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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgagtaatcatggcgtgggaggagtttaatttgtattagtgctcatcaaactagtgtttgatcttttagcattctaaacttcttcctgctgcttgcagTGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTACTTCATATGTGGTTATGTTTGCGTCGCTTGAAGCAAGAGGGAAATGAGGGTGT

Basic information

species Glycine max
transcript GLYMA08G18850.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G18850.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g30790.1 (Oryza sativa), 3'ss of exon 2
-attga--gtaatcatggcgtgggaggagtttaatttgtattagtgctcatcaaactagtgtttgatcttttagca-ttctaaacttcttcctgctgcttgcagTGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTACTTCATATGTGGTTATGTTTGCGTCGCTTGAAGCAAGAGGGAAATGAGGGTGT
 ||| |  | |  | ||   ||| |   ||||  ||  | |   |  |  |     ||   | |  |   |  ||| ||    || | |||||     || |||| ||| | |||||||||||||| ||||||||||| || |||||||| || ||||||||| |   | | |||||||||||  |||| || || || |||||
cattaactgcatacctgttttggtaactgtttgtttcatttccatctttttatgcttaagatatactgggtcggcaatttctgacattttcct----tttacagTTTTTCAGTTGGAGAAAACATTTAAAACAACATTTTCATTACTTGTTCTCCATATGTGGCTTATTCTACGTCGCTTGAAAGAAGAAGGGAAGGATGGTGT

upper sequence: GLYMA08G18850.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv16s0013g01540.t01 (Vitis vinifera), 3'ss of exon 4
attgagtaatcatggcgtgggaggagtttaatttgtattagtgctcatcaaactagtgtttgatcttt-tagcattctaa------acttcttcctgctgcttgcagTGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTACTTCATATGTGGTTATGTTTGCGTCGCTTGAAGCAAGAGGGAAATGAGGGTGT
       ||  |||  |   | |   | | ||||    |  ||||   ||  || |  ||  |||| | ||    |||||      | |   |  |      |||||  ||||||||||||||||| || ||||||||||| ||| | ||| |||||||||||||| | || || || ||||||||  |||| ||||| || |||||
-------aacaatgtagatagtgatttgttattttacatgctgctttccatgctggctttgaatctctatattggtctaatgtaaaattatattatttcatatgcagCATTTAACTTGGAGAAAACCTTTAAAACAACATTTTCTCTGCTTATACTTCATATGTGGCTTTGCTTACGCCGCTTGAAAGAAGATGGAAAGGAAGGTGT
















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|192299113|gb|FG992874.1|FG992874
EST:     TGTGTACCGAAGAATTGTTTCTCAAATTGATAAACCTCCCATTTATGAAG                         TGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTACTTC
genomic: TGTGTACCGAAGAATTGTTTCTCAAATTGATAAACCTCCCATTTATGAAGgtccattctc ... ctgcttgcagTGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTACTTC
EST: gi|213589411|gb|DB961744.1|DB961744
EST:     TGTGTACCGAAGAATTGTTTCTCAAATTGATAAACCTCCCATTTATGAAG                         TGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTACTTC
genomic: TGTGTACCGAAGAATTGTTTCTCAAATTGATAAACCTCCCATTTATGAAGgtccattctc ... ctgcttgcagTGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTACTTC
EST: gi|193640849|gb|FK591470.1|FK591470
EST:     TGTGTACCGAAGAATTGTTTCTCAAATTGATAAACCTCCCATTTATGAAG                         TGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTACTTC
genomic: TGTGTACCGAAGAATTGTTTCTCAAATTGATAAACCTCCCATTTATGAAGgtccattctc ... ctgcttgcagTGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTACTTC
EST: gi|207738357|gb|GD716121.1|GD716121
EST:     TGTGTACCGAAGAATTGTTTCTCAAATTGATAAACCTCCCATTTATGAAG                         TGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTACTTC
genomic: TGTGTACCGAAGAATTGTTTCTCAAATTGATAAACCTCCCATTTATGAAGgtccattctc ... ctgcttgcagTGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTACTTC
EST: gi|14259843|gb|BG882751.1|BG882751
EST:     TGTGTACCGAAGAATTGTTTCTCAAATTGATAAACCTCCCATTTATGAAG                         TGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTACTTC
genomic: TGTGTACCGAAGAATTGTTTCTCAAATTGATAAACCTCCCATTTATGAAGgtccattctc ... ctgcttgcagTGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTACTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcaaactagtgtttgatcttttagcattctaaacttcttcctgctgcttgcagTGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTACTTCATATGTGGTTATGTTTGCGTCGCTTGAAGCAAGAGGGAAATGAGGGTGT
                            ttctaaa  putative branch site (score: 2)
                                   cttcttcctgctgctt  CT-rich tract
                 atctttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgagtaatcatggcgtgggaggagtttaatttgtattagtgctcatcaaactagtgtttgatcttttagcattctaaacttcttcctgctgcttgcagTGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTACTTCATATGTGGTTATGTTTGCGTCGCTTGAAGCAAGAGGGAAATGAGGGTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - gcgtggg
- - - - - - - - - - - - - - - - - - -ttagtgc
- - - - - - - - - - - - - - - - - - - - - - - -tcaaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcattct