Sequence
atgc intronic sequence ATGC exonic sequencegtatttaactgaattattgtcagtttccagtgaatgtaactcatctttataactttttccttacttttagGTTAATAATAAAAAAGTATTTGGAAATCACTCATTTCGCCCCAATCAAAGAGAGATCATTAATGCCTCAATGAGTGGATGTGATGTTTTTGTTCTGATGC
Basic information
species | Glycine max |
transcript | GLYMA08G20070.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G20070.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os04g35420.1 (Oryza sativa), 3'ss of exon 7
---gtatttaactgaattattgtcagtttccagtgaatgtaactcatcttt----ataactt-tttccttactt--ttagGTTAATAATAAAAAAGTATTTGGAAATCACTCATTTCGCCCCAATCAAAGAGAGATCATTAATGCCTCAATGAGTGGATGTGATGTTTTTGTTCTGATGC
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gttattttcttcaaaatcaactgtaattattt-caaacatcatttgtttgtgagaatgacttgtcttgctgcctcatcagGCCAACAACAAAAGAGTATTTGGAAACCGTTCTTTTCGCCCAAATCAACGAGAAATAATCAACGCCACAATGAGTGGGAATGATGTTTTTGTTTTGATGC
upper sequence: GLYMA08G20070.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G319573_T03 (Zea mays), 3'ss of exon 6
---gtatttaactgaattattgtcagtttccagtgaatgtaactcatcttta--------taactttttccttacttttagGTTAATAATAAAAAAGTATTTGGAAATCACTCATTTCGCCCCAATCAAAGAGAGATCATTAATGCCTCAATGAGTGGATGTGATGTTTTTGTTCTGATGC
| || | | || ||| | || | ||| || ||| |||| ||| | | ||| || || | ||| |||||||| || || || |||||||| ||| |||| || || |||||| |||||||||| ||||||||||||| ||||||
gttattttcttcagcatcattttttaattatttacgccatcactgatttttgaatactattaacctttagtgcatatccagGCCAAGAACAGAAATAAGTTTGGAAACCATTCTTTCCGCCCCAACCAACGAGAAATAATCAATGCCACAATGAGTGGGCATGATGTTTTTGTTTTGATGC
upper sequence: GLYMA08G20070.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G10930.1 (Arabidopsis thaliana), 3'ss of exon 8
gtatttaactgaattattgtcagtttccagtgaatgtaactcatctttataactttttccttact---tttagGTTAATAATAAAAAAGTATTTGGAAATCACTCATTTCGCCCCAATCAAAGAGAGATCATTAATGCCTCAATGAGTGGATGTGATGTTTTTGTTCTGATGC
|| || |||| || | | || | || | | | ||||||| | || |||||||||| |||||||| ||||||||||| || ||||| || || || ||||| || || ||||| |||||||||| | ||||||||||||| ||||||
gtgatttgctgagtttctcttttctttgttcacttacgttcaatgtgctcatgtgtttccttgcaaagttcagGTTAATAACAAAAAAGTGTTTGGAAATCATTCGTTTCGACCTAACCAGAGAGAAATTATCAATGCAACAATGAGTGGCTCTGATGTTTTTGTTTTGATGC
upper sequence: GLYMA08G20070.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G60930.1 (Arabidopsis thaliana), 3'ss of exon 8
gtatttaactgaattattgtcagtt--tccagtgaatgtaactcatctttataactttttccttactt-------ttagGTTAATAATAAAAAAGTATTTGGAAATCACTCATTTCGCCCCAATCAAAGAGAGATCATTAATGCCTCAATGAGTGGATGTGATGTTTTTGTTCTGATGC
|| || | | | | ||| | | |||| | | | | | || | || | | || || |||||| |||| ||| ||| |||||||| ||||||||||| ||||| |||||||||||||||||||| |||||||||| ||||||||||||||| ||||||
gtgattggtt-atctgtcgtccgctgttccattatttacatccctcctgtgtactcatgtgctccattgcaatgattagGTCTATAACAAATTAGTGTTTGGAAACCACTCATTTCGACCCAACCAAAGAGAGATCATTAATGCTACAATGAGTGGTTGTGATGTTTTTGTTTTGATGC
upper sequence: GLYMA08G20070.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv12s0035g00400.t01 (Vitis vinifera), 3'ss of exon 4
gtatttaactgaattattgtcag--------tttccagtgaatgtaactc--atctttataacttttt-ccttacttttagGTTAATAATAAAAAAGTATTTGGAAATCACTCATTTCGCCCCAATCAAAGAGAGATCATTAATGCCTCAATGAGTGGATGTGATGTTTTTGTTCTGATGC
|| | | ||| ||| ||| | ||| || || ||||| || || ||| | | | ||| ||| || || || ||||| |||||||| |||||||| |||||||||||||| ||| |||| ||||| |||||||||||| ||||||||||||||| ||||
gtgctcatctgcattgatgtttgaaaatctatttacattgcatgtacttctgattgttacactcactggtcccgttttcagGCCAACAACAAGAAAGTTTTTGGAAACCACTCATTCCGCCCCAATCAAAGGGAGGTCATCAATGCTACAATGAGTGGATATGATGTTTTTGTTCTAATGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgtcagtttccagtgaatgtaactcatctttataactttttccttacttttagGTTAATAATAAAAAAGTATTTGGAAATCACTCATTTCGCCCCAATCAAAGAGAGATCATTAATGCCTCAATGAGTGGATGTGATGTTTTTGTTCTGATGC
tccttac putative branch site (score: 2)
ctttttccttactttt CT-rich tract
atctttataacttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttaactgaattattgtcagtttccagtgaatgtaactcatctttataactttttccttacttttagGTTAATAATAAAAAAGTATTTGGAAATCACTCATTTCGCCCCAATCAAAGAGAGATCATTAATGCCTCAATGAGTGGATGTGATGTTTTTGTTCTGATGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA