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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatattaaaaggaaaaataaaataattttttttggtctcatatgttaataattctctaattgttcttaaattgctaaaatcatattattcaatcatgcagGGAACTTGTGCAAGCAGGGAAAGACATTGAAAGTGCATATTGGGAACTTGTAGTGAAGGATATCCAAGATGCTTGCAAATTATTTGAACCAATCTATGAT

Basic information

species Glycine max
transcript GLYMA08G47790.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G47790.3 (Glycine max), 3'ss of exon 3
lower sequence: AT5G13420.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------gatattaaa---aggaaaaataaaataattttttttggtctcatatgttaataattctct-aattgttcttaaat-tgctaaaatcatattattcaatcatg--cagGGAACTTGTGCAAGCAGGGAAAGACATTGAAAGTGCATATTGGGAACTTGTAGTGAAGGATATCCAAGATGCTTGCAAATTATTTGAACCAATCTATGAT
                 | ||| |     |     ||| |  ||  | ||    ||     |||  |  || | | ||  ||| |   || || |||    |||     ||  ||     |||  ||||||| || | || || |||||||||||||| |||||||||||||| ||||||||||| || ||||| |||||| | ||||| ||||||||||| 
gtatctttttgtgattgtcttagacttgtggttgttaacaacatgctattaaaactttagagttcttctttatatgaaaagttgtctgatatgttaatggtatacctgacatgcactattagGACACTTGTGGAATCGGGAAAGGACATTGAAAGTGCGTATTGGGAACTTGTGGTGAAGGATATTCAGGATGCCTGCAAACTTTTTGAGCCAATCTATGAC

upper sequence: GLYMA08G47790.3 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0150g00190.t01 (Vitis vinifera), 3'ss of exon 3
--gatattaaaaggaaaaataaaataattttttttggtctcatatgttaataattctctaattgttcttaaattgctaaaatcatattattcaatcatgcagGGAACTTGTGCAAGCAGGGAAAGACATTGAAAGTGCATATTGGGAACTTGTAGTGAAGGATATCCAAGATGCTTGCAAATTATTTGAACCAATCTATGAT
  | ||||          |  |  |    |    |   || | ||   | |   ||  | |  |||  |||||     |  | | |   ||  ||  |||||||||||||| | |||||| |||||||||||||||||||| ||||| ||||| |||||||| ||||||||||| |||| | | ||||| ||||||||||||
tagttattctgctcttgcaggacctggaatccaata--ctaacatccgagttgatccttcagagttggtaaatctaacattttaaacctttggattctgcagGGAACTTGTACTAGCAGGAAAAGACATTGAAAGTGCATACTGGGAGCTTGTGGTGAAGGACATCCAAGATGCGTGCAGACTTTTTGAGCCAATCTATGAT
















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|18692732|gb|BM521580.1|BM521580
EST:     ATTTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCAG                         GGAACTTGTGCAAGCAGGGAAAGACATTGAAAGTGCATATTGGGAACTTGT
genomic: ATTTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCAGgtaccatcaa ... aatcatgcagGGAACTTGTGCAAGCAGGGAAAGACATTGAAAGTGCATATTGGGAACTTGT
EST: gi|254326716|gb|GR832868.1|GR832868
EST:     ATTTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCAG                         GGAACTTGTGCAAGCAGGGAAAGACATTGAAAGTGCATATTGGGAACTTGT
genomic: ATTTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCAGgtaccatcaa ... aatcatgcagGGAACTTGTGCAAGCAGGGAAAGACATTGAAAGTGCATATTGGGAACTTGT
EST: gi|254322565|gb|GR837979.1|GR837979
EST:     ATTTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCAG                         GGAACTTGTGCAAGCAGGGAAAGACATTGAAAGTGCATATTGGGAACTTGT
genomic: ATTTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCAGgtaccatcaa ... aatcatgcagGGAACTTGTGCAAGCAGGGAAAGACATTGAAAGTGCATATTGGGAACTTGT
EST: gi|8283342|gb|BE020903.1|BE020903
EST:     ATTTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCAG                         GGAACTTGTGCAAGCAGGGAAAGACATTGAAAGTGCATATTGGGAACTTGT
genomic: ATTTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCAGgtaccatcaa ... aatcatgcagGGAACTTGTGCAAGCAGGGAAAGACATTGAAAGTGCATATTGGGAACTTGT
EST: gi|19271012|gb|BM887268.1|BM887268
EST:     ATTTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCAG                         GGAACTTGTGCAAGCAGGGAAAGACATTGAAAGTGCATATTGGGAACTTGT
genomic: ATTTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCAGgtaccatcaa ... aatcatgcagGGAACTTGTGCAAGCAGGGAAAGACATTGAAAGTGCATATTGGGAACTTGT
EST: gi|17022331|gb|BM093365.1|BM093365
EST:     ATTTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCAG                         GGAACTTGTGCAAGCAGGGAAAGACATTGAAAGTGCATATTGGGAACTTGT
genomic: ATTTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCAGgtaccatcaa ... aatcatgcagGGAACTTGTGCAAGCAGGGAAAGACATTGAAAGTGCATATTGGGAACTTGT
EST: gi|9259167|gb|BE347314.1|BE347314
EST:     ATTTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCAG                         GGAACTTGTGCAAGCAGGGAAAGACATTGAAAGTGCATATTGTGAACTTGT
genomic: ATTTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCAGgtaccatcaa ... aatcatgcagGGAACTTGTGCAAGCAGGGAAAGACATTGAAAGTGCATATTGGGAACTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taataattctctaattgttcttaaattgctaaaatcatattattcaatcatgcagGGAACTTGTGCAAGCAGGGAAAGACATTGAAAGTGCATATTGGGAACTTGTAGTGAAGGATATCCAAGATGCTTGCAAATTATTTGAACCAATCTATGAT
                          tgctaaa  putative branch site (score: 2)
                    ttaaattgctaaaatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatattaaaaggaaaaataaaataattttttttggtctcatatgttaataattctctaattgttcttaaattgctaaaatcatattattcaatcatgcagGGAACTTGTGCAAGCAGGGAAAGACATTGAAAGTGCATATTGGGAACTTGTAGTGAAGGATATCCAAGATGCTTGCAAATTATTTGAACCAATCTATGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG