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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctgcatattcttctaccatgttgtgtcattgtggattctttctttttgtttttttttaaaaatgagttcattttgtttttttttttttcccaatttagGACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCACAATTGGCTCTTAAGCATCGGCAAAATAAAAAGCAACAGCAGAGGATTAT

Basic information

species Glycine max
transcript GLYMA11G08290.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G08290.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0023g03620.t01 (Vitis vinifera), 3'ss of exon 3
tgctgcatattcttctaccatgtt-gtgtcattgtggattctttctttttgtttttttttaaaaatgagttcattttgtttttttttttttcccaatttagGACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCACAATTGGCTCTTAAGCATCGGCAAAATAAAAAGCAACAGCAGAGGATTAT
|  || ||||| || |   || ||  |    || | |||| ||| | | ||| | | | || |  |||  |  ||  | | | | ||||| |  |||| |||  ||||  | ||||||||||||||| |||| || || || || ||||| |||||||||||||||||||| ||||| |||||||| || || ||||| ||
ttttgtatatttttatcagatctttatcctcttcttgatttttt-tatgtgtgtgtatatatatgtgatgtttttaaggtatatatttttacataattcagGTTTAGAGGTGGGTGGTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTCAATTGGCTCTTAAGCATCGACAAAACAAAAAGCAGCAACAAAGGATCAT
















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|151409810|gb|EV279618.1|EV279618
EST:     TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATG                         GACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
genomic: TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATGgtaagtattt ... cccaatttagGACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
EST: gi|14258768|gb|BG881676.1|BG881676
EST:     TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATG                         GACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
genomic: TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATGgtaagtattt ... cccaatttagGACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
EST: gi|213600544|gb|DB960092.1|DB960092
EST:     TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATG                         GACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
genomic: TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATGgtaagtattt ... cccaatttagGACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
EST: gi|193656228|gb|FK603316.1|FK603316
EST:     TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATG                         GACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
genomic: TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATGgtaagtattt ... cccaatttagGACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
EST: gi|213605510|gb|DB970667.1|DB970667
EST:     TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATG                         GACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
genomic: TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATGgtaagtattt ... cccaatttagGACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
EST: gi|298183378|gb|HO028591.1|HO028591
EST:     TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATG                         GACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
genomic: TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATGgtaagtattt ... cccaatttagGACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
EST: gi|298165035|gb|HO011084.1|HO011084
EST:     TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATG                         GACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
genomic: TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATGgtaagtattt ... cccaatttagGACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
EST: gi|193477480|gb|FK443561.1|FK443561
EST:     TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATG                         GACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
genomic: TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATGgtaagtattt ... cccaatttagGACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
EST: gi|213596699|gb|DB964046.1|DB964046
EST:     TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATG                         GACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
genomic: TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATGgtaagtattt ... cccaatttagGACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
EST: gi|4283205|gb|AI440627.1|AI440627
EST:     TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATG                         GACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
genomic: TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATGgtaagtattt ... cccaatttagGACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
EST: gi|208114435|gb|GD908518.1|GD908518
EST:     TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATG                         GACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCTGGTGGCA
genomic: TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATGgtaagtattt ... cccaatttagGACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCA
EST: gi|193384865|gb|FK353223.1|FK353223
EST:     TGATCTGGGCAAGATCTTAGCCTGCATGCATG                         GACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
genomic: TGATCTGGGCAAGATCTTAGCCTGCATGCATGgtaagtattt ... cccaatttagGACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
EST: gi|208274474|gb|GE070164.1|GE070164
EST:     TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATG                         GACTAGATATAGGTGGTGAG
genomic: TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATGgtaagtattt ... cccaatttagGACTAGATATAGGTGGTGAG
EST: gi|298162986|gb|HO011719.1|HO011719
EST:     TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATG                         GACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
genomic: TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATGgtaagtattt ... cccaatttagGACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
EST: gi|209715414|gb|BW684698.1|BW684698
EST:     TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATG                         GACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
genomic: TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATGgtaagtattt ... cccaatttagGACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
EST: gi|193451300|gb|FK420548.1|FK420548
EST:     TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATG                         GACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
genomic: TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATGgtaagtattt ... cccaatttagGACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
EST: gi|193554171|gb|FK511284.1|FK511284
EST:     TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATG                         GACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
genomic: TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATGgtaagtattt ... cccaatttagGACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
EST: gi|151397896|gb|EV267769.1|EV267769
EST:     TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATG                         GACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
genomic: TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATGgtaagtattt ... cccaatttagGACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCAC
EST: gi|208253497|gb|GE054285.1|GE054285
EST:     TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATG                         GACTAGATATAGGTGGTGAG
genomic: TTTGGTTACCCCTACCAGTGATCTGGGCAAGATCTTAGCCTGCATGCATGgtaagtattt ... cccaatttagGACTAGATATAGGTGGTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgtttttttttaaaaatgagttcattttgtttttttttttttcccaatttagGACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCACAATTGGCTCTTAAGCATCGGCAAAATAAAAAGCAACAGCAGAGGATTAT
                       ttcattttgttttttt  CT-rich tract
     tttttttttaaaaatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctgcatattcttctaccatgttgtgtcattgtggattctttctttttgtttttttttaaaaatgagttcattttgtttttttttttttcccaatttagGACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCACAATTGGCTCTTAAGCATCGGCAAAATAAAAAGCAACAGCAGAGGATTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- -tgcatat
- - - - - - - - -ccatgtt