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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacattgcttaccttaaaaagataccaataatgtggttaaactgtcagatgcatgaattattaattcctcctgtgttctagGCATCTGTACAGGCTAATGACTTAAAAAGTGTTGAGAGAAGGTTACCTTTGACTGGGGAGAGCTTAGACTCTAGAGGTCTTTATATTTATGATGATGGCA

Basic information

species Glycine max
transcript GLYMA19G41400.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G41400.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv19s0014g01900.t01 (Vitis vinifera), 3'ss of exon 11
----gtatacattgcttaccttaaaaagataccaataatgtggttaaac-tgtcagatgcatgaattattaattcctcctgtgttctagGCATCTGTACAGGCTAATGACTTAAAAAGTGTTGAGAGAAGGTTACCTTTGACTGGGGAGAGCTTAGACTCTAGAGGTCTTTATATTTATGATGATGGCA------------
        |  |   ||   || ||      ||||| |||   || |    || |    |   || |     | | |    | ||  || || |||  |||||  |||| || |||||            ||||||  |   || |||||||||||| ||||||||||| |||||||||||||||||              
gtaaaggaatttcttttggtttgaattttctccaatcatgccttttactacgtgaatctctaaaactgcatctacatgtcatattgcagCCAACTGCTCAGGCAGATGAGTTGAAAAG------------GTTACCACTAGTTGCGGAGAGCTTAGATTCTAGAGGTCTATATATTTATGATGATGGTTTTCGCTTTGTTA
















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|14999781|gb|BI320595.1|BI320595
EST:     TGAAACTTCTCTATCCTAGCTTGATTCGACTTGATGAATATCTTCTGAAG                         GCATCTGTACAGGCTAATGACTTAAAAAGTGTTGAGAGAAGGTTACCTTTG
genomic: TGAAACTTCTCTATCCTAGCTTGATTCGACTTGATGAATATCTTCTGAAGgtatacattg ... tgtgttctagGCATCTGTACAGGCTAATGACTTAAAAAGTGTTGAGAGAAGGTTACCTTTG
EST: gi|21602683|gb|BQ613014.1|BQ613014
EST:     TGAAACTTCTCTATCCTAGCTTGATTCGACTTGATGAATATCTTCTGAAG                         GCATCTGTACAGGCTAATGACTTAAAAAGTGTTGAGAGAAGGTTACCTTTG
genomic: TGAAACTTCTCTATCCTAGCTTGATTCGACTTGATGAATATCTTCTGAAGgtatacattg ... tgtgttctagGCATCTGTACAGGCTAATGACTTAAAAAGTGTTGAGAGAAGGTTACCTTTG
EST: gi|207702616|gb|GD685682.1|GD685682
EST:     TGAAACTTCTCTATCCTAGCTTGATTCGACTTGGTGAATATCTTCTGAAG                         GCATCTGTACAGGCTAATGACTTAAAAAGTGTTGAGAGAAGGTTACCTTTG
genomic: TGAAACTTCTCTATCCTAGCTTGATTCGACTTGATGAATATCTTCTGAAGgtatacattg ... tgtgttctagGCATCTGTACAGGCTAATGACTTAAAAAGTGTTGAGAGAAGGTTACCTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataatgtggttaaactgtcagatgcatgaattattaattcctcctgtgttctagGCATCTGTACAGGCTAATGACTTAAAAAGTGTTGAGAGAAGGTTACCTTTGACTGGGGAGAGCTTAGACTCTAGAGGTCTTTATATTTATGATGATGGCA
                                tattaat  putative branch site (score: 2)
                                      ttcctcctgtgttct  CT-rich tract
                          atgaattattaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatacattgcttaccttaaaaagataccaataatgtggttaaactgtcagatgcatgaattattaattcctcctgtgttctagGCATCTGTACAGGCTAATGACTTAAAAAGTGTTGAGAGAAGGTTACCTTTGACTGGGGAGAGCTTAGACTCTAGAGGTCTTTATATTTATGATGATGGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT