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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAGgtagttaattatctgtagtatattaaataccccttatgatttttggagccatatttactgcacaaaaatacattcttgctgacttcttgtttgcttcatgcattttaccactaaacag

Basic information

species Glycine max
transcript GLYMA14G36540.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G36540.1 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os08g42410.2 (Oryza sativa), 5'ss of exon 7
ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAGgta-gttaattatctgtagtatattaaataccccttatgatttttggagccatatttactgcacaaaaatacattcttgc-tgacttcttgtttgcttcatgcattttaccactaaacag
 |||||||| |||||||||||||| || |||||||||||||| || || || ||||| || || || || |||||| | |   ||  |||| |   ||          |  | ||| |   | ||  |||      |     | | |    |  |   ||  || | ||| | | |||||| | | |    ||
CTATGGTGAATCATTCCCTGTTTCTGCGGAAGTTCTTGATTCTAGCTTCTGTCTTCCGATTGGGAAGGCTAAGgtatgctgtatagttgtattgatttcgtagtaggatgagttttatttggtcaggtttcggtttctggtttgcctggaagagtttatttctgatggctgctttcatttttcta-tgtgtag

upper sequence: GLYMA14G36540.1 (Glycine max), 5'ss of exon 9
lower sequence: AT5G50850.1 (Arabidopsis thaliana), 5'ss of exon 10
ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAGgtagttaattatctgtagtatattaaataccccttatgatttttggagccatatttactgcacaaaaatacattcttgctgacttcttgtttgcttcatgcattttaccactaaacag
||||||||| ||||||||| |||| |  ||||  |||||||| ||||| || ||||||||||| ||||| |||||| |   | |       | ||||   | |  ||||||  | |        | | | ||    |  | |    |  |  | |  |  | ||||| |    ||                
ATATGGTGAATCATTCCCTATTTCAGAAGAAGCCCTTGATTCAAGTTTCTGTCTTCCCATAGGCAAAGCCAAGgtact--gtcactcagtatctattgtcttcttcttatgtgtctctttcatctttcttctatctagcagttggatgct-ttaatgttgtctttgcctataacag---------------

upper sequence: GLYMA14G36540.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv17s0000g00690.t01 (Vitis vinifera), 5'ss of exon 9
ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAGgtagttaattatctgtagtatattaaataccccttatgatttttggagccatatttactgcacaaaaatacattcttgctgacttcttgtttgcttcatgcattttaccactaaacag
||||||| |||| ||||||||||| |  |||| ||||||||||||||| | |||||| ||||| |||||||||||  ||   | ||| ||  ||  |   | |  || || ||     ||    ||| |  |  |   || ||  ||||| ||  |||||||  |  |  |                    
ATATGGTCAGTCTTTCCCTGTTTCAGAGGAAGCTCTTGATTCCAGTTTCTCCCTTCCAATAGGGAAAGCAAAGgtgctt---tttct-taacattcttgttgctgctgataat-----gatttttatct-ttagatgcaatta--ttcttcct--cttcttggctattgaag-------------------

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|20498733|gb|BQ273663.1|BQ273663
EST:     CGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAG                         ATTGAGAGGGAAGGAAAAGATGTGACTATTACAGCCTATTCAAAAATGGTT
genomic: CGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAGgtagttaatt ... cactaaacagATTGAGAGGGAAGGAAAAGATGTGACTATTACAGCCTATTCAAAAATGGTT
EST: gi|20498857|gb|BQ273787.1|BQ273787
EST:     CGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAG                         ATTGAGAGGGAAGGGAAAGATGTGACTATTACAGCCTATTCAAAAATGGTT
genomic: CGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAGgtagttaatt ... cactaaacagATTGAGAGGGAAGGAAAAGATGTGACTATTACAGCCTATTCAAAAATGGTT
EST: gi|19053203|gb|BM731870.1|BM731870
EST:     CGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAG                         ATTGAGAGGGAAGGAAAAGATGTGACTATTACAGCCTATTCAAAAATGGTT
genomic: CGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAGgtagttaatt ... cactaaacagATTGAGAGGGAAGGAAAAGATGTGACTATTACAGCCTATTCAAAAATGGTT
EST: gi|9439950|gb|BE440462.1|BE440462
EST:     CGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAG                         ATTGAGAGGGAAGGAAAAGATGTGACTATTACAGCCTATTCAAAAATGGTT
genomic: CGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAGgtagttaatt ... cactaaacagATTGAGAGGGAAGGAAAAGATGTGACTATTACAGCCTATTCAAAAATGGTT
EST: gi|37994649|gb|CF806308.1|CF806308
EST:     CGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAG                         ATTGAGAGGGAAGGAAAAGATGTGACTATTACAGCCTATTCAAAAATGGTT
genomic: CGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAGgtagttaatt ... cactaaacagATTGAGAGGGAAGGAAAAGATGTGACTATTACAGCCTATTCAAAAATGGTT
EST: gi|298169681|gb|HO021041.1|HO021041
EST:     CGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAG                         ATTGAGAGGGAAGGAAAAGATGTGACTATTACAGCCTATTCAAAAATGGTT
genomic: CGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAGgtagttaatt ... cactaaacagATTGAGAGGGAAGGAAAAGATGTGACTATTACAGCCTATTCAAAAATGGTT
EST: gi|17962851|gb|BM269607.1|BM269607
EST:     CGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAG                         ATTGAGAGGGAAGGAAAAGATGTGACTATTACAGCCTATTCAAAAATGGTT
genomic: CGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAGgtagttaatt ... cactaaacagATTGAGAGGGAAGGAAAAGATGTGACTATTACAGCCTATTCAAAAATGGTT
EST: gi|5606648|gb|AI900746.1|AI900746
EST:     CGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAG                         ATTGAGAGGGAAGGAAAAGATGTGACTATTACAGCCTATTCAAAAATGGTT
genomic: CGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAGgtagttaatt ... cactaaacagATTGAGAGGGAAGGAAAAGATGTGACTATTACAGCCTATTCAAAAATGGTT
EST: gi|254334369|gb|GR844154.1|GR844154
EST:     CGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAG                         ATTGAGAGGGAAGGAAAAGATGTGACTATTACAGCCTATTCAAAAATGGTT
genomic: CGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAGgtagttaatt ... cactaaacagATTGAGAGGGAAGGAAAAGATGTGACTATTACAGCCTATTCAAAAATGGTT
EST: gi|151396530|gb|EV266407.1|EV266407
EST:     CGGCCGAAGTTCTTGATTCCAGTTTTTGTCTTCCCATAGGAAAAGCAAAG                         ATTGAGAGGGAAGGAAA-GATGTGACTATTACAGCCTATTCAAAA-TGGTT
genomic: CGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAGgtagttaatt ... cactaaacagATTGAGAGGGAAGGAAAAGATGTGACTATTACAGCCTATTCAAAAATGGTT
EST: gi|207714211|gb|GD694990.1|GD694990
EST:     CGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAG                         ATTGAGAGGGAAGGAAAAGATGTGACTATTACAGCCTATTCAAAAAT
genomic: CGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAGgtagttaatt ... cactaaacagATTGAGAGGGAAGGAAAAGATGTGACTATTACAGCCTATTCAAAAAT
EST: gi|207737078|gb|GD713125.1|GD713125
EST:     CGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAG                         ATTGAGAGGGAAGGAAAAGA
genomic: CGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAGgtagttaatt ... cactaaacagATTGAGAGGGAAGGAAAAGA
EST: gi|254335254|gb|GR846751.1|GR846751
EST:     CGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAG                         ATTGAGAGGGAAGGAAAAGATGTGACTATTACAGCCTATTCAAAAATGGTT
genomic: CGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAGgtagttaatt ... cactaaacagATTGAGAGGGAAGGAAAAGATGTGACTATTACAGCCTATTCAAAAATGGTT
EST: gi|10845821|gb|BF068863.1|BF068863
EST:     CGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAG                         ATTGAGAGGGAAGGAAAAGATGTGACTATTACAGCCTATTCAAAAATGGTT
genomic: CGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAGgtagttaatt ... cactaaacagATTGAGAGGGAAGGAAAAGATGTGACTATTACAGCCTATTCAAAAATGGTT
EST: gi|254319588|gb|GR829100.1|GR829100
EST:     CGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAG                         ATTGAGAGGGAAGGAAAAGATGTGACTATTACAGCCTATTCAAAA-TGGTT
genomic: CGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAGgtagttaatt ... cactaaacagATTGAGAGGGAAGGAAAAGATGTGACTATTACAGCCTATTCAAAAATGGTT
EST: gi|207835633|gb|GD805630.1|GD805630
EST:     CGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAG                         ATTGAGAGGGAAGGAAAAGATGTGACTATTACAGCCTATTCAAAAATGGTT
genomic: CGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAGgtagttaatt ... cactaaacagATTGAGAGGGAAGGAAAAGATGTGACTATTACAGCCTATTCAAAAATGGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAGgtagttaattatctgtagtatattaaataccccttatgatttttggagccatatttactgcacaaaaatacattcttgctgacttcttgtttgcttcatgcattttaccactaaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG