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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcctttaaaggtcccaagatctaattttatcatcaacttctcatttaagtaaaatgacatttaaatgatgacaatcactgtcaactttgtttcatgtagGCTACACCAGAGTTGGAGTATGGAAGGATGAATATTGGAAGTCGACCAGCAAAGAGAAGACCTAGTGGAGGCATTGAAACACTGCGTGCAATACCTTGGA

Basic information

species Glycine max
transcript GLYMA12G35840.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G35840.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 10
-gtcctttaaaggtcccaagatctaattttatcatcaacttctcatttaagtaaaatgacatttaaatgatgacaatcactgtcaactttgtttcatgtagGCTACACCAGAGTTGGAGTATGGAAGGATGAATATTGGAAGTCGACCAGCAAAGAGAAGACCTAGTGGAGGCATTGAAACACTGCGTGCAATACCTTGGA
  ||  |     ||| |       |||||  |  |   ||  | |||    |||       | ||||| ||  ||||   ||     ||  | |||  ||||| |||||||||||||| ||||| |||||||||||||||||| | ||| ||||  |||  |||||||||||||||||| |||| |||||||| |||||||
cttcactctgtagtcaccttcataaatttgttattttgctaatgattattctaatggtctgtataaataatctcaatt-ttgcttctttgctgtcaaatagGCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCATCAAAACGAAAGCCTAGTGGAGGCATTGAATCACTTCGTGCAATTCCTTGGA

upper sequence: GLYMA12G35840.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os08g27840.1 (Oryza sativa), 3'ss of exon 8
-----------------------------------------gtcctttaaaggtcccaagatctaattttatcatcaacttctcatttaagtaaaatgacatttaaatgatgacaatcactgtcaactttgtttcatgtagGCTACACCAGAGTTGGAGTATGGAAGGATGAATATTGGAAGTCGACCAGCAAAGAGAAGACCTAGTGGAGGCATTGAAACACTGCGTGCAATACCTTGGA
                                          || | ||| |     |||     | ||    |   | |  |||||| ||  |||  || |||  |   | |   ||  |  ||  |||  |  |   |||| ||||||||| |||||||||||||||||||||| |||||  | ||| | |||||||  || ||||| ||||| ||  |||| ||||| || || ||||
gtgagtgttttgtttcttcataatcatcagacttggaacatttcatataatgcatttaaggc---acttagctaaacattgttcatttcaggcaaa--acctttgtaaattaattttcttta-catttttcatgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCCAAGAGAAAGCCGAGTGGTGGCATCGAGTCACTCCGTGCCATCCCATGGA

upper sequence: GLYMA12G35840.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv19s0014g01390.t01 (Vitis vinifera), 3'ss of exon 8
gtcctttaaaggtcccaagatctaattttatcatcaacttctcatttaagtaaaatgacatttaaatgatgacaatcactgtcaactttgtttcatgtagGCTACACCAGAGTTGGAGTATGGAAGGATGAATATTGGAAGTCGACCAGCAAAGAGAAGACCTAGTGGAGGCATTGAAACACTGCGTGCAATACCTTGGA
      |||   |||    || |   |||  |   |   | | |   |||||||  |   ||   ||  | |  |||    |   || || ||   |||||||||||||||| |||||||||| || ||||| ||||| || || ||| ||||| | |  || ||||| || |||||| | || |||||||| || ||||
-----gtaagtatcctgcaatat--ctttgactcta---tttaaaccaagtaaag-gctgttaccattttaatgatcgtcttgtgctatgatt---gtagGCTACACCAGAGCTGGAGTATGGTAGAATGAACATTGGTAGCCGTCCATCAAAGCGTAAGCCAAGTGGGGGAATTGAATCGCTCCGTGCAATCCCATGGA

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|192324670|gb|FK016831.1|FK016831
EST:     ACCGTTCCATTGTATTCAAGGAACCACGCTTTGTTGAGTATTTCCGCCTG                         GCTACACCAGAGTTGGAGTACGGAAGGATGAATATTGGAAGTCGACCAGCA
genomic: ACCGTTCCATTGTATTCAAGGAACCACGCTTTGTTGAGTATTTCCGCCTGgtaaggacca ... tttcatgtagGCTACACCAGAGTTGGAGTATGGAAGGATGAATATTGGAAGTCGACCAGCA
EST: gi|16347534|gb|BI973129.1|BI973129
EST:     ACCGTTCCATTGTATTCAAGGAACCACGCTTTGTTGAGTATTTCCGCCTG                         GCTACACCAGAGTTGGAGTATGGAAGGATGAATATTGGAAGTCGACCAGCA
genomic: ACCGTTCCATTGTATTCAAGGAACCACGCTTTGTTGAGTATTTCCGCCTGgtaaggacca ... tttcatgtagGCTACACCAGAGTTGGAGTATGGAAGGATGAATATTGGAAGTCGACCAGCA
EST: gi|15813223|gb|BI785498.1|BI785498
EST:     ACCGTTCCATTGTATTCAAGGAACCACGCTTTGTTGAGTATTTCCGCCTG                         GCTACACCAGAGTTGGAGTATGGAAGGATGAATATTGGAAGTCGACCAGCA
genomic: ACCGTTCCATTGTATTCAAGGAACCACGCTTTGTTGAGTATTTCCGCCTGgtaaggacca ... tttcatgtagGCTACACCAGAGTTGGAGTATGGAAGGATGAATATTGGAAGTCGACCAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaagtaaaatgacatttaaatgatgacaatcactgtcaactttgtttcatgtagGCTACACCAGAGTTGGAGTATGGAAGGATGAATATTGGAAGTCGACCAGCAAAGAGAAGACCTAGTGGAGGCATTGAAACACTGCGTGCAATACCTTGGA
                                        ctttgtttc  CT-rich tract
     taaaatgacatttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcctttaaaggtcccaagatctaattttatcatcaacttctcatttaagtaaaatgacatttaaatgatgacaatcactgtcaactttgtttcatgtagGCTACACCAGAGTTGGAGTATGGAAGGATGAATATTGGAAGTCGACCAGCAAAGAGAAGACCTAGTGGAGGCATTGAAACACTGCGTGCAATACCTTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - -catcaac
- - - - - - - - - - - - - - - - - - - - - - - -aagtaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtcaac