Sequence
atgc intronic sequence ATGC exonic sequence...aaaattttaatactgaattttactaaattaatggatgtacaatagaatttatatttatattttttattttttatttttctgacttttgaatctcttgcagATGATACTTTATGACAAACCTGGTGTACTACAGAAGGAAATGCATAAGTTAGACTCAATGATGATGAAAAATGTTCGCAGTGCGGCAGTTAATGCTGACT
Basic information
species | Glycine max |
transcript | GLYMA02G06100.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G06100.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g49220.2 (Oryza sativa), 3'ss of exon 2
aaaattttaatactgaattttactaaattaatggatgtacaatagaatttatatttatattttttattttttatttttctgacttttgaatct-cttgcagATGATACTTTATGACAAACCTGGTGTACTACAGAAGGAAATGCATAAGTTAGACTCAATGATGATGAAAAATGTTCGCAGTGCGGCAGTTAATGCTGACT
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---gtatcaccttttagtttctaaagctttaggattatagactatgaaagggggaaatgttaatttctcactgctaatctgagttatcatttagTTTGCAGATAATACTTTATGACACGCCAGGTGTCATCAAAAAGGAAATGCATAAGCTAGACACAATGATGATGAAGAATGTTAGGAGTGCCGTTGGCAGT-------
upper sequence: GLYMA02G06100.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g49220.1 (Oryza sativa), 3'ss of exon 2
aaaattttaatactgaattttactaaattaatggatgtacaatagaatttatatttatattttttattttttatttttctgacttttgaatct-cttgcagATGATACTTTATGACAAACCTGGTGTACTACAGAAGGAAATGCATAAGTTAGACTCAATGATGATGAAAAATGTTCGCAGTGCGGCAGTTAATGCTGACT
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---gtatcaccttttagtttctaaagctttaggattatagactatgaaagggggaaatgttaatttctcactgctaatctgagttatcatttagtttgcagATAATACTTTATGACACGCCAGGTGTCATCAAAAAGGAAATGCATAAGCTAGACACAATGATGATGAAGAATGTTAGGAGTGCCGTTGGCAGTGCAGATT
upper sequence: GLYMA02G06100.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G66470.1 (Arabidopsis thaliana), 3'ss of exon 2
----aaaattttaatactgaattttactaaattaatggatgtacaatagaatttatatttatattttttatttt--ttatttttctgacttttgaa----tctcttgcagATGATACTTTATGACAAACCTGGTGTACTACAGAAGGAAATGCATAAGTTAGACTCAATGATGATGAAAAATGTTCGCAGTGCGGCAGTTAATGCTGACT
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gtttgtttatctaagcctcattgatttttgactcttaaaagaacca-ggtgttcattgcttggtttgatatagaaattaagatgtcgactgatacaagcttgtgttgcagATGATACTTTATGATACGCCTGGTGTAATTGAGAAGAAGATGCACAGGTTAGATACAATGATGATGAAGAATGTCAGAGATGCTGCCATCAATGCGGACT
upper sequence: GLYMA02G06100.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0023g02120.t01 (Vitis vinifera), 3'ss of exon 2
aaaattttaatactgaattttactaaattaatggatgtaca-atagaatttatatttatattttttattttttatttttctgacttttgaatctcttgcagATGATACTTTATGACAAACCTGGTGTACTACAGAAGGAAATGCATAAGTTAGACTCAATGATGATGAAAAATGTTCGCAGTGCGGCAGTTAATGCTGACT
||| ||| | | | | | ||| ||| || | |||| |||| || | |||| || | |||| |||||||||||||||||| ||||||||| | ||||| ||||||| ||||| ||||| ||||||||||| ||||| |||||||| | ||||||| ||||
aaatacataaacatacacaaccccatgccttcacacacacatataaaagtaatatgc-tattaagctcttaaaaacgcatgaacttatgttttgcttgtagATGATACTTTATGACACACCTGGTGTTATTGAGAAGAAAATGCACAAGTTGGACTCCATGATGATGAAGAATGTCCGCAGTGCTACCATTAATGCGGACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatttatatttatattttttattttttatttttctgacttttgaatctcttgcagATGATACTTTATGACAAACCTGGTGTACTACAGAAGGAAATGCATAAGTTAGACTCAATGATGATGAAAAATGTTCGCAGTGCGGCAGTTAATGCTGACT
ttctgac putative branch site (score: 2)
tctcttgc putative PPT
atatttatatttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaattttaatactgaattttactaaattaatggatgtacaatagaatttatatttatattttttattttttatttttctgacttttgaatctcttgcagATGATACTTTATGACAAACCTGGTGTACTACAGAAGGAAATGCATAAGTTAGACTCAATGATGATGAAAAATGTTCGCAGTGCGGCAGTTAATGCTGACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - -tggatgt