Sequence
atgc intronic sequence ATGC exonic sequence...agctggggtgcacagaaagagcagtaagcatccgtgcattgacatgacggaattcttatctgctttgttctgttgcattttggtgaaatttttttttcagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTAAGATGTGGTCCACTCATCAGCATTTTATAAATTTCTGACACAAATTATGAT
Basic information
species | Glycine max |
transcript | GLYMA03G31550.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G31550.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g40880.2 (Oryza sativa), 3'ss of exon 7
agctggggtgcacagaaagagcagtaagcatccgtgcattgacatgacggaattcttatctgctttgttctgttgcattttggtgaaattttt-ttttcagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTAAGATGTGGTCCACTCATCAGCATTTTATAAATTTCTGACACAAATTATGAT-
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------------------gtgttaccagtttcactgt-caagtattctattacacataac-attgtgttttgactgatcgctgaaacatctttgtctgcagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGTGATCCAGTTGAAA-ATGACATATTTGTAAAGCCGCAGTGAGTTATCATTGCAGATCCAGAAT
upper sequence: GLYMA03G31550.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g40880.1 (Oryza sativa), 3'ss of exon 7
agctggggtgcacagaaagagcagtaagcatccgtgcattgacatgacggaattcttatctgctttgttctgttgcattttggtgaaattttttttt-cagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTAAGATGTGGTCCACTCATCAGCATTTTATAAATTTCTGACACAAATTATGAT
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------------------gtgttaccagtttcactgt-caagtattctattacacataac-attgtgttttgactgatcgctgaaacatctttgtctgcagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGTGATCCAGTTGAAA-ATGACATATTTGTAAA-GCCGCA------------------------
upper sequence: GLYMA03G31550.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G035338_T01 (Zea mays), 3'ss of exon 7
agctggggtgcacagaaagagcagtaagcatccgtgcattgacatgacggaattcttatctgctttgttctgttgcattttgg----tgaaattttt--ttttcagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTAAGATGTGGTCCACTCATCAGCATTTTATAAATTTCTGACACAAATTATGAT
||| | | |||| || || ||||||| | || | || || || | | || | || ||| |||| |||||||||| ||||||||||| ||||||||||| ||||||||| ||| || | | | | |
-----------------------gtatctaccagtgccctgcaatac--aaattcttgaatactgcatgctatttaatctgatcctctaaacatcttggtttgtagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGCGACCCAGTTGAGA-ATGACATATTTGTAAA-GCCACA------------------------
upper sequence: GLYMA03G31550.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G03030.1 (Arabidopsis thaliana), 3'ss of exon 7
agctggggtgcacagaaagagcagtaagcatccgtgcattgacatgacggaattcttatctgctttgttctgttgcattttggtgaaatttt---tttttcagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTAAGATGTGGTCCACTCATCAGCATTTTATAAATTTCTGACACAAATTATGAT
| | ||| | || ||| ||||| | | | || | | || | | | || | | ||| ||| ||||| ||||||||||| ||||||||||| ||||| |||||||| |||||| | | || | | | ||| |
---------gtaaagaggtggttacaaa-atct---tgttgaccttaggatcttgaagttgggagacttacaatagactctgattagttttcaagctttccagGGCTCAGTTTATGTGCCATCATTTGATCATGGAGTTGGGGATCCAGTTGA-AGATGATATCTTTGTTAGCCTCCA-------------------------
upper sequence: GLYMA03G31550.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0141g00310.t01 (Vitis vinifera), 3'ss of exon 7
----------------------------------------------------agctgg--ggtgcacagaaagagcagtaagcatccgtgc-----attgacatgacggaattcttatc-------tgctttgttc-tgttgcattttggtga--aatttttttttcagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTAAGATGTGGTCCACTCATCAGCATTTTATAAATTTCTGACACAAATTATGAT
| |||| |||||| | | | | | | | || | | | |||| | | |||| || | ||||||| || ||| ||| |||| | |||| |||||||||| |||||| ||||| ||||||||||| || |||||| | | || | | | |||||| |
gtgagtagctattgatgttggctgcgtcattttattcttgttgagactttagaactggttggtgcataaacttatctttttttttttttttcaaaaataaaaaataaaaaatttgtggtacatgagtacttttctcatattgcattatgatgagcaatattttctgtagGGGTCAGTTTATGCACCATCGTTTGATCATGGTGTTGGAGATCCAGTTGA-AGATGATATATTTATCAGCCTCCA------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gacggaattcttatctgctttgttctgttgcattttggtgaaatttttttttcagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTAAGATGTGGTCCACTCATCAGCATTTTATAAATTTCTGACACAAATTATGAT
tttttttttc CT-rich tract
attttggtgaaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agctggggtgcacagaaagagcagtaagcatccgtgcattgacatgacggaattcttatctgctttgttctgttgcattttggtgaaatttttttttcagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTAAGATGTGGTCCACTCATCAGCATTTTATAAATTTCTGACACAAATTATGAT
- -tggggtg
- - - - - - - - - - - - - - - tccgtgc
- - - - - - - - - - - - - - - - - - - - -acatgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcattt