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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACATGAGTTTTCAGAACTGGTAAAGCGGGGGTCTACAGCAGAGGACTTAGGTGCAGGTCATGCTGAAGCTGCAAGGGTTCAAGGTCTTGGTTTTGCAAGgtaaagtgactaggaaagaacatattttatggcaataaagtagatttgattttctttatatttactttaatttttttctattttctgtttcagttgtttc...

Basic information

species Glycine max
transcript GLYMA01G06270.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G06270.1 (Glycine max), 5'ss of exon 3
lower sequence: AT3G52220.1 (Arabidopsis thaliana), 5'ss of exon 3
AACATGAGTTTTCAGAACTGGTAAAGCGGGGGTCTACAGCAGAGGACTTAGGTGCAGGTCATGCTGAAGCTGCAAGGGTTCAAGGTCTTGGTTTTGCAAGgtaaagtgact-------aggaaagaacatattttatggcaataaagtagatttgattttctttatatttactt--taatttttttctattttctgtttcagttgtttc-----------------
| || |||||| | ||||| || ||| |||| || |||||||||||||||||||||||  ||||||| ||||   ||||||| |||||||| | ||| | ||||  |   |          ||| |   || ||| |  | ||      | |||   |  ||||||  ||  ||  || |||   | | |    ||| |||  ||| |                  
AGCAAGAGTTTACTGAACTTGTGAAGAGGGGTTCGACAGCAGAGGACTTAGGTGCAGGGAATGCTGATGCTGTGTGGGTTCACGGTCTTGGATATGCTAAgtaagttctttttctttcgtaaaaaactctaatttttaactatgttaatgtttttggtggctttatggtttattggtagtttacctttgtcccttgtctcacatgtctttctccaactctgtacag

upper sequence: GLYMA01G06270.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv13s0101g00090.t01 (Vitis vinifera), 5'ss of exon 3
AACATGAGTTTTCAGAACTGGTAAAGCGGGGGTCTACAGCAGAGGACTTAGGTGCAGGTCATGCTGAAGCTGCAAGGGTTCAAGGTCTTGGTTTTGCAAGgtaaagtgactaggaaagaa-catattttatggcaataaagtagatttgattttctttatattt--actttaatttttttctatt-ttctgtt-tcagttgtttc
| ||||||||||| ||||| || ||||| || ||||| ||||| || || |||||||| ||| ||||||| |||   |||||||||||||||||||| |||||   ||||| ||||||   ||||| || ||||  | | |   | |  | |    ||| | ||  |  || || || || | || ||||| | | |  |  || 
AGCATGAGTTTTCGGAACTTGTGAAGCGAGGCTCTACTGCAGAAGATTTGGGTGCAGGCCATTCTGAAGCAGCACATGTTCAAGGTCTTGGTTTTGCGAGgta---tgactgggaaagtttcatatgtt-tggctttgatgactagtgcaatgatattacacttctatcttgatgttgttttgttgttctgatgttatatactt-
















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|208076621|gb|GD875550.1|GD875550
EST:     GGTGCAGGTCATGCTGAAGCTGCAAGGGTTCAAGGTCTTGGTTTTGCAAG                         AGAACCACGCCCTTGGGAAGAATCCGGTTCTTCTAAGCTTTCACTTAGTGA
genomic: GGTGCAGGTCATGCTGAAGCTGCAAGGGTTCAAGGTCTTGGTTTTGCAAGgtaaagtgac ... tactttgtagAGAACCACGCCCTTGGGAAGAATCCGGTTCTTCTAAGCTTTCACTTAGTGA
EST: gi|208247800|gb|GE044866.1|GE044866
EST:     GGTGCAGGTCATGCTGAAGCTGCAAGGGTTCAAGGTCTTGGTTTTGCAAG                         AGAACCACGCCCTTGGGAAGAATCCGGTTCTTCTAAGCTTTCACTTAGTGA
genomic: GGTGCAGGTCATGCTGAAGCTGCAAGGGTTCAAGGTCTTGGTTTTGCAAGgtaaagtgac ... tactttgtagAGAACCACGCCCTTGGGAAGAATCCGGTTCTTCTAAGCTTTCACTTAGTGA
EST: gi|208265606|gb|GE063134.1|GE063134
EST:     GGTGCAGGTCATGCTGAAGCTGCAAGGGTTCAAGGTCTTGGTTTTGCAAG                         AGAACCACGCCCTTGGGAAGAATCCGGTTCTTCTAAGCTTTCACTTAGTGA
genomic: GGTGCAGGTCATGCTGAAGCTGCAAGGGTTCAAGGTCTTGGTTTTGCAAGgtaaagtgac ... tactttgtagAGAACCACGCCCTTGGGAAGAATCCGGTTCTTCTAAGCTTTCACTTAGTGA
EST: gi|207834252|gb|GD805873.1|GD805873
EST:     GGTGCAGGTCATGCTGAAGCTGCAAGGGTTCAAGGTCTTGGTTTTGCAAG                         AGAACCACGCCCTTGGGAAGAATCCGGTTCTTCTAAGCTTTCACTTAGTGA
genomic: GGTGCAGGTCATGCTGAAGCTGCAAGGGTTCAAGGTCTTGGTTTTGCAAGgtaaagtgac ... tactttgtagAGAACCACGCCCTTGGGAAGAATCCGGTTCTTCTAAGCTTTCACTTAGTGA
EST: gi|208259011|gb|GE052420.1|GE052420
EST:     GGTGCAGGTCATGCTGAAGCTGCAAGGGTACAAGGTCTTGGTTTTGCAAG                         AGAACCACGCCCTTGGGAAGAATCCGGTTCTTCTAAGCTTTCACTTAGTGA
genomic: GGTGCAGGTCATGCTGAAGCTGCAAGGGTTCAAGGTCTTGGTTTTGCAAGgtaaagtgac ... tactttgtagAGAACCACGCCCTTGGGAAGAATCCGGTTCTTCTAAGCTTTCACTTAGTGA
EST: gi|207774642|gb|GD747166.1|GD747166
EST:     GGTGCAGGTCATGCTGAAGCTGCAAGGGTTCAAGGTCTTGGTTTTGCAAG                         AGAACCACGCCCTTGGGAAGAATCCGGTTCTTCTAAGCTTTCACTTAGTGA
genomic: GGTGCAGGTCATGCTGAAGCTGCAAGGGTTCAAGGTCTTGGTTTTGCAAGgtaaagtgac ... tactttgtagAGAACCACGCCCTTGGGAAGAATCCGGTTCTTCTAAGCTTTCACTTAGTGA
EST: gi|193495631|gb|FK461515.1|FK461515
EST:     GGTGCAGGTCATGCTGAAGCTGCAAGGGTTCAAGGTCTTGGTTTTGCAAG                         AGAACCACGCCCTTGGGAAGAATCCGGTTCTTCTAAGCTTTCACTTAG
genomic: GGTGCAGGTCATGCTGAAGCTGCAAGGGTTCAAGGTCTTGGTTTTGCAAGgtaaagtgac ... tactttgtagAGAACCACGCCCTTGGGAAGAATCCGGTTCTTCTAAGCTTTCACTTAG
EST: gi|208172711|gb|GD969342.1|GD969342
EST:     GGTGCAGGTCATGCTGAAGCTGCAAGGGTTCAAGGTCTTGGTTTTGCAAG                         AGAACCACGCCCTTGGGAAGAATCCGGTTCTTCTAAGCTTTCACTTAGTGA
genomic: GGTGCAGGTCATGCTGAAGCTGCAAGGGTTCAAGGTCTTGGTTTTGCAAGgtaaagtgac ... tactttgtagAGAACCACGCCCTTGGGAAGAATCCGGTTCTTCTAAGCTTTCACTTAGTGA
EST: gi|193541703|gb|FK498405.1|FK498405
EST:     GGTGCAGGTCATGCTGAAGCTGCAAGGGTTCAAGGTCTTGGTTTTGCAAG                         AGAACCACGCCCTTGGGAAGAATCCGGTTCTTCTAAGCTTTCACTTAGTGA
genomic: GGTGCAGGTCATGCTGAAGCTGCAAGGGTTCAAGGTCTTGGTTTTGCAAGgtaaagtgac ... tactttgtagAGAACCACGCCCTTGGGAAGAATCCGGTTCTTCTAAGCTTTCACTTAGTGA
EST: gi|298190449|gb|HO032570.1|HO032570
EST:     GGTGCAGGTCATGCTGAAGCTGCAAGGGTTCAAGGTCTTGGTTTTGCAAG                         AGAACCACGCC
genomic: GGTGCAGGTCATGCTGAAGCTGCAAGGGTTCAAGGTCTTGGTTTTGCAAGgtaaagtgac ... tactttgtagAGAACCACGCC
EST: gi|193604205|gb|FK558512.1|FK558512
EST:     GGTGCAGGTCATGCTGAAGCTGCAAGGGTTCAAGGTCTTGGTTTTGCAAG                         AGAACCACGCCCTTGGGAAGAATCCGGTTCTTCTAAGCTTTCACTTAGTGA
genomic: GGTGCAGGTCATGCTGAAGCTGCAAGGGTTCAAGGTCTTGGTTTTGCAAGgtaaagtgac ... tactttgtagAGAACCACGCCCTTGGGAAGAATCCGGTTCTTCTAAGCTTTCACTTAGTGA
EST: gi|207733425|gb|GD713265.1|GD713265
EST:     GGTGCAGGTCATGCTGAAGCTGCAAGGGTTCAAGGTCTTGGTTTTGCAAG                         AGAACCACGCCCTTGGGAAGAATCCGGTTCTTCTAAGCTTTCACTTAGTGA
genomic: GGTGCAGGTCATGCTGAAGCTGCAAGGGTTCAAGGTCTTGGTTTTGCAAGgtaaagtgac ... tactttgtagAGAACCACGCCCTTGGGAAGAATCCGGTTCTTCTAAGCTTTCACTTAGTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACATGAGTTTTCAGAACTGGTAAAGCGGGGGTCTACAGCAGAGGACTTAGGTGCAGGTCATGCTGAAGCTGCAAGGGTTCAAGGTCTTGGTTTTGCAAGgtaaagtgactaggaaagaacatattttatggcaataaagtagatttgattttctttatatttactttaatttttttctattttctgtttcagttgtttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaaagaa