Sequence
atgc intronic sequence ATGC exonic sequence...atgataaaaattggtttgtttttcgtaaaaataattattttatttgttctttaaatttacattttttaaaaattaattgttatctttttggtgctaccagCCACAATCAAAGAATGGTGTCAATAGCTTTGGAGGTCTTGGAGCAACTTTAATAGATTCTCTTGATACACTATATATTATGGGTCTCAACGAACAGTTTC
Basic information
species | Glycine max |
transcript | GLYMA08G23730.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G23730.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g51690.1 (Oryza sativa), 3'ss of exon 3
atgataaaaattggtttgtttttcgtaaaaataattattttatttgttctttaaatttacat-------tttttaaaaattaattgttatctttttggtgcta--------ccagCCACAATCAAAGAATGGTGTCAATAGCTTTGGAGGTCTTGGAGCAACTTTAATAGATTCTCTTGATACACTATATATTATGGGTCTCAACGAACAGTTTC
|||||||| | | |||||| ||| ||| || ||| | | | || | ||| | || || || | | |||||||||||||||||||||||||||||||||||| ||||| || |||||| | | || || ||||||||||| ||||| ||||| || || || | ||||
-------------gtttgtttagtcaacattctgttatttctattgcccttctaacttatctgagtgagctctgaagtgtcttctgtatttttctttgttcaaattattttccagCCACAATCAAAGAATGGTGTCAATAGCTTTGGTGGTCTCGGGGCAACTCTTGTGGACTCACTTGATACACTGTATATAATGGGCCTAAAGGATGAATTTC
upper sequence: GLYMA08G23730.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G130889_T02 (Zea mays), 3'ss of exon 3
-------------atgataaaaattggtt-tgtttttcgtaaaaataattattt--tatttgttctttaaatttacattttttaaaaattaattgttatctttttggtg-ctaccagCCACAATCAAAGAATGGTGTCAATAGCTTTGGAGGTCTTGGAGCAACTTTAATAGATTCTCTTGATACACTATATATTATGGGTCTCAACGAACAGTTTC
| | ||| || || | | | | | |||| || || | | || || || | | | | | ||| | | | | || | |||||||||||| ||||||||| |||| |||||||| |||||||||||||| | | || || |||||||| ||||| || ||||| || || || | ||||
gtttgtttagtcggtactctgtattaattctgatctgcatctggttttacatttcctaactgat-tctagatctaaactgccttctg-tcatttgctttgctcgcgttgattcccagCCACAATCGAAGAATGGTATCAACAGCTTTGGTGGTCTTGGAGCAACCCTTGTTGACTCACTTGATACCCTATACATAATGGGCCTGAAAGATGAATTTC
upper sequence: GLYMA08G23730.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G128914_T02 (Zea mays), 3'ss of exon 3
atgataaaaattggt--ttgtttttcgtaaaaataattattttatttgttctttaaatttacattttttaaaaattaattgttatctttttggtgc--------taccagCCACAATCAAAGAATGGTGTCAATAGCTTTGGAGGTCTTGGAGCAACTTTAATAGATTCTCTTGATACACTATATATTATGGGTCTCAACGAACAGTTTC
| | | ||| | || | | | || || |||| || | | | || |||| ||| | ||| | | || || | | |||||||||||| ||| |||| ||||||| ||||| |||||||||||||| | | || || ||||||||||| ||||| ||||| || || || | ||||
gtttgtttagtcggtagtaattctgatctgcagttgtttttgcatttcttaactgattctaaattta--aaatgtcttctgtcttttgctttgttcacctcaattcccagCCACAATCGAAGGATGGCATCAATAGTTTTGGTGGTCTTGGAGCAACCCTTGTTGACTCACTTGATACACTGTATATAATGGGCCTGAAAGATGAATTTC
upper sequence: GLYMA08G23730.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 3
atgataaaaattggtttgtttttcgtaaaaataattattttatttgttcttt--aaatttacattttttaaaaatta-----attgttatctttttggtgctaccagCCACAATCAAAGAATGGTGTCAATAGCTTTGGAGGTCTTGGAGCAACTTTAATAGATTCTCTTGATACACTATATATTATGGGTCTCAACGAACAGTTTC
||| ||| ||||| || || ||| | || | | ||| | ||| | || || || | || |||| | | ||||| | |||| |||| |||||||||| || |||||||||||| | |||||||| | |||||||| ||||| |||||||| | || |||||||
----caaagatt---ttgttaagaactaagattattttcttcctgaactctgcaaaaaaaatattggtctgaagctattcttgtttctttcctttttttattgtcagCCTCGGACAAAAGATGGCACTGATAGCTTTGGTGGCCTTGGAGCAACTATGGTAGATTCTTTAGATACACTCTATATAATGGGTCTAGATGAGCAGTTTC
upper sequence: GLYMA08G23730.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0054g00370.t01 (Vitis vinifera), 3'ss of exon 3
atgataaaaattg----gtttgtttttcgtaaaaataattattttatttgttctttaaatttacattttttaaaaattaattgttatctttttggtgctaccagCCACAATCAAAGAATGGTGTCAATAGCTTTGGAGGTCTTGGAGCAACTTTAATAGATTCTCTTGATACACTATATATTATGGGTCTCAACGAACAGTTTC
|| | | ||| ||||| |||| | | | |||| | || ||| || || | || | || | | || || |||| || ||||||||||| ||||||||||||||||| |||||||||||||||||||| ||||||||||||||||||||| ||||||| ||||| || | || ||||| |
attcctagatttgtggcatttgtatttcc--atagtgtttatgatgttgtttcattttatccaagttctacaactaaca--tgcaattgttttttccttaacagCCACAATCCAAGAATGGTGTCAATAGTTTTGGAGGTCTTGGAGCAACATTAATAGATTCTCTTGATACATTATATATAATGGGACTAGATGAGCAGTTCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttctttaaatttacattttttaaaaattaattgttatctttttggtgctaccagCCACAATCAAAGAATGGTGTCAATAGCTTTGGAGGTCTTGGAGCAACTTTAATAGATTCTCTTGATACACTATATATTATGGGTCTCAACGAACAGTTTC
aattaat putative branch site (score: 3)
ttaaatttacattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgataaaaattggtttgtttttcgtaaaaataattattttatttgttctttaaatttacattttttaaaaattaattgttatctttttggtgctaccagCCACAATCAAAGAATGGTGTCAATAGCTTTGGAGGTCTTGGAGCAACTTTAATAGATTCTCTTGATACACTATATATTATGGGTCTCAACGAACAGTTTC
- -ataaaaa
- - - - - -tggtttg
- - - - - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaattaa