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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgttattcaactctccatttttttgttttgaatttcaaacatgattatttgcatatgaaaacactgttatttgactaagttttcatgtttttatttagGTCTTCATCATCGGACCAGTGAAGGAGGTGAGGAAAGCCGAGGCCATGATACGGGGTAGAATCTTGGATATATAGTTAAGAAATGTGTTATTTCTCTTCC

Basic information

species Glycine max
transcript GLYMA17G34990.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G34990.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G081924_T01 (Zea mays), 3'ss of exon 9
-tctgttattcaactctccatttttttgttttgaatttcaaacatgattatttgcatatgaaaacactgttatttgac-taagttttcatgt---ttttatttagGTCTTCATCATCGGACCAGTGAAGGAGGTGAGGAAAGCCGAGGCCATGATACGGGGTAGAATCTTGGATATATAGTTAAGAAATGTGTTATTTCTCTTCC
 |  |||| |  |  |  || |  || ||   |||  |   |  |||  ||   |||||   |    ||||| |   | |   ||||  |||    |  || ||||| |||||||| ||| ||||||| || || |||||||||||||||||  |  | ||  ||||  ||||  | |||  | |  |    ||    | | |  
tttagttaatataagcaacaatcgtt-gtgcagaaact--gatctga--atgaacatatttcagttttgttactgatcctgtttttttttgtgtgctaaatgtagGTTTTCATCATTGGATCAGTGAATGAAGTCAGGAAAGCCGAGGCCATCTTCAGAGGCCGAATGCTGGAGTTCTAGAGATGTTACCCTTTGCGCCCCATGT

upper sequence: GLYMA17G34990.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv04s0008g00650.t01 (Vitis vinifera), 3'ss of exon 9
tctgttattcaactctccatttttttg----ttttgaatttcaaacatgattatttgcatatgaaaacactgttatttgactaagttttcatgtttttatttagGTCTTCATCATCGGACCAGTGAAGGAGGTGAGGAAAGCCGAGGCCATGATACGGGGTAGAATCTTGGATATATAGTTAAGAAATGTGTTATTTCTCTTCC-
 |   | ||  | |  |||| | |       ||   ||||| | |  | |    || |||  | ||    |  ||  |    |   | |  | | ||  |  |||| |||||||||||||| |||||| ||||||||||||| || |||||  || ||||  ||||  |||| || || || || ||    || |    |||   
gcaaatttttgagttcccatgtgtcccaactttcccaatttgacatctaacc-cttccattcgtaa---ttcctaaataggcattatatattatgttggtgcagGTGTTCATCATCGGACCGGTGAAGCAGGTGAGGAAAGCAGAAGCCATATTAAGGGGACGAATGCTGGAAATGTA-TTGAGGAAAAACTTGTAGTGCTTGTG
















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|9901090|gb|BE610058.1|BE610058
EST:     TGCCGAAATTCTCACGGGAGGTCCCAAGGGCCCACCTGACAAG                         GTCTTCATCATCGGACCAGTGA
genomic: TGCCGAAATTCTCACGGGAGGTCCCAAGGGCCCACCTGACAAGgttcgtatat ... ttttatttagGTCTTCATCATCGGACCAGTGA
EST: gi|31457746|gb|CD399774.1|CD399774
EST:     TGCAATGCCGAAATTCTCACGGGAGGTCCCAAGGGCCCACCTGACAAG                         GTCTTCATTATCGGACCAGTGAAGGAGGTGAGGAAAGCCGAGGCCATGATA
genomic: TGCAATGCCGAAATTCTCACGGGAGGTCCCAAGGGCCCACCTGACAAGgttcgtatat ... ttttatttagGTCTTCATCATCGGACCAGTGAAGGAGGTGAGGAAAGCCGAGGCCATGATA
EST: gi|193611774|gb|FK565389.1|FK565389
EST:     TGCCGAAATTCTCACGGGAGGTCCCAAGGGCCCACCTGACAAG                         GTCTTCATCATCGGACCAGTGAAGGAGGTGAGGAAAGCCGAGGCCATGATA
genomic: TGCCGAAATTCTCACGGGAGGTCCCAAGGGCCCACCTGACAAGgttcgtatat ... ttttatttagGTCTTCATCATCGGACCAGTGAAGGAGGTGAGGAAAGCCGAGGCCATGATA
EST: gi|5760980|gb|AI966343.1|AI966343
EST:     TGCCGAAATTCTCACGGGAGGTCCCAAGGGCCCACCTGACAAG                         GTCTTCATCATCGGACCAGTGA
genomic: TGCCGAAATTCTCACGGGAGGTCCCAAGGGCCCACCTGACAAGgttcgtatat ... ttttatttagGTCTTCATCATCGGACCAGTGA
EST: gi|254339166|gb|GR847883.1|GR847883
EST:     TGCCGAAATTCTCACGGGAGGTCCCAAGGGCCCACCTGACAAG                         GTCTTCATCATCGGACCAGTGAAGGAGGTGAGGAAAGCCGAGGCCATGATA
genomic: TGCCGAAATTCTCACGGGAGGTCCCAAGGGCCCACCTGACAAGgttcgtatat ... ttttatttagGTCTTCATCATCGGACCAGTGAAGGAGGTGAGGAAAGCCGAGGCCATGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatttgcatatgaaaacactgttatttgactaagttttcatgtttttatttagGTCTTCATCATCGGACCAGTGAAGGAGGTGAGGAAAGCCGAGGCCATGATACGGGGTAGAATCTTGGATATATAGTTAAGAAATGTGTTATTTCTCTTCC
                         atttgac  putative branch site (score: 4)
                                            tttttattt  putative PPT
                                taagttttcatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgttattcaactctccatttttttgttttgaatttcaaacatgattatttgcatatgaaaacactgttatttgactaagttttcatgtttttatttagGTCTTCATCATCGGACCAGTGAAGGAGGTGAGGAAAGCCGAGGCCATGATACGGGGTAGAATCTTGGATATATAGTTAAGAAATGTGTTATTTCTCTTCC

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