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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtaatcattgacagaaagaatagtacccattatgacattgatcttttgtaattgtccttttcattattttatttgttctcctgtaacatgattttacagATTTGAAGTACTGGATGAGGAACCAGGCGATGATGAAGAAAGCAGTGGCCAAAG

Basic information

species Glycine max
transcript GLYMA16G07460.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G07460.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G27460.2 (Arabidopsis thaliana), 3'ss of exon 5
tgtaatcattgacagaaagaatagtac--ccattatgacattgatcttttgtaattgtccttttcattattttatttgttctcctgtaacatgattttacagATTTGAAGTACTGGATGAGGAACCAGGCGATGATGAAGAAAGCAGTGGCCAAAG
|  | |  | || ||     ||    |    ||  | |   || |  | |   || |     |  ||   | ||  |    |     ||  |  ||| ||||| |||||||||| ||||| |||||||| |||||||||||| |  ||||||| ||
taaactggtagatagccgttatgacgcagttatggtaaatatgttgctcttccatagattcatatatgggtctaaataaagtttc--aaacttttttcacagAGTTGAAGTACTTGATGAAGAACCAGGAGATGATGAAGAAGGAGGTGGCCAGAG

upper sequence: GLYMA16G07460.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G40550.2 (Arabidopsis thaliana), 3'ss of exon 5
-----------------------------------------------------------------------------------tgtaa-tcattgacagaaagaatagtacccattatgacattgatcttt---tgtaattgtccttttcattattttatttgttctcctgtaacatgattttacagATTTGAAGTACTGGATGAGGAACCAGGCGATGATGAAGAAAGCAGTGGCCAAAG
                                                                                   || || | |||    |     |    || ||  |      || |  ||   || ||  |     |  || | | ||  | |  |  |  ||| |  || | |||| |||||||||| ||||| |||||||| |||||||||||| | || || || ||
gtaagccttcgaacctttcttctgtatgatgttatgcctaatttttgaatatcacacaaatgcatatctgatagtttagtagctgaaacttatttgttgctgccaacacacacaaaagagttgtgcttgttaagtgcaaaggcttcatctatgaatctaaatatgtt--taaaacttt-ttatccagAGTTGAAGTACTTGATGAAGAACCAGGAGATGATGAAGAAGGAAGCGGTCAGAG

upper sequence: GLYMA16G07460.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0066g00210.t01 (Vitis vinifera), 3'ss of exon 6
tgtaatcattgacagaaagaatagtacccattatgacattgatc----ttttgtaattgtccttttcattattttatttgttctcctgtaaca--tgattttacagATTTGAAGTACTGGATGAGGAACCAGGCGATGATGAAGAAAGCAGTGGCCAAAG
   ||   ||      || | |   |   ||| || | || |      ||  | |    | | ||  ||| ||  ||   |  |  || ||||  |   | | ||||||||||||||| ||||||||||| || ||||||||||| || |||||||||||
---aactttt--ttataacagtgcgattgattgtgccctttaataaaattcagcatacatgccttgtattgttc-ataaatattgatggaacaactatatatgcagATTTGAAGTACTTGATGAGGAACCTGGTGATGATGAAGAGAGTAGTGGCCAAAG

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|208166859|gb|GD960409.1|GD960409
EST:     GACGAGTGGTTTGTCGTAAAAGTGATTCATTTTGATAAGGAATCAAAGGA                         ATTTGAAGTACTGGATGAGGAACCAGGCGATGATGAAGAAAGCAGTGGCCA
genomic: GACGAGTGGTTTGTCGTAAAAGTGATTCATTTTGATAAGGAATCAAAGGAgtaagtatac ... gattttacagATTTGAAGTACTGGATGAGGAACCAGGCGATGATGAAGAAAGCAGTGGCCA
EST: gi|207800304|gb|GD773685.1|GD773685
EST:     GACGAGTGGTTTGTCGTAAAAGTGATTCATTTTGATAAGGAATCAAAGGA                         ATTTGAAGTACTGGATGAGGAACCAGGCGATGATGAAGAAAGCAGTGGCCA
genomic: GACGAGTGGTTTGTCGTAAAAGTGATTCATTTTGATAAGGAATCAAAGGAgtaagtatac ... gattttacagATTTGAAGTACTGGATGAGGAACCAGGCGATGATGAAGAAAGCAGTGGCCA
EST: gi|151405976|gb|EV275791.1|EV275791
EST:     GACGAGTGGTTTGTCGTAAAAGTGATTCATTTTGATAAGGAATCAAAGGA                         ATTTGAAGTACTGGATGAGGAACCAGGCGATGATGAAGAAAGCAGTGGCCA
genomic: GACGAGTGGTTTGTCGTAAAAGTGATTCATTTTGATAAGGAATCAAAGGAgtaagtatac ... gattttacagATTTGAAGTACTGGATGAGGAACCAGGCGATGATGAAGAAAGCAGTGGCCA
EST: gi|208101773|gb|GD900644.1|GD900644
EST:     GACGAGTGGTTTGTCGTAAAAGTGATTCATTTTGATAAGGAATCAAAGGA                         ATTTGAAGTACTAGATGAGGAACCAGGTGATGATGAAGAAAGCAGTGGCCA
genomic: GACGAGTGGTTTGTCGTAAAAGTGATTCATTTTGATAAGGAATCAAAGGAgtaagtatac ... gattttacagATTTGAAGTACTGGATGAGGAACCAGGCGATGATGAAGAAAGCAGTGGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtaattgtccttttcattattttatttgttctcctgtaacatgattttacagATTTGAAGTACTGGATGAGGAACCAGGCGATGATGAAGAAAGCAGTGGCCAAAG
                                    ctgtaac  putative branch site (score: 3)
             ttttcattattttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtaatcattgacagaaagaatagtacccattatgacattgatcttttgtaattgtccttttcattattttatttgttctcctgtaacatgattttacagATTTGAAGTACTGGATGAGGAACCAGGCGATGATGAAGAAAGCAGTGGCCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - -agaaagaa