACAAAGTTGTGGAACCAGTAATTGGAACTGATG                         GAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTG
genomic: TGCTGTAGGGAGAGGCAACAAAGTTGTGGAACCAGTAATTGGAACTGATGgtataaattt ... tttgctatagGAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTG
EST: gi|120532018|gb|EH260151.1|EH260151
EST:     TGCTGTAGGGAGAGGCAACAAAGTTGTGGAACCAGTAATTGGAACTGATG                         GAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTG
genomic: TGCTGTAGGGAGAGGCAACAAAGTTGTGGAACCAGTAATTGGAACTGATGgtataaattt ... tttgctatagGAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTG
EST: gi|19346936|gb|BM891747.1|BM891747
EST:     TGCTGTAGGGAGAGGCAACAAAGTTGTGGAACCAGTAATTGGAACTGATG                         GAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTG
genomic: TGCTGTAGGGAGAGGCAACAAAGTTGTGGAACCAGTAATTGGAACTGATGgtataaattt ... tttgctatagGAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTG
EST: gi|58023434|gb|CX710175.1|CX710175
EST:     TGCTGTAGGGAGAGGCAACAAAGTTGTGGAACCAGTAATTGGAACTGATG                         GAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTG
genomic: TGCTGTAGGGAGAGGCAACAAAGTTGTGGAACCAGTAATTGGAACTGATGgtataaattt ... tttgctatagGAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccactaaatgctaaaatttcaggttgtgttaacgttggtatttatttgctatagGAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTGATCATCGTGTTTTTGATGGCAAAGTTGGAG
                           tgttaac  putative branch site (score: 2)
                                         tttattt  putative PPT
     taaatgctaaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataaatttatggatgttctctatgtgccactaaatgctaaaatttcaggttgtgttaacgttggtatttatttgctatagGAATTGAGAAGCCATCAATTGCCACTAAGTTGAGCTTAACATTGTCTGCTGATCATCGTGTTTTTGATGGCAAAGTTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG