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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaagtcattcttgaagtttctcatattgaattctaatatttaattttaattgtttggatattttttgtatttcagCCTATTGCTGCATTGCCTTATCTGGACAGGGAGCTTTCACCGGCACTGTATAGGTCCTTTTTCATTCCTTACCTTTGGCAAGAGAAGAATGTTTTTGGAA

Basic information

species Glycine max
transcript GLYMA13G34570.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G34570.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv19s0014g01410.t01 (Vitis vinifera), 3'ss of exon 9
-----------------gtaaaagtcattcttgaagtttctcatattgaatt--ctaatatttaattttaa-ttgtttg--gatattttttgtatttcagCCTATTGCTGCATTGCCTTATCTGGACAGGGAGCTTTCACCGGCACTGTATAGGTCCTTTTTCATTCCTTACCTTTGGCAAGAGAAGAATGTTTTTGGAA
                  |  |  |  ||  |   || | |    |  ||||  ||   || |||| | |  |||  |    | ||||| |||  || || || |||| |  ||||||||||||||||||||||||||||| |||   ||| |||| |||||||| || || || ||| |    | |||||||||||| |
ttttttctacttttcttctttattttctttcttttgtattttccctcaaattttctgggatctaatataaccttggctactaaaattttatgtgctttagGCTGTTGCGGTGTTGCCTTATCTGGACAGGGAGCTTTCACCTGCAACTTATCGGTCTTTTTTCATCCCATATCTCTGGGAGCGTAGGAATGTTTTTGGCA
















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|208185706|gb|GD986349.1|GD986349
EST:     AGCTAGAGCGGCCTTACCTGACTCGTGGAAGTGACTTGTCAACATGGGAG                         CCTATTGCTGCATTGCCTTATCTGGACAGGGAGCTTTCACCGGCACTGTAT
genomic: AGCTAGAGCGGCCTTACCTGACTCGTGGAAGTGACTTGTCAACATGGGAGgtaaaagtca ... tgtatttcagCCTATTGCTGCATTGCCTTATCTGGACAGGGAGCTTTCACCGGCACTGTAT
EST: gi|10253488|gb|BE821254.1|BE821254
EST:     AGCTAGAGCGGCCTTACCTGACTCGTGGAAGTGACTTGTCAACATGGGAG                         CCTATTGCTGCATTGCCTTATCTGGACAGGGAGCTTTCACCGGCACTGTAT
genomic: AGCTAGAGCGGCCTTACCTGACTCGTGGAAGTGACTTGTCAACATGGGAGgtaaaagtca ... tgtatttcagCCTATTGCTGCATTGCCTTATCTGGACAGGGAGCTTTCACCGGCACTGTAT
EST: gi|193550904|gb|FK507199.1|FK507199
EST:     AGCTAGAGCGGCCTTACCTGACTCGTGGAAGTGACTTGTCAACATGGGAG                         CCTATTGCTGCATTGCCTTATCTGGACAGGGAGCTTTCACCGGCACTGTAT
genomic: AGCTAGAGCGGCCTTACCTGACTCGTGGAAGTGACTTGTCAACATGGGAGgtaaaagtca ... tgtatttcagCCTATTGCTGCATTGCCTTATCTGGACAGGGAGCTTTCACCGGCACTGTAT
EST: gi|51342060|gb|CO983327.1|CO983327
EST:     AGCTAGAGCGGCCTTACCTGACTCGTGGAAGTGACTTGTCAACATGGGAG                         CCTATTGCTGCATTGCCTTATCTGGACAGGGAGCTTTCACCGGCACTGTAT
genomic: AGCTAGAGCGGCCTTACCTGACTCGTGGAAGTGACTTGTCAACATGGGAGgtaaaagtca ... tgtatttcagCCTATTGCTGCATTGCCTTATCTGGACAGGGAGCTTTCACCGGCACTGTAT
EST: gi|7926538|gb|AW832564.1|AW832564
EST:     AGCTAGAGCGGCCTTACCTGACTCGTGGAAGTGACTTGTCAACATGGGAG                         CCTATTGCTGCAT
genomic: AGCTAGAGCGGCCTTACCTGACTCGTGGAAGTGACTTGTCAACATGGGAGgtaaaagtca ... tgtatttcagCCTATTGCTGCAT
EST: gi|208199908|gb|GE000388.1|GE000388
EST:     AGCTAGAGCGGCCTTACCTGACTCGTGGAAGTGACTTGTCAACATGGGAG                         CCTATTGCTGCATTGCCTTATCTGGACAGGGAGCTTTCACCGGCACTGTAT
genomic: AGCTAGAGCGGCCTTACCTGACTCGTGGAAGTGACTTGTCAACATGGGAGgtaaaagtca ... tgtatttcagCCTATTGCTGCATTGCCTTATCTGGACAGGGAGCTTTCACCGGCACTGTAT
EST: gi|21887490|gb|BQ740703.1|BQ740703
EST:     AGTGACTTGTCAACATGGGAG                         CCTATTGCTGCATTGCCTTATCTGGACAGGGAGCTTTCACCGGCACTGTAT
genomic: AGTGACTTGTCAACATGGGAGgtaaaagtca ... tgtatttcagCCTATTGCTGCATTGCCTTATCTGGACAGGGAGCTTTCACCGGCACTGTAT
EST: gi|208073152|gb|GD869855.1|GD869855
EST:     AGCTAGAGCGGCCTTACCTGACTCGTGGAAGTGACTTGTCAACATGGGAG                         CCTATTGCTGCATTGCCTTATCTGGACAGGGAGCTTTCACCGGCACTGTAT
genomic: AGCTAGAGCGGCCTTACCTGACTCGTGGAAGTGACTTGTCAACATGGGAGgtaaaagtca ... tgtatttcagCCTATTGCTGCATTGCCTTATCTGGACAGGGAGCTTTCACCGGCACTGTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatattgaattctaatatttaattttaattgtttggatattttttgtatttcagCCTATTGCTGCATTGCCTTATCTGGACAGGGAGCTTTCACCGGCACTGTATAGGTCCTTTTTCATTCCTTACCTTTGGCAAGAGAAGAATGTTTTTGGAA
                                      tatttttt  CT-rich tract
             taatatttaattttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaagtcattcttgaagtttctcatattgaattctaatatttaattttaattgtttggatattttttgtatttcagCCTATTGCTGCATTGCCTTATCTGGACAGGGAGCTTTCACCGGCACTGTATAGGTCCTTTTTCATTCCTTACCTTTGGCAAGAGAAGAATGTTTTTGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA