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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatatctgttgcatgctgtatgctttgtccatgaagcaaagtgatggagtagtgtatgatttgcttggacttattggtggtttgctttcattttttcagATTATTACCACCTTCAGTGTAGTGGATAACATAAAACAGCAGTTTTATGCTCAACAGGGGAGAATTTCCAG

Basic information

species Glycine max
transcript GLYMA20G38530.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38530.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv13s0067g03850.t01 (Vitis vinifera), 3'ss of exon 16
caatatctgttgcatgctgtatgctttgtccatgaagcaaagtgatggagtagtgtatgatttgcttggac--ttattggtggtttgcttt--cattttttcagATTATTACCACCTTCAGTGTAGTGGATAACATAAAACAGCAGTTTTATGCTCAACAGGGGAGAATTTCCAG
|||| | |      |  |  |  | | |  ||  |  |||| |  |   ||  |  |  ||| || ||  |  | ||| ||| |||  |||  | ||||| ||||| || ||||||||||||||||| |||||||| ||| |||| |||||||||||||| |||| |||||||||
caatttgttaattctattcaacacctag--caatacacaaa-ttctattgtctta-actattggcatgaccaatgattagtgattttttttttcctttttgcagATAATAACCACCTTCAGTGTAGTTGATAACATGAAAGAGCAATTTTATGCTCAACAAGGGAAAATTTCCAG
















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|9985234|gb|BE659342.1|BE659342
EST:     TAAGTCCAAGGAGAAATCTTGAGGAGGAATATTTGACCTATGAAGCCAAG                         ATTATTACCACCTTCAGTGTAGTGGATAACATAAAACAGCAGTTTTATGCT
genomic: TAAGTCCAAGGAGAAATCTTGAGGAGGAATATTTGACCTATGAAGCCAAGgtatatatgt ... attttttcagATTATTACCACCTTCAGTGTAGTGGATAACATAAAACAGCAGTTTTATGCT
EST: gi|254327727|gb|GR834692.1|GR834692
EST:     TAAGTCCAAGGAGAAATCTTGAGGAGGAATATTTGACCTATGAAGCCAAG                         ATTATTACCACCTTCAGTGTAGTGGATAACATAAAACAGCAGTTTTATGCT
genomic: TAAGTCCAAGGAGAAATCTTGAGGAGGAATATTTGACCTATGAAGCCAAGgtatatatgt ... attttttcagATTATTACCACCTTCAGTGTAGTGGATAACATAAAACAGCAGTTTTATGCT
EST: gi|209727141|gb|BW660147.1|BW660147
EST:     GACCTATGAAGCCAAG                         ATTATTACCACCTTCAGTGTAGTGGATAACATAAAACAGCAGTTTTATGCT
genomic: GACCTATGAAGCCAAGgtatatatgt ... attttttcagATTATTACCACCTTCAGTGTAGTGGATAACATAAAACAGCAGTTTTATGCT
EST: gi|57575890|gb|CX548861.1|CX548861
EST:     TAAGTCCAAGGAGAAATCTTGAGGAGGAATATTTGACCTATGAAGCCAAG                         ATTATTACCACCTTCAGTGTAGTGGATAACATAAAACAGCAGTTTTATGCT
genomic: TAAGTCCAAGGAGAAATCTTGAGGAGGAATATTTGACCTATGAAGCCAAGgtatatatgt ... attttttcagATTATTACCACCTTCAGTGTAGTGGATAACATAAAACAGCAGTTTTATGCT
EST: gi|151410338|gb|EV280153.1|EV280153
EST:     TAAGTCCAAGGAGAAATCTTGAGGAGGAATATTTGACCTATGAAGCCAAG                         ATTATTGCCACCTTCAGTGTAGTGGATAACATAAAACAGCAGTTTTATGCT
genomic: TAAGTCCAAGGAGAAATCTTGAGGAGGAATATTTGACCTATGAAGCCAAGgtatatatgt ... attttttcagATTATTACCACCTTCAGTGTAGTGGATAACATAAAACAGCAGTTTTATGCT
EST: gi|58025300|gb|CX712041.1|CX712041
EST:     TAAGTCCAAGGAGAAATCTTGAGGAGGAATATTTGACCTATGAAGCCAAG                         ATTATTACCACCTTCAGTGTAGTGGATAACATAAAACAGCAGTTTTATGCT
genomic: TAAGTCCAAGGAGAAATCTTGAGGAGGAATATTTGACCTATGAAGCCAAGgtatatatgt ... attttttcagATTATTACCACCTTCAGTGTAGTGGATAACATAAAACAGCAGTTTTATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggagtagtgtatgatttgcttggacttattggtggtttgctttcattttttcagATTATTACCACCTTCAGTGTAGTGGATAACATAAAACAGCAGTTTTATGCTCAACAGGGGAGAATTTCCAG
                                    tttgctttcatttttt  CT-rich tract
                                         tttcatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caatatctgttgcatgctgtatgctttgtccatgaagcaaagtgatggagtagtgtatgatttgcttggacttattggtggtttgctttcattttttcagATTATTACCACCTTCAGTGTAGTGGATAACATAAAACAGCAGTTTTATGCTCAACAGGGGAGAATTTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - -gcatgct
- - - - - - - - - gtatgct
- - - - - - - - - - - - - - -ccatgaa
- - - - - - - - - - - - - - - - - - - - - -gatggag
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgtatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttggtgg