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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttatggctgatgcttggtttttgatttatatttaatttattctctttgtaattggaccctatttacattttgcttttaattattctttatctcttatagGCATACATGTTCAAATACGATTCTACTCATGGTCCATTCAAGGGGTCCATTAATATTTTGGATGACTCTACTTTGGAAATTAATGGGAAGCATGTTAAAG

Basic information

species Glycine max
transcript GLYMA03G22790.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv19s0085g00600.t01 (Vitis vinifera), 3'ss of exon 5
-tttatggctgatgcttggtttttgatttatatttaatttattctctttgtaattggaccctatttacattttgcttttaattattctttatctcttatagGCATACATGTTCAAATACGATTCTACTCATGGTCCATTCAAGGGGTCCATTAATATTTTGGATGACTCTACTTTGGAAATTAATGGGAAGCATGTTAAAG
 | ||||| |  |    | || ||||  ||  | | |       ||    | |  |      | |   | |    | ||  || |  ||||| |     |||| ||||||||||| || ||||||||||||||    ||||||||  |||| ||  | |||||||| || ||||||||||| ||||| |||||  | ||||
ttgtatgg-tagtttaggattcttgagctagttgttaggatccttcaactttagagagaaggaatggtagtgatatgttggttttcgtttattttacgcagGCTTACATGTTCAAGTATGATTCTACTCATGGAGTTTTCAAGGGAACCATCAAGGTATTGGATGAGTCCACTTTGGAAATCAATGGCAAGCAGATAAAAG
















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|298183719|gb|HO028932.1|HO028932
EST:     ATGTTGATGTTGTTGCAATTAATGATCCATTTATTGATGCGAAATATATG                         GCATACATGTTCAAATACGATTCTACTCATGGTCCATTCAAGGGGTCCATT
genomic: ATGTTGATGTTGTTGCAATTAATGATCCATTTATTGATGCGAAATATATGgtatgtaaat ... tctcttatagGCATACATGTTCAAATACGATTCTACTCATGGTCCATTCAAGGGGTCCATT
EST: gi|192322626|gb|FK014363.1|FK014363
EST:     ATGTTGATGTTGTTGCAATTAATGATCCATTTACTGATGCGAAATATATG                         GCATACATGTTCAAATACGATTCTACTCATGGTCCATTCAAGGGGTCCATT
genomic: ATGTTGATGTTGTTGCAATTAATGATCCATTTATTGATGCGAAATATATGgtatgtaaat ... tctcttatagGCATACATGTTCAAATACGATTCTACTCATGGTCCATTCAAGGGGTCCATT
EST: gi|208297585|gb|GE090588.1|GE090588
EST:     GCGAAATATATG                         GCATACATGTTCAAATACGATTCTACTCATGGTCCATTCAAGGGGTCCATT
genomic: GCGAAATATATGgtatgtaaat ... tctcttatagGCATACATGTTCAAATACGATTCTACTCATGGTCCATTCAAGGGGTCCATT
EST: gi|151407697|gb|EV277512.1|EV277512
EST:     TGTTGATGTTGTTGCAATTAATGATCCATTTTATTGATGCGAAATATATG                         GCATAAATGTTCAAATACGATTCTACTCATGGTCCATTCAAGGGGTCCATT
genomic: TGTTGATGTTGTTGCAATTAATGATCCATTT-ATTGATGCGAAATATATGgtatgtaaat ... tctcttatagGCATACATGTTCAAATACGATTCTACTCATGGTCCATTCAAGGGGTCCATT
EST: gi|207800666|gb|GD775055.1|GD775055
EST:     GCGAAATATATG                         GTCATACATGTTCAAATACGATTCTACTCATGGTCCATTCAAGGGGTCCAT
genomic: GCGAAATATATGgtatgtaaat ... tctcttatagG-CATACATGTTCAAATACGATTCTACTCATGGTCCATTCAAGGGGTCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtaattggaccctatttacattttgcttttaattattctttatctcttatagGCATACATGTTCAAATACGATTCTACTCATGGTCCATTCAAGGGGTCCATTAATATTTTGGATGACTCTACTTTGGAAATTAATGGGAAGCATGTTAAAG
                             ttttaat  putative branch site (score: 3)
                                   ttattctttatctctt  CT-rich tract
               tatttacattttgctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttatggctgatgcttggtttttgatttatatttaatttattctctttgtaattggaccctatttacattttgcttttaattattctttatctcttatagGCATACATGTTCAAATACGATTCTACTCATGGTCCATTCAAGGGGTCCATTAATATTTTGGATGACTCTACTTTGGAAATTAATGGGAAGCATGTTAAAG

- - - -ctgatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctttt