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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatagatttaacttggtacaatataatttttcatcctacagatttaaagtaccatgatgctattatcatccaatgtacatttgtggttccctttctgtagGTGTTGCTGCAAGGCCTGGAAAGGTTGTGGGTTCGGTAATGCGTTACAACAACTGTGGGGTAGCCGGGACGGCCGAGGCTGAACAGCGTCGGGTGGTCAG

Basic information

species Glycine max
transcript GLYMA13G28120.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G28120.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 9
---tatagatttaacttggtacaatataatttttcatcctacagatttaaagtaccatgatgctattatcatccaatgtacatttgtggttccctttctgtagGTGTTGCTGCAAGGCCTGGAAAGGTTGTGGGTTCGGTAATGCGTTACAACAACTGTGGGGTAGCCGGGACGGCCGAGGCT---GAACAGCGTCGGGTGGTCAG
   |   | | |   |   |    |    |||  |||||||      |     ||||       || ||   |   | ||  | |    | | | |  || ||| | |||||||||||||||||||||||| ||||| ||  ||||||||||||||||||| | ||| |   | || |||| |   ||||||||  |  ||||   
ctctcatgctcttgttccttctcttgatctttgccatcctat---cctttgtcaccagatcttaataattggcttctctaattataaactgctcctagtgcagGAGGTGCTGCAAGGCCTGGAAAGGTTGTTGGTTCAGTGTTGCGTTACAACAACTGTGGAGCAGCTGCAGCAGCAGAGGTTCTTGAACAGCGGAGAATGGT---
















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|254316052|gb|GR825861.1|GR825861
EST:     TGCCATCCCTATGTCTCGACTTCCTTTACAAGCACCACAAAATATTCAAG                         GTGTTGCTGCAAGGCCTGGAAAGGTTGTGGGTTCGGTAATGCGTTACAACA
genomic: TGCCATCCCTATGTCTCGACTTCCTTTACAAGCACCACAAAATATTCAAGgtgtgatgat ... ctttctgtagGTGTTGCTGCAAGGCCTGGAAAGGTTGTGGGTTCGGTAATGCGTTACAACA
EST: gi|193409165|gb|FK372483.1|FK372483
EST:     TCCCTATGTCTAGGCTTCCTTTACAAGCACCACAAAAATATTCAAG                         GTGTTGCTGCAAGGCCTGGAAAGGTTGTGGGTTCGGTAATGCGTTACAACA
genomic: TCCCTATGTCTCGACTTCCTTTACAAGCACCAC-AAAATATTCAAGgtgtgatgat ... ctttctgtagGTGTTGCTGCAAGGCCTGGAAAGGTTGTGGGTTCGGTAATGCGTTACAACA
EST: gi|192296005|gb|FG993383.1|FG993383
EST:     TGCCATCCCTATGTCTCGACTTCCTTTACAAGCACCACAAAATATTCAAG                         GTGTCGCTGCAAGGCCTGGAAAGGTTGTGGGTTCGGTAATGTGTTACAACA
genomic: TGCCATCCCTATGTCTCGACTTCCTTTACAAGCACCACAAAATATTCAAGgtgtgatgat ... ctttctgtagGTGTTGCTGCAAGGCCTGGAAAGGTTGTGGGTTCGGTAATGCGTTACAACA
EST: gi|192296006|gb|FG993384.1|FG993384
EST:     TGCCATCCCTATGTCTCGACTTCCTTTACAAGCACCACAAAATATTCAAG                         GTGTCGCTGCAAGGCCTGGAAAGGTTGTGGGTTCGGTAATGTGTTACAACA
genomic: TGCCATCCCTATGTCTCGACTTCCTTTACAAGCACCACAAAATATTCAAGgtgtgatgat ... ctttctgtagGTGTTGCTGCAAGGCCTGGAAAGGTTGTGGGTTCGGTAATGCGTTACAACA
EST: gi|151410759|gb|EV280574.1|EV280574
EST:     TGCCATCCCTATGTCTCGACTTCCTTTACAAGCACCACAAAATATTCAAG                         GTGTTGCTGCAAGGCCTGGAAAGGTTGTGGGTTCGGTAATGCGTTACAACA
genomic: TGCCATCCCTATGTCTCGACTTCCTTTACAAGCACCACAAAATATTCAAGgtgtgatgat ... ctttctgtagGTGTTGCTGCAAGGCCTGGAAAGGTTGTGGGTTCGGTAATGCGTTACAACA
EST: gi|51345005|gb|CO985738.1|CO985738
EST:     TGCCATCCCTATGTCTCGACTTCCTTTACAAGCACCACAAAATATTCAAG                         GTGTTGCTGCAAGGCCTGGAAAGGTTGTGGGTTCGGTAATGCGTTACAACA
genomic: TGCCATCCCTATGTCTCGACTTCCTTTACAAGCACCACAAAATATTCAAGgtgtgatgat ... ctttctgtagGTGTTGCTGCAAGGCCTGGAAAGGTTGTGGGTTCGGTAATGCGTTACAACA
EST: gi|58025025|gb|CX711766.1|CX711766
EST:     TGCCATCCCTATGTCTCGACTTCCTTTACAAGCACCACAAAATATTCAAG                         GTGTTGCTGCAAGGCCTGGAAAGGTTGTGGGTTCGGTAATGCGTTACAACA
genomic: TGCCATCCCTATGTCTCGACTTCCTTTACAAGCACCACAAAATATTCAAGgtgtgatgat ... ctttctgtagGTGTTGCTGCAAGGCCTGGAAAGGTTGTGGGTTCGGTAATGCGTTACAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagtaccatgatgctattatcatccaatgtacatttgtggttccctttctgtagGTGTTGCTGCAAGGCCTGGAAAGGTTGTGGGTTCGGTAATGCGTTACAACAACTGTGGGGTAGCCGGGACGGCCGAGGCTGAACAGCGTCGGGTGGTCAG
                                         ttccctttctgt  CT-rich tract
               tattatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatagatttaacttggtacaatataatttttcatcctacagatttaaagtaccatgatgctattatcatccaatgtacatttgtggttccctttctgtagGTGTTGCTGCAAGGCCTGGAAAGGTTGTGGGTTCGGTAATGCGTTACAACAACTGTGGGGTAGCCGGGACGGCCGAGGCTGAACAGCGTCGGGTGGTCAG

- - - - - - - - - - - - - - - - -tcctaca
- - - - - - - - - - - - - - - - - - - - - - - - - -ccatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggttcc