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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctagtgtagtctactgtttcttttctttttttggtttcttctttaggtgattttaaattttatttacctgttttttcttctttttttgctgatattgtggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAACG

Basic information

species Glycine max
transcript GLYMA06G10930.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G10930.3 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G107473_T01 (Zea mays), 3'ss of exon 1
-------------gtctagtgtagtctactgtttcttttctttttttg-gtttcttctttaggtgattttaaattttatttacctgttttttcttctttttttgctgatattgtggaatttc----agCCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAACG
               | |   | |    |    || |  ||   |  |  | |     ||        |       |   | ||  ||||   |     |    ||   || |     || |    |||||||||| |  |||||||||||||| || ||||||||||||||||| || |||| ||| ||| | |  ||  |
gtaacagcagcacccccatcttcgctctcctcctcctccctccatgcgtatctgcatcttcctccccctcccccgatgcgtgccgcttttgattgaccatcaaactcgcatcgctccgttgcgcgcagCCGTCGGAGGCTATCAGGAAGGTGGTGTTCGGGGGTCAGGTCACCGAGGAGGAGGCCGACAGCCTCACCAAGAG

upper sequence: GLYMA06G10930.3 (Glycine max), 3'ss of exon 2
lower sequence: AT1G78150.2 (Arabidopsis thaliana), 3'ss of exon 2
gtctagtgtagtctactgtttcttttctttttttggtttcttctttaggtgattttaaattttatttacctgttttttcttctttttttg---ctgatattgtggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAACG
                   | |||      ||| |   |       |  | | ||| | ||| ||  | ||| |  |  |  || |||      || | |  ||   ||  |||| ||||||||||| || || ||||| ||||| ||||| |||||||||||||| || |||||||| ||     |
------------------gtacttgcaccgtttcgaaattcatgaaatttcactttgattttgatcaatctggtaatagtatttgtttcaattttggtttaatgtgtttgtagCCATCGGATGGGATTAGCAAAGTGGTGTTTGGTGGTCAAGTCACCGATGAAGAAGTTGAGAGCTTGAACCGCAG

upper sequence: GLYMA06G10930.3 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g05480.t01 (Vitis vinifera), 3'ss of exon 1
gtctagtgtagtctactgtttcttttctttttttggtttcttctttaggtgattttaaattttatttacctgttttttcttctttttttgctgatattgtggaatttca-gCCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAACG
                 ||  ||  | |||    ||  |  |  |   ||  |      |||| |||   | |  |    |  |||   | | | |||      ||  | ||| || ||||||||||| |||||||| ||||| || ||||| || ||||||||||  |||   ||    ||| |
-----------------gtacctcatttttccccggactggtaatggagttgtacgtttttttttttttttttgatcgtgtaatttagggtttaaatttcatttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAAGAGGCGGAGGCTTTGTCGAAAAG

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|193341668|gb|FK305942.1|FK305942
EST:     CCTTCCTCCGCCGTTCGTTCTCACCAG                         CCGTCGGATGGGGTCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
genomic: CCTTCCTCCGCCGTTCGTTCTCACCAGgtctagtgta ... ggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
EST: gi|5605824|gb|AI899922.1|AI899922
EST:     CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAG                         CCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
genomic: CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAGgtctagtgta ... ggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
EST: gi|9204366|gb|BE330590.1|BE330590
EST:     CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAG                         CCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
genomic: CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAGgtctagtgta ... ggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
EST: gi|207831332|gb|GD801638.1|GD801638
EST:     CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAG                         CCGTCGGATGGGATCAGGAAGGTGGTTTTTGGGG-TCAGGTCACCGATGAA
genomic: CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAGgtctagtgta ... ggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
EST: gi|51345323|gb|CO986056.1|CO986056
EST:     CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAG                         CCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
genomic: CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAGgtctagtgta ... ggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
EST: gi|213607251|gb|DB967044.1|DB967044
EST:     CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAG                         CCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
genomic: CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAGgtctagtgta ... ggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
EST: gi|208149384|gb|GD948116.1|GD948116
EST:     ATCCTTCCTCCGCCGTTCGTTCTCACCAG                         CCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
genomic: ATCCTTCCTCCGCCGTTCGTTCTCACCAGgtctagtgta ... ggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
EST: gi|213593687|gb|DB971709.1|DB971709
EST:     CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAG                         CCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
genomic: CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAGgtctagtgta ... ggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
EST: gi|209722915|gb|BW669461.1|BW669461
EST:     CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAG                         CCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
genomic: CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAGgtctagtgta ... ggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
EST: gi|208156520|gb|GD956830.1|GD956830
EST:     CATCCTTCCTCCGCCGTTCGTTCTCACCAG                         CCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
genomic: CATCCTTCCTCCGCCGTTCGTTCTCACCAGgtctagtgta ... ggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
EST: gi|298181167|gb|HO022606.1|HO022606
EST:     CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAG                         CCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
genomic: CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAGgtctagtgta ... ggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
EST: gi|298178909|gb|HO024644.1|HO024644
EST:     CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAG                         CCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
genomic: CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAGgtctagtgta ... ggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
EST: gi|192329307|gb|FK020226.1|FK020226
EST:     CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAG                         CCGTCGGATGGGATCAGGAAGGTGGTATTTGGGG-TCAGGTCACCGATGAA
genomic: CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAGgtctagtgta ... ggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
EST: gi|208271227|gb|GE066189.1|GE066189
EST:     CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAG                         CCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
genomic: CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAGgtctagtgta ... ggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
EST: gi|213589447|gb|DB973183.1|DB973183
EST:     CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAG                         CCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
genomic: CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAGgtctagtgta ... ggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
EST: gi|192314071|gb|FK010351.1|FK010351
EST:     CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAG                         CCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
genomic: CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAGgtctagtgta ... ggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
EST: gi|298191866|gb|HO035948.1|HO035948
EST:     CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAG                         CCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
genomic: CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAGgtctagtgta ... ggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
EST: gi|209714511|gb|BW684874.1|BW684874
EST:     CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAG                         CCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
genomic: CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAGgtctagtgta ... ggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
EST: gi|151408216|gb|EV278024.1|EV278024
EST:     CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAG                         CCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA
genomic: CAATTTCTCATTCCCCAACTCATCCTTCCTCCGCCGTTCGTTCTCACCAGgtctagtgta ... ggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaattttatttacctgttttttcttctttttttgctgatattgtggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAACG
                                 tgctgat  putative branch site (score: 3)
                 ttttttcttctttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctagtgtagtctactgtttcttttctttttttggtttcttctttaggtgattttaaattttatttacctgttttttcttctttttttgctgatattgtggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT