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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcatctgatgtcacaactcacaataactctttgatgattttccaaagtgtagatttgggtctgttactcaatcatttagctgatgtatatgctcttcagGTCATAATTACAAGTATAAATATAGACGGGATTCTTCTCCTCATTGGCAGTCATCAAAAAGAAAAG

Basic information

species Glycine max
transcript GLYMA11G33970.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G33970.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv14s0006g01660.t01 (Vitis vinifera), 3'ss of exon 8
-----tgcatctgatgtcacaactcacaataactctttgatgattttccaaagtgtagatttgggtctgttactcaatcatttagctgatgtatatgctcttcagGTCATAATTACAAGTATAAATATAGACGGGATTCTTCTCCTCATTGGCAGTCATCAAAAAGAAAAG
     || | |||||    |   |   | ||| |  || ||| | ||      | |   | |   | |||  |  ||  || ||  |  |   ||||  |  |||||  | || ||||| ||||| || || |||| |||||||||||||||||||||||| |||||||||
atctatg-aactgatcagccttgttttattaagttattaatg-tctttttttttttcattcttaatttgtggcataag-atgtaaatttttactatgtcc--cagGTTGTCATAACAAGCATAAACATGGAAGGGAATCTTCTCCTCATTGGCAGTCATCAGAAAGAAAAG
















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|209718099|gb|BW677396.1|BW677396
EST:     GACATGGGCGGGAGGCCTGTAGGCTTCTCCATGCAGCTGGGCCTTCAAAG                         GTCATAATTACAAGTATAAATATAGACGGGATTCTTCTCCTCATTGGCAGT
genomic: GACATGGGCGGGAGGCCTGTAGGCTTCTCCATGCAGCTGGGCCTTCAAAGgtttgctttt ... tgctcttcagGTCATAATTACAAGTATAAATATAGACGGGATTCTTCTCCTCATTGGCAGT
EST: gi|58016835|gb|CX703577.1|CX703577
EST:     GACATGGGCGGGAGGCCTGTAGGCTTCTCCATGCAGCTGGGCCTTCAAAG                         GTCATAATTACAAGTATAAATATAGACGGGATTCTTCTCCTCATTGGCAGT
genomic: GACATGGGCGGGAGGCCTGTAGGCTTCTCCATGCAGCTGGGCCTTCAAAGgtttgctttt ... tgctcttcagGTCATAATTACAAGTATAAATATAGACGGGATTCTTCTCCTCATTGGCAGT
EST: gi|58023232|gb|CX709973.1|CX709973
EST:     GACATGGGCGGGAGGCCTGTAGGCTTCTCCATGCAGCTGGGCCTTCAAAG                         GTCATAATTACAAGTATAAATATAGACGGGATTCTTCTCCTCATTGGCAGT
genomic: GACATGGGCGGGAGGCCTGTAGGCTTCTCCATGCAGCTGGGCCTTCAAAGgtttgctttt ... tgctcttcagGTCATAATTACAAGTATAAATATAGACGGGATTCTTCTCCTCATTGGCAGT
EST: gi|151404004|gb|EV273814.1|EV273814
EST:     GGCGGGAGGCCTGTAGGCTTCTCCATGCAGCTGGGCCTTCAAAG                         GTCATAATTACAAGTATAAATATAGACGGGATTCTTCTCCTCATTGGCAGT
genomic: GGCGGGAGGCCTGTAGGCTTCTCCATGCAGCTGGGCCTTCAAAGgtttgctttt ... tgctcttcagGTCATAATTACAAGTATAAATATAGACGGGATTCTTCTCCTCATTGGCAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtgtagatttgggtctgttactcaatcatttagctgatgtatatgctcttcagGTCATAATTACAAGTATAAATATAGACGGGATTCTTCTCCTCATTGGCAGTCATCAAAAAGAAAAG
                                 agctgat  putative branch site (score: 4)
                                             tgctcttc  putative PPT
                         aatcattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcatctgatgtcacaactcacaataactctttgatgattttccaaagtgtagatttgggtctgttactcaatcatttagctgatgtatatgctcttcagGTCATAATTACAAGTATAAATATAGACGGGATTCTTCTCCTCATTGGCAGTCATCAAAAAGAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA