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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtacttgtacaaatgttgaagtttaatttatgtggatttcatcttgttaaaatgcttaaagttgactatcatgcttttcttttagGTTGAGTTCCAGACTGCTTCAGGACAGATGATAGATCTGATCACCACACTGGAAGGAGAAAAAGACCTGTCTAAATACACATTAACACT

Basic information

species Glycine max
transcript GLYMA15G12780.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G12780.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G47770.1 (Arabidopsis thaliana), 3'ss of exon 5
gttgtacttgtacaaatgttgaagtttaatttatgtggatttca-tcttgttaaaatgcttaaagttgactatcatgcttttcttttagGTTGAGTTCCAGACTGCTTCAGGACAGATGATAGATCTGATCACCACACTGGAAGGAGAAAAAGACCTGTCTAAATACACATTAACACT
        |   |   | | | || |  | |  | |   || || | ||| ||   |      |||  | |||     ||    | ||||||||||| || || ||||  || |||||||||||| ||||||||||  | ||||||||||| ||  || | || ||| ||||  || |
-------gtaatctgttttggcagatctactattctcttttccacttttgatattttatcctcagtctattattccatttgctgtctagGTTGAGTTGCAAACAGCTTGTGGCCAGATGATAGATTTGATCACCACCTTTGAAGGAGAAAAGGATTTGGCCAAGTACTCATTGTCAAT
















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|208102994|gb|GD901432.1|GD901432
EST:     ACTTCAGGGGAAAGCCATATTACGTTGATCTTCTTGATTTGTTTAATGAG                         GTTGAGTTCCAGACTGCTTCAGGACAGATGATAGATCTGATCACCACACTG
genomic: ACTTCAGGGGAAAGCCATATTACGTTGATCTTCTTGATTTGTTTAATGAGgttgtacttg ... tttcttttagGTTGAGTTCCAGACTGCTTCAGGACAGATGATAGATCTGATCACCACACTG
EST: gi|298187020|gb|HO034169.1|HO034169
EST:     ACTTCAGGGGAAAGCCATATTACGTTGATCTTCTTGATTTGTTTAATGAG                         GTTGAGTTCCAGACTGCTTCAGGACAGATGATAGATCTGATCACCACACTG
genomic: ACTTCAGGGGAAAGCCATATTACGTTGATCTTCTTGATTTGTTTAATGAGgttgtacttg ... tttcttttagGTTGAGTTCCAGACTGCTTCAGGACAGATGATAGATCTGATCACCACACTG
EST: gi|13789758|gb|BG652349.1|BG652349
EST:     CCTTTAGGG-AAAGCCATATTACGTTGATCTTCTTGATTTGTTTAATGAA                         GTTGAGTTCCAGACTGCTTCAGGGCAGATGATA
genomic: C-TTCAGGGGAAAGCCATATTACGTTGATCTTCTTGATTTGTTTAATGAGgttgtacttg ... tttcttttagGTTGAGTTCCAGACTGCTTCAGGACAGATGATA
EST: gi|9902003|gb|BE610971.1|BE610971
EST:     ACTTCAGGGGAAAGCCATATTACGTTGATCTTCTTGATTTGTTTAATGAG                         GGTGAGTTCCAGACTGCTTCAGGACAGATGATAGATCTGATCACCACACTT
genomic: ACTTCAGGGGAAAGCCATATTACGTTGATCTTCTTGATTTGTTTAATGAGgttgtacttg ... tttcttttagGTTGAGTTCCAGACTGCTTCAGGACAGATGATAGATCTGATCACCACACT-
EST: gi|193512996|gb|FK470544.1|FK470544
EST:     ATATTACGTTGATCTTCTTGATTTGTTTAATGAG                         GTTGAGTTCCAGACTGCTTCAGGACAGATGATAGATCTGATCACCACACTG
genomic: ATATTACGTTGATCTTCTTGATTTGTTTAATGAGgttgtacttg ... tttcttttagGTTGAGTTCCAGACTGCTTCAGGACAGATGATAGATCTGATCACCACACTG
EST: gi|192294520|gb|FG987449.1|FG987449
EST:     ACTTCAGGGGAAAGCCATATTACGTTGATCTTCTTGATTTGTTTAATGAG                         GTTGAGTTCCAGACTGCTTCAGGACAGATGATAGATCTGATCACCACACTG
genomic: ACTTCAGGGGAAAGCCATATTACGTTGATCTTCTTGATTTGTTTAATGAGgttgtacttg ... tttcttttagGTTGAGTTCCAGACTGCTTCAGGACAGATGATAGATCTGATCACCACACTG
EST: gi|19345889|gb|BM890769.1|BM890769
EST:     ACTTCAGGGGAAAGCCATATTACGTTGATCTTCTTGATTTGTTTAATGAA                         GTTGAGTTCCAG
genomic: ACTTCAGGGGAAAGCCATATTACGTTGATCTTCTTGATTTGTTTAATGAGgttgtacttg ... tttcttttagGTTGAGTTCCAG
EST: gi|298181906|gb|HO026081.1|HO026081
EST:     ACTTCAGGGGAAAGCCATATTACGTTGATCTTCTTGATTTGTTTAATGAG                         GTTGAGTTCCAGACTGCTTCAGGACAGATGATAGATCTGATCACCACACTG
genomic: ACTTCAGGGGAAAGCCATATTACGTTGATCTTCTTGATTTGTTTAATGAGgttgtacttg ... tttcttttagGTTGAGTTCCAGACTGCTTCAGGACAGATGATAGATCTGATCACCACACTG
EST: gi|7233280|gb|AW568628.1|AW568628
EST:     ACTTCAGGGGAAAGCCATATTACGTTGATCTTCTTGATTTGTTTAATGAG                         GTTGAGTTCCAGACTGCTTCAGGACAGATGATAGATCTGATCACCACACTG
genomic: ACTTCAGGGGAAAGCCATATTACGTTGATCTTCTTGATTTGTTTAATGAGgttgtacttg ... tttcttttagGTTGAGTTCCAGACTGCTTCAGGACAGATGATAGATCTGATCACCACACTG
EST: gi|5606131|gb|AI900229.1|AI900229
EST:     ACTTCAGGGGAAAGCCATATTACGTTGATCTTCTTGATTTGTTTAATGAG                         GGTGAGTTCCAGACTGCTTCANGACAGATGATAGATCTGATCACCACACTG
genomic: ACTTCAGGGGAAAGCCATATTACGTTGATCTTCTTGATTTGTTTAATGAGgttgtacttg ... tttcttttagGTTGAGTTCCAGACTGCTTCAGGACAGATGATAGATCTGATCACCACACTG
EST: gi|15814471|gb|BI786746.1|BI786746
EST:     ACTTCAGGGGAAAGCCATATTACGTTGATCTTCTTGATTTGTTTAATGAG                         GTTGAGTTCCAGACTGCTTCAGGACAGATGATAGATCTGATCACC
genomic: ACTTCAGGGGAAAGCCATATTACGTTGATCTTCTTGATTTGTTTAATGAGgttgtacttg ... tttcttttagGTTGAGTTCCAGACTGCTTCAGGACAGATGATAGATCTGATCACC
EST: gi|9565120|gb|BE474629.1|BE474629
EST:     ACTTCAGGGGAAAGCCATATTACGTTGATCTTCTTGATTTGTTTAATGAG                         GTTGAGTTCCAGACTGCTTCAGGACAGATGATAGATCTGATCACCACACTG
genomic: ACTTCAGGGGAAAGCCATATTACGTTGATCTTCTTGATTTGTTTAATGAGgttgtacttg ... tttcttttagGTTGAGTTCCAGACTGCTTCAGGACAGATGATAGATCTGATCACCACACTG
EST: gi|208045687|gb|GD838961.1|GD838961
EST:     ACTTCAGGGGAAAGCCATATTACGTTGATCTTCTTGATTTGTTTAATGAG                         GTTGAGTTCCAGACTGCTTCAGGACAGATGATAGATCTGATCACCACACTG
genomic: ACTTCAGGGGAAAGCCATATTACGTTGATCTTCTTGATTTGTTTAATGAGgttgtacttg ... tttcttttagGTTGAGTTCCAGACTGCTTCAGGACAGATGATAGATCTGATCACCACACTG
EST: gi|14259182|gb|BG882090.1|BG882090
EST:     ACTTCAGGGGAAAGCCATATTACGTTGATCTTCTTGATTTGTTTAATGAG                         GTTGAGTTCCAGACTGCTTCAGGACAGATGATAGATCTGATCACCACACTG
genomic: ACTTCAGGGGAAAGCCATATTACGTTGATCTTCTTGATTTGTTTAATGAGgttgtacttg ... tttcttttagGTTGAGTTCCAGACTGCTTCAGGACAGATGATAGATCTGATCACCACACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtggatttcatcttgttaaaatgcttaaagttgactatcatgcttttcttttagGTTGAGTTCCAGACTGCTTCAGGACAGATGATAGATCTGATCACCACACTGGAAGGAGAAAAAGACCTGTCTAAATACACATTAACACT
                             agttgac  putative branch site (score: 4)
                                      tcatgcttttctttt  putative PPT
                ttaaaatgcttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtacttgtacaaatgttgaagtttaatttatgtggatttcatcttgttaaaatgcttaaagttgactatcatgcttttcttttagGTTGAGTTCCAGACTGCTTCAGGACAGATGATAGATCTGATCACCACACTGGAAGGAGAAAAAGACCTGTCTAAATACACATTAACACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA