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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatcaatttgtggattatgttttttttattcgatataaatgcatttatcgtatttatcttatcttgaacagtcatacgtataggatgcaccttatctcctacagttagtgttttttttttatcttgaattattctcatgattttgttaaatgcaatgttaatagATGAGCAATCTTACCAAGGAAGAGTTCGTCCACGTGCTTCGCCGACAAAGCACTGGATTTCCGAGAGGAAGCTCCAAATATAGAGGTGTCACTTTGCACA

Basic information

species Glycine max
transcript GLYMA17G18640.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G18640.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g55560.2 (Oryza sativa), 3'ss of exon 4
gtgatcaatttgtggattatgttttttttattcgatataaatgcatttatcgtatttatcttatcttgaacagtcatacgta--taggatgcaccttatctcctacagttagtgttttttttttatcttgaattattctcatgat-----tttgttaaatgcaatgttaatagATGAGCAATCTTACCAAGGAAGAGTTCGTCCACGTGCTTCGCCGACAAAGCACTGGATTTCCGAGAGGAAGCTCCAAATATAGAGGTGTCACTTTGCACA
                                                          |   | |  || |  | ||   ||  |    |   | || | | |   |||        |||  |||  |   | || | | |   |        | | || |  ||  |   |||||||||| || |||||||| ||||||||||||||||| || || || ||||| || || ||  | ||||||||||| || || || || ||  | ||||
---------------------------------------------------------gtgagagcgcgatcgattattattacctgaactttcctttcttttcatgagtcgccacggtttcgttagatcatactactattactgtagctgcaagattaacgggatcattgcagATGAGCAACCTGACCAAGGAGGAGTTCGTCCACGTGCTCCGGCGGCAGAGCACGGGGTTCCCCCGGGGAAGCTCCAAGTACAGGGGCGTGACGCTCCACA

upper sequence: GLYMA17G18640.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G36920.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgatcaatttgtggattatgttttttttattcgatataaatgcatttatcgtatttatcttatcttgaacagtcatacgtataggatgcaccttatctcctacagttagtgttttttttttatcttgaattattctcatgattt-tgttaaatgcaatgttaatagATGAGCAATCTTACCAAGGAAGAGTTCGTCCACGTGCTTCGCCGACAAAGCACTGGATTTCCGAGAGGAAGCTCCAAATATAGAGGTGTCACTTTGCACA
                                                                                  ||  ||  |  ||||   ||| | || || ||| ||    || || ||   ||     ||||  | || ||    |  || ||||||||  ||| | ||||||||||||||||| ||||| ||||||||||||||||| || || ||  ||||||| || || |||||||||||||||||||| |
---------------------------------------------------------------------------------gtaa-atataaattataaactata-ttggtttttattaacgatttttaaaggtttgggagattaatattgaaattgaattttatagATGACTAATTTAACCAAGGAAGAGTTCGTACACGTACTTCGCCGACAAAGCACAGGCTTCCCTCGAGGAAGTTCGAAGTATAGAGGTGTCACTTTGCATA

upper sequence: GLYMA17G18640.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G67180.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgatcaatttgtggattatgttttttttattcgatataaatgcatttatcgtatttatcttatcttgaacagtcatacgtataggatgcaccttatctcctacagttagtgt--tttttttttatcttgaattattctca-tgattttgttaaatgcaatgttaatagATGAGCAATCTTACCAAGGAAGAGTTCGTCCACGTGCTTCGCCGACAAAGCACTGGATTTCCGAGAGGAAGCTCCAAATATAGAGGTGTCACTTTGCACA
                                                          |  ||| |    |  | ||   |||   ||  || |||  |  |||   || | |  ||  ||  ||    |||  |  | || |||  |  |    |    | ||   ||||| | ||| | || |||||||||||  | || || ||| |  | ||||||||||| ||||| ||||| || || ||||| |||||||| ||||||||||
---------------------------------------------------------gttctatataagtcttttatggatat---atctactttaggttatactagtaatttaattacttactactcagaagaaaacacaatgaaatattggttttttttttttgcagATGGGAAATTTGACAAAGGAAGAGTTTATGCATGTACTTAGAAGGCAAAGCACTGGGTTTCCAAGAGGCAGTTCTAAATACAGAGGTGTTACTTTGCACA

upper sequence: GLYMA17G18640.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0031g00220.t01 (Vitis vinifera), 3'ss of exon 4
gtgatcaatttgtggattatgttttttttattcgatataaatgcatttatcgtatttatcttatcttgaacagtcatacgtataggatgcaccttatc--tcctacagttagtgttttttttttatcttgaattattctcatgattttgttaaatgcaatgttaatagATGAGCAATCTTACCAAGGAAGAGTTCGTCCACGTGCTTCGCCGACAAAGCACTGGATTTCCGAGAGGAAGCTCCAAATATAGAGGTGTCACTTTGCACA
          |   ||     ||    ||||    || |  | ||  | |    | ||   ||| ||||   |   | |  || |     |  | |    |   | |  |   |          |  | || |  || |||||  |   |  ||||     |  | ||||| ||||||| |||||||||||||| || || || |||||||||||||| ||||| |||||||||||||||||||| ||||||||||| || || ||||
---------gtagagaggggcttcaccttatcttgtacagttccacct-tatcttctacagtattttgattcgcttttctgattgttgctagttgagaaatagcaaaaatgaagaaaaaaaagaaagtggattgtttttcatgtatacatgtaatgttgaatgcacagATGGGCAATCTAACCAAGGAAGAGTTTGTGCATGTCCTTCGCCGACAAAGTACTGGTTTTCCGAGAGGAAGCTCCAAGTATAGAGGTGTAACCTTACACA

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|193447296|gb|FK414555.1|FK414555
EST:     AGGCTGACATTAACTTCAATATTGAAGACTATGAAGATGACTTGAAGCAG                         ATGAGCAATCTTACCAAGGAAGAGTTCGTCCACGTGCTTCGCCGCCAAAGC
genomic: AGGCTGACATTAACTTCAATATTGAAGACTATGAAGATGACTTGAAGCAGgtgatcaatt ... atgttaatagATGAGCAATCTTACCAAGGAAGAGTTCGTCCACGTGCTTCGCCGACAAAGC
EST: gi|193374560|gb|FK341542.1|FK341542
EST:     AGGCTGACATTAACTTCAATATTGAAGACTATGAAGATGACTTGAAGCAG                         ATGAGCAATCTTACCAAGGAAGAGTTCGTCCACGTGCTTCGCCGCCAAAGC
genomic: AGGCTGACATTAACTTCAATATTGAAGACTATGAAGATGACTTGAAGCAGgtgatcaatt ... atgttaatagATGAGCAATCTTACCAAGGAAGAGTTCGTCCACGTGCTTCGCCGACAAAGC
EST: gi|193629340|gb|FK572870.1|FK572870
EST:     AGGCTGACATTAACTTCAATATTGAAGACTATGAAGATGACTTGAAGCAG                         ATGAGCAATCTTACCAAGGAAGAGTTCGTCCACGTGCTTCGCCGCCAAAGC
genomic: AGGCTGACATTAACTTCAATATTGAAGACTATGAAGATGACTTGAAGCAGgtgatcaatt ... atgttaatagATGAGCAATCTTACCAAGGAAGAGTTCGTCCACGTGCTTCGCCGACAAAGC
EST: gi|120494213|gb|EH222380.1|EH222380
EST:     AGGCTGACATTAACTTCAATATTGAAGACTATGAAGATGACTTGAAGCAG                         ATGAGCAATCTTACCAAGGAAGAGTTCGTCCACGTGCTTCGCCGACAAAGC
genomic: AGGCTGACATTAACTTCAATATTGAAGACTATGAAGATGACTTGAAGCAGgtgatcaatt ... atgttaatagATGAGCAATCTTACCAAGGAAGAGTTCGTCCACGTGCTTCGCCGACAAAGC
EST: gi|208054805|gb|GD852794.1|GD852794
EST:     AGGCTGACATTAACTTCAATATTGAGGACTATGAAGATGACTTGAAGCAG                         ATGAGCAATCTTACCAAGGAAGAGTTCGTCCACGTGCTTCGCCGCCAAAGC
genomic: AGGCTGACATTAACTTCAATATTGAAGACTATGAAGATGACTTGAAGCAGgtgatcaatt ... atgttaatagATGAGCAATCTTACCAAGGAAGAGTTCGTCCACGTGCTTCGCCGACAAAGC
EST: gi|193638071|gb|FK585389.1|FK585389
EST:     AGGCTGACATTAACTTCAATATTGAAGACTATGAAGATGACTTGAAGCAG                         ATGAGCAATCTTACCAAGGAAGAGTTCGTCCACGTGCTTCGCCGCCAAAGC
genomic: AGGCTGACATTAACTTCAATATTGAAGACTATGAAGATGACTTGAAGCAGgtgatcaatt ... atgttaatagATGAGCAATCTTACCAAGGAAGAGTTCGTCCACGTGCTTCGCCGACAAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttttttttatcttgaattattctcatgattttgttaaatgcaatgttaatagATGAGCAATCTTACCAAGGAAGAGTTCGTCCACGTGCTTCGCCGACAAAGCACTGGATTTCCGAGAGGAAGCTCCAAATATAGAGGTGTCACTTTGCACA
     ttttttatcttgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatcaatttgtggattatgttttttttattcgatataaatgcatttatcgtatttatcttatcttgaacagtcatacgtataggatgcaccttatctcctacagttagtgttttttttttatcttgaattattctcatgattttgttaaatgcaatgttaatagATGAGCAATCTTACCAAGGAAGAGTTCGTCCACGTGCTTCGCCGACAAAGCACTGGATTTCCGAGAGGAAGCTCCAAATATAGAGGTGTCACTTTGCACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA