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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacatcacaggttccattttgtagtctattttgggaggttttaatcaatggtagatattcagttctcttgtcattacattgattttaatttattttttagGTTTTGGCACTGTTCCCATCATCTCAAGGTTTGGAAGTGACTTGGTCTTCTGTTGTTAAAATTGGCCAATCTCTGTACCGTGAGGGGCCTGGTAAAGATC

Basic information

species Glycine max
transcript GLYMA10G30220.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G30220.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv14s0030g01740.t01 (Vitis vinifera), 3'ss of exon 12
cacatcacaggttccatttt-gtagtctattttggg--aggttttaatcaatggtagatattcagttctcttgtcattacattgattttaatttattttttagGTTTTGGCACTGTTCCCATCATCTCAAGGTTTGGAAGTGACTTGGTCTTCTGTTGTTAAAATTGGCCAATCTCTGTACCGTGAGGGGCCTGGTAAAGATC
    | |   | ||||| || || |  | ||||  |  |      || |||   ||   ||||  || |||| |   |   ||  ||||   ||  |||| |||||||||   | |||||||| || |||||||| ||||| |||||||| |||||||| ||||| |||||||| || || |||||||| |||||||||||||
--tctaatttgctccatcttagttgcatgttttcagtcaaacaacaaacaaatataatcattcttttttcttttttcttttttt-ttttctcttccttttcagGTTTTGGTTTTATTCCCATCCTCCCAAGGTTTAGAAGTTACTTGGTCATCTGTTGTCAAAATCGGCCAATCCCTATATCGTGAGGGACCTGGTAAAGATC
















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|9899120|gb|BE608147.1|BE608147
EST:     CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAG                         GTTTTGGCACTGTTCCCATCATCTCAAGGTTTGGAAGTGACTTGGTCTTCT
genomic: CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGgttggttaaa ... tattttttagGTTTTGGCACTGTTCCCATCATCTCAAGGTTTGGAAGTGACTTGGTCTTCT
EST: gi|192309148|gb|FG999081.1|FG999081
EST:     CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAG                         GTTTTGGCACTGTTCCCATCATCTCAAGGTTTGGAAGTGACTTGGTCTTCT
genomic: CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGgttggttaaa ... tattttttagGTTTTGGCACTGTTCCCATCATCTCAAGGTTTGGAAGTGACTTGGTCTTCT
EST: gi|209702721|gb|BW652764.1|BW652764
EST:     AATTATTGCAAGGGTAGCAAAACAG                         GTTTTGGCACTGTTCCCATCATCTCAAGGTTTGGAAGTGACTTGGTCTTCT
genomic: AATTATTGCAAGGGTAGCAAAACAGgttggttaaa ... tattttttagGTTTTGGCACTGTTCCCATCATCTCAAGGTTTGGAAGTGACTTGGTCTTCT
EST: gi|151411529|gb|EV281340.1|EV281340
EST:     CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAG                         GTTTTGGCACTGTTCCCATCATCTCAAGGTTTGGAAGTGACTTGGTCTTCT
genomic: CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGgttggttaaa ... tattttttagGTTTTGGCACTGTTCCCATCATCTCAAGGTTTGGAAGTGACTTGGTCTTCT
EST: gi|209717714|gb|BW671532.1|BW671532
EST:     CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAG                         GTTTTGGCACTGTTCCCATCATCTCAAGGTTTGGAAGTGACTTGGTCTTCT
genomic: CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGgttggttaaa ... tattttttagGTTTTGGCACTGTTCCCATCATCTCAAGGTTTGGAAGTGACTTGGTCTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatggtagatattcagttctcttgtcattacattgattttaatttattttttagGTTTTGGCACTGTTCCCATCATCTCAAGGTTTGGAAGTGACTTGGTCTTCTGTTGTTAAAATTGGCCAATCTCTGTACCGTGAGGGGCCTGGTAAAGATC
                                     ttttaat  putative branch site (score: 3)
                                           tttatttttt  CT-rich tract
                    tcttgtcattacattg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacatcacaggttccattttgtagtctattttgggaggttttaatcaatggtagatattcagttctcttgtcattacattgattttaatttattttttagGTTTTGGCACTGTTCCCATCATCTCAAGGTTTGGAAGTGACTTGGTCTTCTGTTGTTAAAATTGGCCAATCTCTGTACCGTGAGGGGCCTGGTAAAGATC

cacatca
- - - - - - - - - - - - - - - - gggaggt