Sequence
atgc intronic sequence ATGC exonic sequencegtaatgtgtcacacttaccaactttactcttctaatttgtttactcaatcattacattgaccatagctaaaagcatcttttgttgcatgatttgttttgatactatatagGAAGAAAGAAAAACTCTTGACCGGGAGTTAGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACA
Basic information
species | Glycine max |
transcript | GLYMA08G05100.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 6
gtaatgtgtcacacttaccaactttactcttctaatttgtttactcaatcattacattgaccatagctaaaagcatcttttgttgcatgatttgttttgatactatatagGAAGAAAGAAAAACTCTTGACCGGGAGTTAGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACA
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-------------gtaacatcctttactgttgctttcggataatct--tcactgttctgtacgcaaa-aaagttgacccatgcta-atctctaaccatggcac-acttagGAGGAAAGAAAAATTCTTGACCGTGAGCTTGCGCGGGCAAAAGTTACAGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACA
upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g44340.1 (Oryza sativa), 3'ss of exon 6
gtaatgtgtcacacttaccaactttactcttctaatttgtttactcaatcattacattgaccatagctaaaagcatcttttgttgcatgatttgttttgatactatatagGAAGAAAGAAAAACTCTTGACCGGGAGTTAGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACA
|||||| | | | | | || | || || ||||| || | | || | || | | || || | || | |||| | ||||||||| ||||||||||| || || |||||||||| ||||| | ||||| ||||| || |||||||| ||||||||||||||||||| ||||| |
gtaatgcatgatgcc--ctgagcacacgttcctgat--gtttattctacc--taatagaatggtaattgatgccaatttac--------acttatgctgatgtca----gGAAGAAAGGAAAACTCTTGATCGTGAACTAGCTCGTGCGAAGGTTTCGGCAAATAGAGTTGCAGTAGTGGTGGCAAATGAATGGAAAGATGGCAATGATA
upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g14080.1 (Oryza sativa), 3'ss of exon 6
gtaatgtgtcacactt--accaactttactcttctaatttgtttactcaatcattacattgaccatagctaaaagcatcttttgttgcatgatttgttttgatactatatagGAAGAAAGAAAAACTCTTGACCGGGAGTTAGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACA
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gtaacaacctattctttgactattgcatatgtcatcatgtcttcatgagctcttccccccttctataggaacagttcactcatgcttatttaacatttatgatcattaccagGACCAAAAAAAGACACTTGAATGTGAACTTGCTCGTGCAAAAGTTACAGCAAACAGGGTTGCTGTTGTGGTTGCCAACGAGTGGAAAGATTCTAATGACA
upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G017525_T01 (Zea mays), 3'ss of exon 2
gtaatgtgtcacacttaccaactttactcttctaatttgtttactcaatcattacattg---accatagctaaaagcatcttttgttgcatgatttgttttgatactatatagGAAGAAAGAAAAACTCTTGACCGGGAGTTAGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACA
||||| | | | | | || | | | || | | || ||| ||||| |||| ||| |||| | | | || | ||||| |||| ||||||||||| || ||| |||||||||| ||||| ||||||| || || || |||||||| |||||||| |||||||||| |||| |
gtaatacatgaatcctgatgtccttggaaatgcattatgcgttttaggatatctacttgagcaccatgactaat-gcaagttttacaacgtttcctattct---------tagGAGGAAATGAAAACTCTTGATCGTGAGCTAGCTCGTGCAAAGGTTTCAGCAAATAGGGTTGCAGTAGTGGTGGCAAATGAGTGGAAAGATGGCGATGATA
upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaatgtgtcacacttaccaactttactcttctaatttgtttactcaatcattacattgaccatagctaaaagcatcttttgttgcatgatttgttttgatactatatagGAAGAAAGAAAAACTCTTGACCGGGAGTTAGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACA
|||| | ||| || || | | | || | ||||||||| | | || | || ||| | || | | ||| | |||||||| ||||||||||||||||||| | || ||||| ||||| |||||||||||||| || |||||||||||||||||||||||||| |||||| |
gtaagttaatacattt-ccgaaaaaagaagtatagaatctttactcaact---------------gatgaaggaatattt-----cttgctctacttt-------tgcagGAAGAACGAAAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATA
upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaatgtgtcacacttaccaactttactcttctaatttgtttactcaatcattacattgaccatagctaaaagcatcttttgttgcatgatttgttttgatactatatagGAAGAAAGAAAAACTCTTGACCGGGAGTTAGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACA
|||| ||||||| | | | |||||||| || | ||| ||| | | || || | | | ||||| ||||| | | ||||||| | |||||||||||||||||| | || ||||| ||||| |||||||||||||| || ||||| |||||||| |||||||||| |||||| |
gtaactaaacacactt-----cataaagtctctaatttcttgtcacaacaattgc-ctactgatg--taggaataattcttgtt------tttgtct--------ttcagGAAGAGCGGAAAACTCTTGACCGGGAGCTTGCACGTGCAAAGGTTACAGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATA
upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 6
gtaatgtgtcacacttac-caac-----tttactcttctaatttgttt---actca-atcattacattgac----cata-gctaaaagcatctt--ttgttgcatgatttgttttgatactata------tagGAAGAAAGAAAAACTCTTGACCGGGAGTTAGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACA
|||||||| || ||| ||| || | || || | ||| || | || || ||| | |||| || | | | |||||| | | | | | | | | |||| ||||||||||| || ||| ||||| | || ||||| |||||||| |||||||| || || ||||| || ||||||||||||||||||||||||||||
gtaatgtgccatttttaaacaataaatattgaacattgcaagtcatttcaggcttatatttttgcatctagttggcatatgccatgtgttctatcattgttgagttgtctttccttttcttttggaccttcagGAGGAAAGAAAAACCCTCGACAGGGAGCTGGCCCGTGCAAAGGTAACTGCAAACAGGGTGGCAGTAGTTGTAGCAAATGAATGGAAAGATGCTAATGACA
upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ18059 (Selaginella moellendorffii), 3'ss of exon 6
gtaatgtgtcacacttaccaactttactcttctaatttgtttactcaatcattacattgaccatagctaaaagcatcttttgttgcatgatttgttttgatactatatagGAAGAAAGAAAAACTCTTGACCGGGAGTTAGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACA
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-----------------------------------------------gtagtgccgccagccac--ctttgggtcgcactcaccccaca--ttgtctttttaccat-tagGAAGAGAAACGGACGCTTGAGCGGGAACTGGCGCGTGCCAAGGTAACAGCAAACAGAGTGGCAGTCGTCGTTGCAAACGAATGGAAGGATGCAAACGACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgaccatagctaaaagcatcttttgttgcatgatttgttttgatactatatagGAAGAAAGAAAAACTCTTGACCGGGAGTTAGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACA
ttttgatactatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgtgtcacacttaccaactttactcttctaatttgtttactcaatcattacattgaccatagctaaaagcatcttttgttgcatgatttgttttgatactatatagGAAGAAAGAAAAACTCTTGACCGGGAGTTAGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG