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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgttttatcttttctcatgtttgattaattagttaatttgtttatttttaagctatgtgcactaactttttactgtcatcttggtgtgtgtcccgcagGCACATCCATATTTCTCTCAGGTAAGGGCAGCTGAAAGTAGCAGAATGAGGACACAGTAACTTGATCACATATGGATCCATAAACTTGAGTTAATATATT

Basic information

species Glycine max
transcript GLYMA11G05340.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G05340.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv07s0129g00410.t01 (Vitis vinifera), 3'ss of exon 9
---------attgttttatcttttctcatgtttgattaattagttaatttgtttatttttaagctatgtgcactaactttttactgtcatcttggtgtgtgtcccgcagGCACATCCATATTTCTCTCAGGTAAGGGCAGCTGAAAGTAGCAGAATGAGGACACAGTAAC---TTGATCACATATGGATCCATAAACTTGAGTTAATATATT
         ||| ||  |    | | || | |   ||   |  | |      ||  ||          | |||| || | ||| | ||| |||  ||| |   | | |||||||||||||||||| ||| || ||||| || || |||||||| ||| | |||||||| |   || |||   | || || ||||||    ||   || |   
gaaaagaaaatttttggaaaactgcacaagctctgtttgatgataagaacaattgctt-------gattacactgacatgttattctcaactta-tgt-tccgctgtagGCACATCCATATTTCTTTCAAGTGAGGGCTGCAGAGAGTAGCAGGATGCGAACACAGTAGCCTCTTCATCTTGTGTGCATACATAAAAAC-AGCGCATGTC--
















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|193383360|gb|FK347265.1|FK347265
EST:     AGCTCCTTCGATATGATCACCAGGACAGGCTAACAGCTAGAGAAGCAATG                         GCACATCCATATTTCTCTCAGGTAAGGGCGAGCTGAAAGTAGCAGAATGAG
genomic: AGCTCCTTCGATATGATCACCAGGACAGGCTAACAGCTAGAGAAGCAATGgtaatgataa ... tgtcccgcagGCACATCCATATTTCTCTCAGGTAAGGGC-AGCTGAAAGTAGCAGAATGAG
EST: gi|213605531|gb|DB974274.1|DB974274
EST:     AGCTCCTTCGATATGATCACCAGGACAGGCTAACAGCTAGAGAAGCAATG                         GCACATCCATATTTCTCTCAGGTAAGGGCAGCTGAAAGTAGCAGAATGAGG
genomic: AGCTCCTTCGATATGATCACCAGGACAGGCTAACAGCTAGAGAAGCAATGgtaatgataa ... tgtcccgcagGCACATCCATATTTCTCTCAGGTAAGGGCAGCTGAAAGTAGCAGAATGAGG
EST: gi|10233590|gb|BE802478.1|BE802478
EST:     AGCTCCTTCGATATGATCACCAGGACAGGCTAACAGCTAGAGAAGCAATG                         GCACATCCATATTTCTCTCAGGTAAGGGCAGCTGAGAGTAGCAGAATGAGG
genomic: AGCTCCTTCGATATGATCACCAGGACAGGCTAACAGCTAGAGAAGCAATGgtaatgataa ... tgtcccgcagGCACATCCATATTTCTCTCAGGTAAGGGCAGCTGAAAGTAGCAGAATGAGG
EST: gi|38193563|gb|CF922769.1|CF922769
EST:     AGCTCCTTCGATATGATCACCAGGACAGGCTAACAGCTAGAGAAGCAATG                         GCACATCCATATTTCTCTCAGGTAAGGGCAGCTGAAAGTAGCAGAATGAGG
genomic: AGCTCCTTCGATATGATCACCAGGACAGGCTAACAGCTAGAGAAGCAATGgtaatgataa ... tgtcccgcagGCACATCCATATTTCTCTCAGGTAAGGGCAGCTGAAAGTAGCAGAATGAGG
EST: gi|193321178|gb|FK283564.1|FK283564
EST:     AGCTCCTTCGATATGATCACCAGGACAGGCTAACAGCTAGAGAAGCAATG                         GCACATCCATATTTCTCTCAGGTAAGGGCAGCTGAAAGTAGCAGAATGAGG
genomic: AGCTCCTTCGATATGATCACCAGGACAGGCTAACAGCTAGAGAAGCAATGgtaatgataa ... tgtcccgcagGCACATCCATATTTCTCTCAGGTAAGGGCAGCTGAAAGTAGCAGAATGAGG
EST: gi|214009784|gb|DB986911.1|DB986911
EST:     AGCTCCTTCGATATGATCACCAGGACAGGCTAACAGCTAGAGAAGCAATG                         GCACATCCATATTTCTCTCAGGTAAGGGCAGCTGAAAGTAGCAGAATGAGG
genomic: AGCTCCTTCGATATGATCACCAGGACAGGCTAACAGCTAGAGAAGCAATGgtaatgataa ... tgtcccgcagGCACATCCATATTTCTCTCAGGTAAGGGCAGCTGAAAGTAGCAGAATGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttaagctatgtgcactaactttttactgtcatcttggtgtgtgtcccgcagGCACATCCATATTTCTCTCAGGTAAGGGCAGCTGAAAGTAGCAGAATGAGGACACAGTAACTTGATCACATATGGATCCATAAACTTGAGTTAATATATT
                cactaac  putative branch site (score: 1)
                   taacttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgttttatcttttctcatgtttgattaattagttaatttgtttatttttaagctatgtgcactaactttttactgtcatcttggtgtgtgtcccgcagGCACATCCATATTTCTCTCAGGTAAGGGCAGCTGAAAGTAGCAGAATGAGGACACAGTAACTTGATCACATATGGATCCATAAACTTGAGTTAATATATT

- - - - - - - - tcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - ctatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cactaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tactgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgtg