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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agctcattgtatgactctgtatgccttcttttttctagatataataaactttatgcagtgttaaataaaaaatgattcatgcagtgttttcatttaacagGCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCTTCTTGTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAA

Basic information

species Glycine max
transcript GLYMA17G04720.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G04720.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g14150.5 (Oryza sativa), 3'ss of exon 2
------------------------------------------------agctcattgtatgactctgtatgccttcttttttctagatataataaactttatgcagtgttaaataaaaaatgattcatgcagtgttttcatttaa----cagGCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCTTCTTGTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAA
                                                ||   || || |  |  | |  ||||| |   |  || |  |   |   ||||        |      | |   | |||    ||  ||   || ||    |||||||| || |||||     | || || ||  ||||||||||||| || || |||||||| || ||||| ||||||||||||||| | || || || || |
gtgaaatgctttatttatctgtcactgctcgtaaatcatttgttcatgagaatat-gtgtatccgtttgggccttttgcgtgttaaacttcgaattgtttaccacaccattttcggatagctactcacattgtcgttctgttaaattttcagGCTTGCAAAAAGCTCGGAAAAATCGAGCTCTCAGATTGTGAAATTTACGCGTCTTGTGAGCCATGCCCAATGTGCTTTGGTGCAGTTCATCTCTCCCGGA

upper sequence: GLYMA17G04720.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G840909_T01 (Zea mays), 3'ss of exon 5
------------------------------------------------------agctc---attgtatgactctgtatgccttcttttttctagatataataaactttatgcagtgttaaataaaaaatgattcatg---------cagtgt---tttcatttaacagGCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCTTCTTGTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAA
                                                      || ||   | | | |  |  |   ||    ||   ||||| || || |   | ||     || | |   || | |  | ||||          || |||   |||  |  |  ||||||| || ||||||  | | || || ||  | ||||||||||| ||||| |||||||| || ||||| ||||| ||||||||  | || || || || |
gtcactgaacctaaaaaaagtatcgtgtttgttccgcctaacttttggcattatagttctgaaatatttttcattcagtgttcgctgcattctacat-tagttttcctttcattgt-taaggcaagagaatactcatctcttataaccaatgtatcttttgtaaactagGCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCATCTTGTGAGCCATGCCCAATGTGTTTTGGTGCTGTTCATCTATCCCGGA

upper sequence: GLYMA17G04720.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G840909_T02 (Zea mays), 3'ss of exon 3
----agctcattgtatgactctgtatgccttcttttttctagatataataaactttatgcagtgttaaataaaaaatgattcatgcagtgttttcatttaacagGCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCTTCTTGTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAA
       ||| |||  |   |  | | | ||  |||| ||    ||  | ||    |   | |  | | |     || |   ||| |    |||  |  |  ||||||| || ||||||  | | || || ||  | ||||||||||| ||||| |||||||| || ||||| ||||| ||||||||  | || || || || |
ttttcattcagtgttcgctgcattctacattagttttccttt-cattgttaaggcaagagaatactca-tctcttataaccaatgtatc--ttttgtaaactagGCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCATCTTGTGAGCCATGCCCAATGTGTTTTGGTGCTGTTCATCTATCCCGGA

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|298176038|gb|HO015443.1|HO015443
EST:     TGTGTAACACAGACCCAACTGCTCATGCTGAGGTGACAGCAATAAGAGAG                         GCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT
genomic: TGTGTAACACAGACCCAACTGCTCATGCTGAGGTGACAGCAATAAGAGAGgttagatttt ... catttaacagGCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT
EST: gi|192328192|gb|FK020439.1|FK020439
EST:     TGTGTAACACAGACCCAACTGCTCATGCTGAGGTGACAGCAATAAGAGAG                         GCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT
genomic: TGTGTAACACAGACCCAACTGCTCATGCTGAGGTGACAGCAATAAGAGAGgttagatttt ... catttaacagGCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT
EST: gi|16347143|gb|BI972738.1|BI972738
EST:     TGTGTAACACAGACCCAACTGCTCATGCTGAGGTGACAGCAATAAGAGAG                         GCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT
genomic: TGTGTAACACAGACCCAACTGCTCATGCTGAGGTGACAGCAATAAGAGAGgttagatttt ... catttaacagGCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT
EST: gi|16347848|gb|BI973443.1|BI973443
EST:     TGTGTAACACAGACCCAACTGCTCATGCTGAGGTGACAGCAATAAGAGAG                         GCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT
genomic: TGTGTAACACAGACCCAACTGCTCATGCTGAGGTGACAGCAATAAGAGAGgttagatttt ... catttaacagGCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT
EST: gi|5752974|gb|AI960261.1|AI960261
EST:     TGTGTAACACAGACCCAACTGCTCATGCTGAGGTGACAGCAATAAGAGAG                         GCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT
genomic: TGTGTAACACAGACCCAACTGCTCATGCTGAGGTGACAGCAATAAGAGAGgttagatttt ... catttaacagGCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT
EST: gi|6964020|gb|AW432713.1|AW432713
EST:     TGTGTAACACAGACCCAACTGCTCATGCTGAGGTGACAGCAATAAGAGAG                         GCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT
genomic: TGTGTAACACAGACCCAACTGCTCATGCTGAGGTGACAGCAATAAGAGAGgttagatttt ... catttaacagGCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT
EST: gi|14126393|gb|BG790831.1|BG790831
EST:     TGTGTAACACAGACCCAACTGCTCATGCTGAGGTGACAGCAATAAGAGAG                         GCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT
genomic: TGTGTAACACAGACCCAACTGCTCATGCTGAGGTGACAGCAATAAGAGAGgttagatttt ... catttaacagGCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT
EST: gi|21888734|gb|BQ741947.1|BQ741947
EST:     TGTGTAACACAGACCCAACTGCTCATGCTGAGGTGACAGCAATAAGAGAG                         GCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT
genomic: TGTGTAACACAGACCCAACTGCTCATGCTGAGGTGACAGCAATAAGAGAGgttagatttt ... catttaacagGCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT
EST: gi|209723270|gb|BW651277.1|BW651277
EST:     TGTGTAACACAGACCCAACTGCTCATGCTGAGGTGACAGCAATAAGAGAG                         GCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT
genomic: TGTGTAACACAGACCCAACTGCTCATGCTGAGGTGACAGCAATAAGAGAGgttagatttt ... catttaacagGCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT
EST: gi|209723271|gb|BW651278.1|BW651278
EST:     GAGGTGACAGCAATAAGAGAG                         GCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT
genomic: GAGGTGACAGCAATAAGAGAGgttagatttt ... catttaacagGCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT
EST: gi|151400238|gb|EV270052.1|EV270052
EST:     TGTGTAACACAGACCCAACTGCTCATGCTGAGGTGACAGCAATAAGAGAG                         GCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT
genomic: TGTGTAACACAGACCCAACTGCTCATGCTGAGGTGACAGCAATAAGAGAGgttagatttt ... catttaacagGCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT
EST: gi|14990698|gb|BI316371.1|BI316371
EST:     TGTGTAACACAGACCCAACTGCTCATGCTGAGGTGACAGCAATAAGAGAG                         GCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT
genomic: TGTGTAACACAGACCCAACTGCTCATGCTGAGGTGACAGCAATAAGAGAGgttagatttt ... catttaacagGCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT
EST: gi|151407408|gb|EV277223.1|EV277223
EST:     TGTGTAACACAGACCCAACTGCTCATGCTGAGGTGACAGCAATAAGAGAG                         GCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT
genomic: TGTGTAACACAGACCCAACTGCTCATGCTGAGGTGACAGCAATAAGAGAGgttagatttt ... catttaacagGCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT
EST: gi|120532313|gb|EH260446.1|EH260446
EST:     TGTGTAACACAGACCCAACTGCTCATGCTGAGGTGACAGCAATAAGAGAG                         GCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT
genomic: TGTGTAACACAGACCCAACTGCTCATGCTGAGGTGACAGCAATAAGAGAGgttagatttt ... catttaacagGCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT
EST: gi|21888733|gb|BQ741946.1|BQ741946
EST:     TGTGTAACACAGACCCAACTGCTCATGCTGAGGTGACAGCAATAAGAGAG                         GCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT
genomic: TGTGTAACACAGACCCAACTGCTCATGCTGAGGTGACAGCAATAAGAGAGgttagatttt ... catttaacagGCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT
EST: gi|14990622|gb|BI316295.1|BI316295
EST:     TGTGTAACACAGACCCAACTGCTCATGCTGAGGTGACAGCAATAAGAGAG                         GCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT
genomic: TGTGTAACACAGACCCAACTGCTCATGCTGAGGTGACAGCAATAAGAGAGgttagatttt ... catttaacagGCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaactttatgcagtgttaaataaaaaatgattcatgcagtgttttcatttaacagGCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCTTCTTGTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAA
                                         ttttcattt  CT-rich tract
             tgttaaataaaaaatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agctcattgtatgactctgtatgccttcttttttctagatataataaactttatgcagtgttaaataaaaaatgattcatgcagtgttttcatttaacagGCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCTTCTTGTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAA

- - - -tgtatga
- - - - - - - - - gtatgcc
- - - - - - - - - - - - - - - - - - - - - - - - -tttatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgca