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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataagatcataaaaaccttgttcatttcctctaatcctttctagttgatgtaccaagtttaatcatatgatgcctgtgctttagGTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAG

Basic information

species Glycine max
transcript GLYMA20G18980.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G18980.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM5G848768_T02 (Zea mays), 3'ss of exon 9
---gtataagatcataaaaaccttgttcatttcctctaatcctttcta-gttgatgtaccaagtttaatcatatgatgcctgtgctttagGTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAG
    |      |  |    ||| |  |  |        ||  |||||  | |||      |  | | || |    ||     || | |||| ||||| ||||| |||||||||||||||| ||||||||| || |||||||||  ||| ||  || | || ||||| |||||||||||||| |||||
gtattgcttttttctggtgaccctccttttgcagctagattttttctctgctgaaacgtta--tctgataaaccaatcaaactg-tgtagGCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAG

upper sequence: GLYMA20G18980.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G152442_T01 (Zea mays), 3'ss of exon 2
-------------------------------------------------------gtataagatcataaaaaccttgttca------tttcctct---------aatcctttctagttgatgtaccaagtttaatcatatgatgcctgtgctttagGTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAG---
                                                         |||  |  |  ||| | || |||         |||| |         | | || |||   | ||| | | |  |     | |  |  |      | |||| ||||| ||||| |||||||||||||||| ||||||||| || |||||||||  ||| ||  |  | || ||||| |||||||||||||| |||||   
gtgagttcctcattaagcatcaactgtatgaattaattatcttggattttctagttaatataacaactaaagcttttttctggtgaccctccttttgcagctagatttctctctctctaatgaatcgatatatgataaaccaatcaaactgtgtagGCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAAGATCTGTGGCTCTTAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGGTT

upper sequence: GLYMA20G18980.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G152442_T02 (Zea mays), 3'ss of exon 2
------------------------------gtataagatcataaaaaccttgttca------tttcctct---------aatcctttctagttgatgtaccaagtttaatcatatgatgcctgtgctttagGTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAG
                                |||  |  |  ||| | || |||         |||| |         | | || |||   | ||| | | |  |     | |  |  |      | |||| ||||| ||||| |||||||||||||||| ||||||||| || |||||||||  ||| ||  |  | || ||||| |||||||||||||| |||||
gtatgaattaattatcttggattttctagttaatataacaactaaagcttttttctggtgaccctccttttgcagctagatttctctctctctaatgaatcgatatatgataaaccaatcaaactgtgtagGCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAAGATCTGTGGCTCTTAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAG

upper sequence: GLYMA20G18980.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G33150.1 (Arabidopsis thaliana), 3'ss of exon 9
gtataagatcataaaaaccttgttcatttcctctaatcctttctagttgatgtaccaagtttaatcatat-gatgcctgtgcttt---------agGTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAG
|||      |  ||  |  |  ||||||   |  || ||    |  ||  | |  ||| |||||    || | | | | || | |         ||| ||||| || || || ||||||||||| | ||| ||||| || ||||| |||||||||||  ||||||| || || ||| ||||||||||||||||
gtacttttcccgaatcaattgtttcatt--atggaaaccacagttcttattatcacaattttaaatccattgcttcatttgttctgtcgcaaacagGAAATTCCAGCCAAGTAAGTGATGGTGCAGGAGCGGTTCTCCTAATGAAGAGAAGTGTTGCAATGCAAAAAGGACTTCCCGTTCTTGGTGTATTCAG

upper sequence: GLYMA20G18980.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv05s0051g00720.t01 (Vitis vinifera), 3'ss of exon 9
gtataagatcataaaaaccttgttcatttcctctaatcctttctagttgatgtaccaagtttaatcatatgatgcctgtgctttagGTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAG
|||| |||     | |      ||| ||   || ||    || |  ||| |  |     ||| |  || || ||| | || | |||| |||||||| || |||||||||||||||| ||||||||| || ||||| |||||||||||  |||  || ||| |||| |||||||||||||||||
gtattagacggccatatataatttctttctttcaaaatgattgt--ttgttccattccattttactatttggtgcttttggtgtagGGAATTCTAGCCAAGTGAGTGATGGTGCTGGAGCTGTTCTCCTCATGAAGAGAAGTGTTGCAATGCGTAAAGGGTTACCTATTCTTGGTGTATTCAG

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|51336044|gb|CO979910.1|CO979910
EST:     TCTAGGAAGGCTCAAACCTGTGTTCAAGAAAGACGGAAGCACTACTGCTG                         GTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAA
genomic: TCTAGGAAGGCTCAAACCTGTGTTCAAGAAAGACGGAAGCACTACTGCTGgtataagatc ... tgtgctttagGTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAA
EST: gi|192310414|gb|FG999157.1|FG999157
EST:     TCTAGGAAGGCTCAAACCTGTGTTCAAGAAAGACGGAAGCACTACTGCTG                         GTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAA
genomic: TCTAGGAAGGCTCAAACCTGTGTTCAAGAAAGACGGAAGCACTACTGCTGgtataagatc ... tgtgctttagGTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAA
EST: gi|254331906|gb|GR843649.1|GR843649
EST:     AGAAAGACGGAAGCACTACTGCTG                         GT-ATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTG-TCTGCTGATGAAAA
genomic: AGAAAGACGGAAGCACTACTGCTGgtataagatc ... tgtgctttagGTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAA
EST: gi|308099050|gb|HO760891.1|HO760891
EST:     TCTAGGAAGGCTCANACCTGTGTTCAAGAAAGACGGAAGCACTACTGCTG                         GTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAA
genomic: TCTAGGAAGGCTCAAACCTGTGTTCAAGAAAGACGGAAGCACTACTGCTGgtataagatc ... tgtgctttagGTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAA
EST: gi|254319377|gb|GR828997.1|GR828997
EST:     AAAGACGGAAGCACTACTGCTG                         GT-A-TCTAGTCAGGTGAGTGATGGTGCTGCAGCTG-TCTGCTGATGAAAA
genomic: AAAGACGGAAGCACTACTGCTGgtataagatc ... tgtgctttagGTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAA
EST: gi|298174872|gb|HO014789.1|HO014789
EST:     TCTAGGAAGGCTCAAACCTGTGTTCAAGAAAGACGGAAGCACTACTGCTG                         GTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAA
genomic: TCTAGGAAGGCTCAAACCTGTGTTCAAGAAAGACGGAAGCACTACTGCTGgtataagatc ... tgtgctttagGTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAA
EST: gi|51335173|gb|CO979039.1|CO979039
EST:     TCTAGGAAGGCTCAAACCTGTGTTCAAGAAAGACGGAAGCACTACTGCTG                         GTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAA
genomic: TCTAGGAAGGCTCAAACCTGTGTTCAAGAAAGACGGAAGCACTACTGCTGgtataagatc ... tgtgctttagGTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAA
EST: gi|4397476|gb|AI496473.1|AI496473
EST:     TCTAGGAAGGCTCAAACNTGTGTACAAGAAAGACGGAAGCACTACTGCTG                         GT-ATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAA
genomic: TCTAGGAAGGCTCAAACCTGTGTTCAAGAAAGACGGAAGCACTACTGCTGgtataagatc ... tgtgctttagGTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAA
EST: gi|254346644|gb|GR856366.1|GR856366
EST:     GTTCAAGAAAGACGGAAGCACTACTGCTG                         GTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAA
genomic: GTTCAAGAAAGACGGAAGCACTACTGCTGgtataagatc ... tgtgctttagGTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaatcctttctagttgatgtaccaagtttaatcatatgatgcctgtgctttagGTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAG
                         aagtttaatcatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataagatcataaaaaccttgttcatttcctctaatcctttctagttgatgtaccaagtttaatcatatgatgcctgtgctttagGTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT