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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgatgttatatggagactgctcaggctgataggatctgtcattaatgttaccagctgaatgtgagtctgttaacaagttctgttatttctcgtaccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAAATCCAGATGAAGTGATGGAGATTGTAAAAGTTATAACTACAAAAATACT

Basic information

species Glycine max
transcript GLYMA20G22090.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G22090.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0068g00220.t01 (Vitis vinifera), 3'ss of exon 2
-tttgatgttatatgg--agactgctcaggctgataggatctgtcattaatgttaccagctgaatgtgagtctgttaacaagttctgttatttctcgtaccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAAATCCAGATGAAGTGATGGAGATTGTAAAAGTTATAACTACAAAAATACT
      | ||    |   |   ||  ||     | |  |||    |  |       |  ||  || | | |   |     | || | |  ||| |  | |||||| | |||| |||||||||| ||||||| |||||||| || ||| | |||| |||||||||||   ||||||| | |||  ||||| || |||||||   
aagcagttttggtcgatcaagttgtgcaaa--aacaaaatcaagtaagatgaagttcctctttatataaatg-atatctgatttatatattttttaatcccagATCTTGAGTGCATCTTCACTGTCATCTGTAATCTTGTCACGAAGTCTGAAAGTCCAGATGAAGCATTGGAGATGGCAAAGTTTATATCTGCAAAAATTAC
















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|151404862|gb|EV274676.1|EV274676
EST:     ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAG                         ATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAA
genomic: ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAGgtagagtcat ... ctcgtaccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAA
EST: gi|15000159|gb|BI320973.1|BI320973
EST:     ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAG                         ATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAA
genomic: ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAGgtagagtcat ... ctcgtaccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAA
EST: gi|208278659|gb|GE080370.1|GE080370
EST:     ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAG                         ATATAGAGTCCATCTTC
genomic: ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAGgtagagtcat ... ctcgtaccagATATAGAGTCCATCTTC
EST: gi|15000274|gb|BI321088.1|BI321088
EST:     ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAG                         ATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAA
genomic: ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAGgtagagtcat ... ctcgtaccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAA
EST: gi|193531663|gb|FK491413.1|FK491413
EST:     ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAG                         ATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACTAAAGACCGAA
genomic: ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAGgtagagtcat ... ctcgtaccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTAC-AAAGACCGAA
EST: gi|19271164|gb|BM887420.1|BM887420
EST:     ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAG                         ATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAA
genomic: ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAGgtagagtcat ... ctcgtaccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAA
EST: gi|193464573|gb|FK431913.1|FK431913
EST:     ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAG                         ATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAA
genomic: ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAGgtagagtcat ... ctcgtaccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAA
EST: gi|298176542|gb|HO023129.1|HO023129
EST:     ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAG                         ATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAA
genomic: ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAGgtagagtcat ... ctcgtaccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAA
EST: gi|9819641|gb|BE555154.1|BE555154
EST:     ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAG                         ATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAA
genomic: ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAGgtagagtcat ... ctcgtaccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAA
EST: gi|8283494|gb|BE021053.1|BE021053
EST:     ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAG                         ATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAA
genomic: ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAGgtagagtcat ... ctcgtaccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAA
EST: gi|19452639|gb|BM954049.1|BM954049
EST:     ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAG                         ATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAA
genomic: ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAGgtagagtcat ... ctcgtaccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAA
EST: gi|209729516|gb|BW651856.1|BW651856
EST:     ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAG                         ATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAA
genomic: ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAGgtagagtcat ... ctcgtaccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAA
EST: gi|7684961|gb|AW755609.1|AW755609
EST:     ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAG                         ATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAA
genomic: ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAGgtagagtcat ... ctcgtaccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAA
EST: gi|192326394|gb|FK015911.1|FK015911
EST:     ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAG                         ATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAA
genomic: ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAGgtagagtcat ... ctcgtaccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAA
EST: gi|298176621|gb|HO023208.1|HO023208
EST:     ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAG                         ATATAGAGTCCATCTTCACTATCACCTGCAATCTTGTTACAAAGACCGAAA
genomic: ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAGgtagagtcat ... ctcgtaccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAA
EST: gi|208087969|gb|GD891097.1|GD891097
EST:     TTTTCTCGAAGGTTTCTGAAAAAG                         ATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAA
genomic: TTTTCTCGAAGGTTTCTGAAAAAGgtagagtcat ... ctcgtaccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAA
EST: gi|208313706|gb|GE113000.1|GE113000
EST:     TTGATGATTACCTCTGCTGAATTGATTTTCNCGAAGGTTTCTGAAAAAAG                         ATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAA
genomic: TTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTG-AAAAAGgtagagtcat ... ctcgtaccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAA
EST: gi|298175563|gb|HO018274.1|HO018274
EST:     ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAG                         ATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAA
genomic: ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAGgtagagtcat ... ctcgtaccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAA
EST: gi|15202225|gb|BI425289.1|BI425289
EST:     ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAG                         ATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAA
genomic: ATTGATGATTACCTCTGCTGAATTGATTTTCTCGAAGGTTTCTGAAAAAGgtagagtcat ... ctcgtaccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgttaccagctgaatgtgagtctgttaacaagttctgttatttctcgtaccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAAATCCAGATGAAGTGATGGAGATTGTAAAAGTTATAACTACAAAAATACT
                        tgttaac  putative branch site (score: 2)
                                  ttctgttatttctc  putative PPT
                                     tgttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgatgttatatggagactgctcaggctgataggatctgtcattaatgttaccagctgaatgtgagtctgttaacaagttctgttatttctcgtaccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTTACAAAGACCGAAAATCCAGATGAAGTGATGGAGATTGTAAAAGTTATAACTACAAAAATACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- tgatgtt
- - - - - - - - - ctgctca
- - - - - - - - - - - - - gctgata
- - - - - - - - - - - - - - - - - - tctgtca
- - - - - - - - - - - - - - - - - - - - - - - - - - -cagctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gagtctg