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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatgtcttattgaagtatttcctgatagcaagcacatgcttcctgcattttgtctaaatgctacctctaatagttattaaagatggtcatctgctgtagGTAGCTTGGGAGCATGAACAGTTTTCAAGGCTGAGAGTTACTGCGGCCACCCTCTCTGAACTCTCTACAGCACCTGAATTTCTAGAGAAGACTGGTGGCT

Basic information

species Glycine max
transcript GLYMA11G18710.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G18710.1 (Glycine max), 3'ss of exon 8
lower sequence: AT3G44330.1 (Arabidopsis thaliana), 3'ss of exon 8
--tcatgtc----ttattga-agtatttcctgatagcaagcacatgcttcctgcattttgtctaaatgctacctctaatagttattaaagatggtcatctgctgtagGTAGCTTGGGAGCATGAACAGTTTTCAAGGCTGAGAGTTACTGCGGCCACCCTCTCTGAACTCTCTACAGCACCTGAATTTCTAGAGAAGACTGGTGGCT
    |||      ||||||| |||| ||  |||    |   |  | ||  || | |    | || |  |    ||||||  | | |   | || | |  |  | ||||| ||||||||||||||||| |||||||| || ||||| ||||| |||||  | |||||||| || ||  |||| || || || || ||  ||||  |  
tcctatgctggggttattgagagtagtt--tgactttac-tatgttctctctccgtca-atttatagaccctttctaat--tgaattgtgttgctgaattatt-tagGTTGCTTGGGAGCATGAACAATTTTCAAGACTCAGAGTAACTGCAGCCACATTATCTGAACTTTCAACTCCACCCGAGTTACTGGAAAATGCTGGAAGTC

upper sequence: GLYMA11G18710.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv06s0080g00880.t01 (Vitis vinifera), 3'ss of exon 8
tcatgtcttattg-aagtatttcctgatagcaagcacatgcttcctg----cattttgtctaaatgctacctctaatagttattaaagatggtcatctgctgtagGTAGCTTGGGAGCATGAACAGTTTTCAAGGCTGAGAGTTACTGCGGCCACCCTCTCTGAACTCTCTACAGCACCTGAATTTCTAGAGAAGACTGGTGGCT
     | || ||| ||     |    |||   ||  | | |    ||    ||| |||        ||   |  | | | |  ||||  || |    |||||||||||||||||||||||||||||||||||||||| ||||||||||| |||||||| ||||||||||||   || |||||| |  |||| |  ||||| ||  
-----tttttttgtaaactgctgtaaatatgtagtgctttcagtgtggtcccatattgagatcgcactgtttagacttggtgctaaatctgttgccgtgctgtagGTAGCTTGGGAGCATGAACAGTTTTCAAGGCTAAGAGTTACTGCTGCCACCCTTTCTGAACTCTCTGTTGCGCCTGAACTGTTAGAAAGAACTGGCGGTC
















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|11687645|gb|BF595321.1|BF595321
EST:     GCTTTAAAGTGAATCTGAAGCATAAGAAAATTAACATTTGCAATCCCCGA                         GTAGCTTGGGAGCATGAACAGTTTTCAAGGCTGAGAGTTACTGCAGCCACC
genomic: GCTTTAAAGTGAATCTGAAGCATAAGAAAATTAACATTTCCAATCCCCGAgtaagtgata ... tctgctgtagGTAGCTTGGGAGCATGAACAGTTTTCAAGGCTGAGAGTTACTGCGGCCACC
EST: gi|8284372|gb|BE021931.1|BE021931
EST:     GCTNTAAAGTGAATCTGAAGCATAAGAAAATTAACATTTCCAATCCCCGA                         GTAGCTTGGGAGCATGAACAGTTTTCAAGGCTGAGAGTTTCTGCGGCCACC
genomic: GCTTTAAAGTGAATCTGAAGCATAAGAAAATTAACATTTCCAATCCCCGAgtaagtgata ... tctgctgtagGTAGCTTGGGAGCATGAACAGTTTTCAAGGCTGAGAGTTACTGCGGCCACC
EST: gi|21993710|gb|BQ785238.1|BQ785238
EST:     GCTTTAAAGTGAATCTGAAGCATAAGAAAATTAACATTTCCAATCCCCGA                         GTAGCTTGGGAGCATGAACAGTTTTCAAGGCTGAGAGTTACTGCGGCCACC
genomic: GCTTTAAAGTGAATCTGAAGCATAAGAAAATTAACATTTCCAATCCCCGAgtaagtgata ... tctgctgtagGTAGCTTGGGAGCATGAACAGTTTTCAAGGCTGAGAGTTACTGCGGCCACC
EST: gi|33388989|gb|CA852196.1|CA852196
EST:     GCTTTAAAGTGAATCTGAAGCATAAGAAAATTAACATTTCCAATCCCCGA                         GTAGCTTGGGAGCATGAACAGTTTTCAAGGCTGAGAGTTACTGCGGCCACC
genomic: GCTTTAAAGTGAATCTGAAGCATAAGAAAATTAACATTTCCAATCCCCGAgtaagtgata ... tctgctgtagGTAGCTTGGGAGCATGAACAGTTTTCAAGGCTGAGAGTTACTGCGGCCACC
EST: gi|254343175|gb|GR859337.1|GR859337
EST:     AAGAAAATT-ACATTTCC-ATCCCCGA                         GTAGC-TGGGAGCATGAACAGTTTTCAAGGCTGAGAGTTACTGCGGCCACC
genomic: AAGAAAATTAACATTTCCAATCCCCGAgtaagtgata ... tctgctgtagGTAGCTTGGGAGCATGAACAGTTTTCAAGGCTGAGAGTTACTGCGGCCACC
EST: gi|151406228|gb|EV276043.1|EV276043
EST:     GCTTTAAAGTGAATCTGAAGCATAAGAAAATTAACATTTCCAATCCCCGA                         GTAGCTTGGGAGCATGAACAGTTTTCAAGGCTGAGAGTTACTGCGGCCACC
genomic: GCTTTAAAGTGAATCTGAAGCATAAGAAAATTAACATTTCCAATCCCCGAgtaagtgata ... tctgctgtagGTAGCTTGGGAGCATGAACAGTTTTCAAGGCTGAGAGTTACTGCGGCCACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcattttgtctaaatgctacctctaatagttattaaagatggtcatctgctgtagGTAGCTTGGGAGCATGAACAGTTTTCAAGGCTGAGAGTTACTGCGGCCACCCTCTCTGAACTCTCTACAGCACCTGAATTTCTAGAGAAGACTGGTGGCT
                    ctctaat  putative branch site (score: 3)
                       taatagttattaaaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatgtcttattgaagtatttcctgatagcaagcacatgcttcctgcattttgtctaaatgctacctctaatagttattaaagatggtcatctgctgtagGTAGCTTGGGAGCATGAACAGTTTTCAAGGCTGAGAGTTACTGCGGCCACCCTCTCTGAACTCTCTACAGCACCTGAATTTCTAGAGAAGACTGGTGGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
tcatgtc
- - - - - - - - - - -cctgata
- - - - - - - - - - - - - - -caagcac
- - - - - - - - - - - - - - - - - - - - -tcctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctacc