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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtagtgaatttatagaacattctttaaatttcccctgccagttttgtttgaggtacatcaagaggccttccaagttatgagtcaatgactgggaaagccaaaagctgattggttatcactgaatatactaaatgtagtaacttcttttttattcatttgctcttcaatacatagCAAGGGTGCAGAAAAATATTTCAAGCGAGGATCGCGACTAAGATGGCCTGAAGGAGCTGTTTCAAGGGAGAGCATTAGTGCAGTGAAGAAGCTTGGTCAT

Basic information

species Glycine max
transcript GLYMA06G08480.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G08480.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv04s0008g04220.t01 (Vitis vinifera), 3'ss of exon 10
gtaagtagtgaatttatagaacattctttaaatttcccctgccagttttgtttgaggtacatcaagaggccttccaagttatgagtcaatgactgggaaagccaaaagctgattggttatcactgaatatactaaatgtagtaacttcttttttattcatttgctcttcaatacatagCAAGGGTGCAGAAAAATATTTCAAGCGAGGATCGCGACTAAGATGGCCTGAAGGAGCTGTTTCAAGGGAGAGCATTAGTGCAGTGAAGAAGCTTGGTCAT
                                                                        ||   | | |   || ||   ||       | |||  |      | ||   |  ||||            | | | |  |    | || |     |  ||    |||    |||  ||||| ||||||| | ||||||| ||  | |  |||||||||||||| ||||| ||||| || || || ||||||||||||||||  | |
-------------------------------------------------------------------cttgatcattgctgtccctctatttttgtatgcatctaaaattcgagaatgatgtttcgatat-----------caccctttaatgccattatatatctgtatatttgcagCCGAAGTGTTGAAAAGTATTTCAGGGGAGGATCACGGTTGAATTGGCCTGAAGGAGCAGTTTCTAGGGAAAGTATCAGAGCAGTGAAGAAGCTTGACCGT
















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|208061980|gb|GD856362.1|GD856362
EST:     ATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAA                         CAAGGGTGCAGAAAAATATTTCAAGCGAGGATCGCGACTAGGATGGCCTGA
genomic: ATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAAgtaagtagtg ... caatacatagCAAGGGTGCAGAAAAATATTTCAAGCGAGGATCGCGACTAAGATGGCCTGA
EST: gi|193724330|gb|FK657590.1|FK657590
EST:     ATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAA                         CAAGGGTGCAGAAAAATATTTCAAGCGAGGATCGCGACTAAGATGGCCTGA
genomic: ATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAAgtaagtagtg ... caatacatagCAAGGGTGCAGAAAAATATTTCAAGCGAGGATCGCGACTAAGATGGCCTGA
EST: gi|9985118|gb|BE659226.1|BE659226
EST:     ATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAA                         CAAGGGTGCAGAAAAATATTTCAAGCGAGGATCGCGACTAAGATGGCCTGA
genomic: ATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAAgtaagtagtg ... caatacatagCAAGGGTGCAGAAAAATATTTCAAGCGAGGATCGCGACTAAGATGGCCTGA
EST: gi|193529120|gb|FK484311.1|FK484311
EST:     ATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAA                         CAAGGGTGCAGAAAAATATTTCAAGCGAGGATCGCGACTAAGATGGCC
genomic: ATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAAgtaagtagtg ... caatacatagCAAGGGTGCAGAAAAATATTTCAAGCGAGGATCGCGACTAAGATGGCC
EST: gi|13481114|gb|BG510457.1|BG510457
EST:     ATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAA                         CAAGGGTGCAGAAAAATATTTCAAGCGAGGATCGCGACTAAGATGGCCTGA
genomic: ATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAAgtaagtagtg ... caatacatagCAAGGGTGCAGAAAAATATTTCAAGCGAGGATCGCGACTAAGATGGCCTGA
EST: gi|193571532|gb|FK532763.1|FK532763
EST:     ATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAA                         CAAGGGTGCAGAAAAATATTTCAAGCGAGGATCGCGACTAAGATGGCCTGA
genomic: ATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAAgtaagtagtg ... caatacatagCAAGGGTGCAGAAAAATATTTCAAGCGAGGATCGCGACTAAGATGGCCTGA
EST: gi|22933892|gb|BU551031.1|BU551031
EST:     ATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAA                         CAAGGGTGCAGAAAAATATTTCAAGCGAGGATCGCGACTAAGATGGCCTGA
genomic: ATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAAgtaagtagtg ... caatacatagCAAGGGTGCAGAAAAATATTTCAAGCGAGGATCGCGACTAAGATGGCCTGA
EST: gi|193521719|gb|FK479492.1|FK479492
EST:     ATGGAAAGGGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAA                         CAAGGGTGCAGAAAAATATTTCAAGCGAGGATCGCGACTAAGATGGCCTGA
genomic: ATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAAgtaagtagtg ... caatacatagCAAGGGTGCAGAAAAATATTTCAAGCGAGGATCGCGACTAAGATGGCCTGA
EST: gi|207729049|gb|GD706385.1|GD706385
EST:     ATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAA                         CAAGGGTGCAGAAAAATATTTCAAGCGAGGATCGCGACTAAGATGGCCTGA
genomic: ATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAAgtaagtagtg ... caatacatagCAAGGGTGCAGAAAAATATTTCAAGCGAGGATCGCGACTAAGATGGCCTGA
EST: gi|120529842|gb|EH257976.1|EH257976
EST:     ATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAA                         CAAGGGTGCAGAAAAATATTTCAAGCGAGGATCGCGACTAAGATGGCCTGA
genomic: ATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAAgtaagtagtg ... caatacatagCAAGGGTGCAGAAAAATATTTCAAGCGAGGATCGCGACTAAGATGGCCTGA
EST: gi|208289609|gb|GE086756.1|GE086756
EST:     ATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAA                         CAAGGGTGCAGAAAAATATTTCAAGCGAGGATCGCGACTAAGATGGCCTGA
genomic: ATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAAgtaagtagtg ... caatacatagCAAGGGTGCAGAAAAATATTTCAAGCGAGGATCGCGACTAAGATGGCCTGA
EST: gi|208167418|gb|GD959554.1|GD959554
EST:     ACCTATTCCAGAGCATATGATTTGCAGGTCTAA                         CAAGGGTGCAGAAAAATATTTCAAGCGAGGATCGCGACTAAGATGGCCTGA
genomic: ACCTATTCCAGAGCATATGATTTGCAGGTCTAAgtaagtagtg ... caatacatagCAAGGGTGCAGAAAAATATTTCAAGCGAGGATCGCGACTAAGATGGCCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatatactaaatgtagtaacttcttttttattcatttgctcttcaatacatagCAAGGGTGCAGAAAAATATTTCAAGCGAGGATCGCGACTAAGATGGCCTGAAGGAGCTGTTTCAAGGGAGAGCATTAGTGCAGTGAAGAAGCTTGGTCAT
               tagtaac  putative branch site (score: 1)
                     cttcttttttattcat  CT-rich tract
                  taacttcttttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtagtgaatttatagaacattctttaaatttcccctgccagttttgtttgaggtacatcaagaggccttccaagttatgagtcaatgactgggaaagccaaaagctgattggttatcactgaatatactaaatgtagtaacttcttttttattcatttgctcttcaatacatagCAAGGGTGCAGAAAAATATTTCAAGCGAGGATCGCGACTAAGATGGCCTGAAGGAGCTGTTTCAAGGGAGAGCATTAGTGCAGTGAAGAAGCTTGGTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC