Sequence
atgc intronic sequence ATGC exonic sequencegtagtcatttctttctatgcactagtcctttcctgcatatcagcttaagtaattcgtttttttttttttttttgcctttgtgttcgtgttaatattatttctgtttgtgtttagCTTGGTGAGACCATTCATCCAATGAAGGAGGATTTTATCATGGTTCACTTGCAGCATAGTTGCACACATTGCTGTACGCTGATGGTAACTGGAAATCGTT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G16710.2 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 12
-------------------------------------------gtagtcatttctttctatgcactagtcctttcctgcatatcagcttaagtaattcgtttttttttttttttttgcc--tttgtgttcgtgttaatattatttctgtttgtgtttagCTTGGTGAGACCATTCATCCAATGAAGGAGGATTTTATCATGGTTCACTTGCAGCATAGTTGCACACATTGCTGTACGCTGATGGTAACTGGAAATCGTT
| | || | | || || || ||| ||||| | | | | | ||| ||||||| ||| | | | | | | | | | || ||| ||||||| || |||||| ||||||||||||| ||||| || |||||||| |||||| || || | || || ||||| || ||||| ||||||| ||||
gtaggattgtacagtggtttgcgtgctccttattttgatagatcacatggctgctagcactctacccctctttccctttctatcatccttgctcagt-atttgtttttttcactttactggatggcatctttaccatgaacttgatttgttatgtgcagCTTGGGGAAACCATTTATCCAATGAAGGAAGATTTCATTATGGTTCATTTGCAGTATTCGTGTAGTCACTGTTGTACCCTTATGGTGTCTGGAAAACGTT
upper sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 12
gtagtcatttctttctatgcactagtcctttcctgcatatcagcttaagtaattcgtttttttttttttttttgcctttgtgttcgtgttaatattatttctgtttgtgtttagCTTGGTGAGACCATTCATCCAATGAAGGAGGATTTTATCATGGTTCACTTGCAGCATAGTTGCACACATTGCTGTACGCTGATGGTAACTGGAAATCGTT
| ||| || || || ||||| | | | | || |||| || | | | | | | || ||| | || | | | | |||||||||| |||||| ||||||||||| ||||||||||||||||| ||||||||| ||||| |||||||||| || ||||| |||| || ||||
----------caaattatat-cttctcacttattgcat-ttaacatttatatggggtttccttgagtggaaatagcaatttccttgtaataaagct--tttgatctctatccagCTTGGTGAAACCATTTGCCCAATGAAGGAAGATTTTATCATGGTTCATTTGCAGCATGCATGCACTCATTGCTGTATTCTAATGGTGTCTGGCAACCGTT
upper sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 14
gtagtcatttctttctatgcactagtcctttcctgcatatcagcttaagtaattcgtttttttttttttttttgcctttgtgttcgtgttaatattatttctgtttgtgtttagCTTGGTGAGACCATTCATCCAATGAAGGAGGATTTTATCATGGTTCACTTGCAGCATAGTTGCACACATTGCTGTACGCTGATGGTAACTGGAAATCGTT
| |||| | | | | || |||| |||| | | || || || | | || || || || | || | ||| ||| || | ||| | |||||||||| |||||| ||||||||||| |||||||| |||||||| ||||||||| || || || |||| | ||||| |||| || ||||
--aaacattaatattgtttcctta---ctttactgctt------tcaaata-tttatctgttaggttccttatgtttgataatttcttataaaattcttgatctttct--ccagCTTGGTGAAACCATTTCCCCAATGAAGGAAGATTTTATTATGGTTCATTTGCAGCATGCATGTACTAGCTGTTGTATTTTAATGGTGTCTGGCAACCGTT
upper sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 11
--gtagtcatttctttctatgcactagtcctttcctgcatatcagcttaagtaattcgtttttttttttttttttgcctttgtgttcgtgttaatattatttctgtttgtgtttagCTTGGTGAGACCATTCATCCAATGAAGGAGGATTTTATCATGGTTCACTTGCAGCATAGTTGCACACATTGCTGTACGCTGATGGTAACTGGAAATCGTT
| | | | || || | | | || | | || | | | ||| | |||| || || | ||| || || | | |||||||||| ||||| ||||||||||| |||||||| |||||||||||||| ||| || || ||||| ||| ||||||||| ||||||| ||||
tttcaaacgtcttcactgatattatattttctcctgacacttttgaacaaatgaaa-----gtcaatttctgtttgttcttatg---------aagctat--ctattcttctccagCTTGGTGAAACCATAAGCCCAATGAAGGAAGATTTTATAATGGTTCACTTGCAACATGCATGTACTCATTGTTGTCATCTGATGGTATCTGGAAACCGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttttttttttgcctttgtgttcgtgttaatattatttctgtttgtgtttagCTTGGTGAGACCATTCATCCAATGAAGGAGGATTTTATCATGGTTCACTTGCAGCATAGTTGCACACATTGCTGTACGCTGATGGTAACTGGAAATCGTT
tgttaat putative branch site (score: 3)
tttctgttt putative PPT
ttaatattatttctgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagtcatttctttctatgcactagtcctttcctgcatatcagcttaagtaattcgtttttttttttttttttgcctttgtgttcgtgttaatattatttctgtttgtgtttagCTTGGTGAGACCATTCATCCAATGAAGGAGGATTTTATCATGGTTCACTTGCAGCATAGTTGCACACATTGCTGTACGCTGATGGTAACTGGAAATCGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT