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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctctctctctcactctccctctgaatttatcaacagctagtacgattttagaagtgatccttttttaatcttcttgtgtggccaccagataatattccccaagaatatgctgattgaccataactgtaaagtaactttttttgttataaaaatatttataaaatttctgagtattttctcttatttgatcagAGGATTTCAGATCTCTGCAAGAATGCTGGCTCTTGGCTTGTTGTTGATAATACATACGA

Basic information

species Glycine max
transcript GLYMA15G01520.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G01520.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G107639_T01 (Zea mays), 3'ss of exon 6
gtctctctctctcactctccctctgaatttatcaacagctagtacgattttagaagtgatccttttttaatcttcttgtgtggccaccagataatattccccaagaatatgctgattgaccataactgtaaagtaactttttttgttataaaaatatttataaaatttctgagtattttctcttatttgatcagAGGATTTCAGATCTCTGCAAGAATGCTGGCTCTTGGCTTGTTGTTGATAATACATACGA
                                                                                                                        |||  || |  | ||||  || | |||   ||  | | |  || ||||   | ||||   |  |  ||   ||||||||||||||||| ||||| ||||||||  | |||||||| ||||| ||||| || ||
----------------------------------------------------------------------------------------------------------------------gtcatctctctccactaacacttgt-gtttggaatctctatccaacattttctaatattgcattgtcatt--ccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAATACCTATGA

upper sequence: GLYMA15G01520.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0002g05250.t01 (Vitis vinifera), 3'ss of exon 6
gtctctctctctcactctccctctgaatttatcaacagctagtacgattttagaagtgatccttttttaatcttcttgtgtggccaccagataatattccccaagaatatgctgattgaccataactgtaaagtaactttttttgttataaaaatatttataaaatttctgagtattttctcttatttgatcagAGGATTTCAGATCTCTGCAAGAATGCTGGCTCTTGGCTTGTTGTTGATAATACATACGA
                                      ||    |     |    ||  |  | | |   | | |  ||||| |  |       ||  |    ||||||   |  | ||  |||  ||  || |  | ||||   || |  |  |  ||  |||  |     ||  ||| | || ||| |  ||||| || ||||||||||||  |||||||| |||||||||||||| ||||||||||| ||
------------------------------------gtctctctctcccctctgtgtcgttgtgtgtgtgtgtgcacgtgtgcctgct------tacactgttagaataaattt-tagaaaatagttg--aactttcgttttccttttttcagtttgtttcaaacctaactggtcctttgttttctttaagtagAGGTTTGCAGATCTCTGCAGAAATGCTGGATCTTGGCTTGTTGTAGATAATACATATGA
















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|19938456|gb|BQ081728.1|BQ081728
EST:     TAAATCCAGGCAATCCATCTGGAACTTACATTCCAGAGCCCCTTCTAAAG                         AGGATTTCAGATCTCTGCAAGAATGCTGGC
genomic: TAAATCCAGGCAATCCATCTGGAACTTACATTCCAGAGCCCCTTCTAAAGgtctctctct ... atttgatcagAGGATTTCAGATCTCTGCAAGAATGCTGGC
EST: gi|26058655|gb|CA801569.1|CA801569
EST:     TAAATCCAGGCAATCCATCTGGAACTTACATTCCAGAGCCCCTTCTAAAG                         AGGATTTCAGATCTCTGCAAGAATGCTGGCTCTTGGCTTGTTGTTGATAAT
genomic: TAAATCCAGGCAATCCATCTGGAACTTACATTCCAGAGCCCCTTCTAAAGgtctctctct ... atttgatcagAGGATTTCAGATCTCTGCAAGAATGCTGGCTCTTGGCTTGTTGTTGATAAT
EST: gi|4313781|gb|AI460900.1|AI460900
EST:     TAAATCCAGGCAATCCATCTGGAACTTACATTCCAGAGCCCCTTCTAAAG                         AGGATTTCAGATCTCTGCAAGAATGCTGGCTCTTGGCTTGTTGTTGATAAT
genomic: TAAATCCAGGCAATCCATCTGGAACTTACATTCCAGAGCCCCTTCTAAAGgtctctctct ... atttgatcagAGGATTTCAGATCTCTGCAAGAATGCTGGCTCTTGGCTTGTTGTTGATAAT
EST: gi|37995957|gb|CF807546.1|CF807546
EST:     TAAATCCAGGCAATCCATCTGGAACTTACATTCCAGAGCCCCTTCTAAAG                         AGGATTTCAGATCTCTGCAAGAATGCTGGCTCTTGGCTTGTTGTTGATAAT
genomic: TAAATCCAGGCAATCCATCTGGAACTTACATTCCAGAGCCCCTTCTAAAGgtctctctct ... atttgatcagAGGATTTCAGATCTCTGCAAGAATGCTGGCTCTTGGCTTGTTGTTGATAAT
EST: gi|208247343|gb|GE048959.1|GE048959
EST:     TAAATCCAGGCAATCCATCTGGAACTTACATTCCAGAGCCCCTTCTAAAG                         AGGATTTCAGATCTCTGCAAGAATGCTGGCTCTTGGCTTGTTGTTGATAAT
genomic: TAAATCCAGGCAATCCATCTGGAACTTACATTCCAGAGCCCCTTCTAAAGgtctctctct ... atttgatcagAGGATTTCAGATCTCTGCAAGAATGCTGGCTCTTGGCTTGTTGTTGATAAT
EST: gi|151399034|gb|EV268905.1|EV268905
EST:     TAAATCCAGGCAATCCATCTGGAACTTACATTCCAGAGCCCCTTCTAAAG                         AGGATTTCAGATCTCTGCAAGAATGCTGGCTCTTGGCTTGTTGTTGATAAT
genomic: TAAATCCAGGCAATCCATCTGGAACTTACATTCCAGAGCCCCTTCTAAAGgtctctctct ... atttgatcagAGGATTTCAGATCTCTGCAAGAATGCTGGCTCTTGGCTTGTTGTTGATAAT
EST: gi|13477614|gb|BG507424.1|BG507424
EST:     TAAATCCAGGCAATCCATCTGGAACTTACATTCCAGAGCCCCTTCTAAAG                         AGGATTTCAGATCTCTGCAAGAATGCTGGCTCTTGGCTTGTTGTTGATAAT
genomic: TAAATCCAGGCAATCCATCTGGAACTTACATTCCAGAGCCCCTTCTAAAGgtctctctct ... atttgatcagAGGATTTCAGATCTCTGCAAGAATGCTGGCTCTTGGCTTGTTGTTGATAAT
EST: gi|7233283|gb|AW568631.1|AW568631
EST:     TAAATCCAGGCAATCCATCTGGAACTTACATTCCAGAGCCCCTTCTAAAG                         AGGATTTCAGATCTCTGCAAGAATGCTGGCTCTTGGCTTGTTGTTGATAAT
genomic: TAAATCCAGGCAATCCATCTGGAACTTACATTCCAGAGCCCCTTCTAAAGgtctctctct ... atttgatcagAGGATTTCAGATCTCTGCAAGAATGCTGGCTCTTGGCTTGTTGTTGATAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgttataaaaatatttataaaatttctgagtattttctcttatttgatcagAGGATTTCAGATCTCTGCAAGAATGCTGGCTCTTGGCTTGTTGTTGATAATACATACGA
                                  tattttctcttattt  CT-rich tract
      ttataaaaatatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctctctctctcactctccctctgaatttatcaacagctagtacgattttagaagtgatccttttttaatcttcttgtgtggccaccagataatattccccaagaatatgctgattgaccataactgtaaagtaactttttttgttataaaaatatttataaaatttctgagtattttctcttatttgatcagAGGATTTCAGATCTCTGCAAGAATGCTGGCTCTTGGCTTGTTGTTGATAATACATACGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG