Sequence
atgc intronic sequence ATGC exonic sequence...tttttgcattatttgtcttccctgcagtcaaagtggctgcagagatggtgatctttgtctctgtatatttttgaataataacatattttcacactctcagATTCTCGTGGCTACACCCGGAAGGCTCAAAGACCATATCGACAACACTTCTGGATTTGCAACAAGGTTGATGGGTGTGAAAGTCCTTGTGCTTGATGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G08620.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G08620.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os06g33520.1 (Oryza sativa), 3'ss of exon 4
tttttgcattatttgtcttccctgcagtcaaagtggctgcagagatggtgatctttgtctctgtatatttttgaataataacatattttcacactctcagATTCTCGTGGCTACACCCGGAAGGCTCAAAGACCATATCGACAACACTTCTGGATTTGCAACAAGGTTGATGGGTGTGAAAGTCCTTGTGCTTGATGAAG
| | ||| || | ||| | ||| ||| | | | ||| | || || || | | |||||||| || |||||||| |||||||| || || ||||| || |||||| | || ||||| || || ||||||||||| ||||||||| | ||||||||||
----------------gtgattggaagt--aacttactgaattatcctggatatttctacatttggattgtgtgatgtaaaaatgctgctg-atgtgcagATTCTAGTAGCTACACCAGGAAGGCTTAAGGATCATATGGAGAACACTCCAGGGTTTGCTACTAGATTGATGGGTGTCAAAGTCCTTATTCTTGATGAAG
upper sequence: AT5G08620.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G06240.1 (Glycine max), 3'ss of exon 4
tttttgcattatttgtcttccctgcagtcaaagtggctgcagagatggtgatctttgtctctgtatatttttgaataataacat--attttcacactct-cagATTCTCGTGGCTACACCCGGAAGGCTCAAAGACCATATCGACAACACTTCTGGATTTGCAACAAGGTTGATGGGTGTGAAAGTCCTTGTGCTTGATGAAG
| | | ||| | || |||| | | || | | | || ||| || | | | || | | | | |||| || ||| | ||||| || || || ||||| |||||||| | ||| |||| || || ||| |||| |||||||| ||| ||||||||||||| ||| | |||||||||||||
taactac-ttactagttttccagactttgttggttgattattgacttctg--cttaagctacatgttctgttcacacacattgttaatttgcatactatacagATCCTTGTTGCCACACCTGGAAGGCTTAGAGATCATACTGAGAATACTGCTGGTTTTGCAACTAGGCTGATGGGTGTGAAGGTCTTGGTGCTTGATGAAG
upper sequence: AT5G08620.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G02880.1 (Glycine max), 3'ss of exon 4
tttttgcattatttgtcttccctgcagtcaaagtggctgcagagatggtgatctttgtct---ctgtatatttt-tgaataataacat---attttcacactct-cagATTCTCGTGGCTACACCCGGAAGGCTCAAAGACCATATCGACAACACTTCTGGATTTGCAACAAGGTTGATGGGTGTGAAAGTCCTTGTGCTTGATGAAG
| || | | ||| | | | || || ||| | || | || || || | | | | | | |||| || ||| | ||||| || || ||||| || |||||||| | ||| |||| || || ||| |||| |||||||| ||| ||||||||||||| ||| | |||||||||||||
-----taactactaactagtttttcagact---ttgttgattgaatattgagttctgcttaagctacatgttctgttgacacccatttttaatttgcatactgtacagATCCTTGTTGCTACTCCTGGAAGGCTAAGAGATCATACTGAGAATACTGCTGGTTTTGCAACTAGGCTGATGGGTGTGAAGGTCTTGGTGCTTGATGAAG
upper sequence: AT5G08620.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv15s0046g01010.t01 (Vitis vinifera), 3'ss of exon 5
--tttttgcattatttgt-cttccctgcagtcaaagtggctgcagagatggtgatctttgtctctgtatatttttgaataataacatattttcacactctcagATTCTCGTGGCTACACCCGGAAGGCTCAAAGACCATATCGACAACACTTCTGGATTTGCAACAAGGTTGATGGGTGTGAAAGTCCTTGTGCTTGATGAAG
| |||| | | | || | | |||| | | || | || | ||||||| | | | || | | | | |||||||| || ||||| || ||| |||| || |||||||| || || || | ||||||||||| | |||||||||| ||||||||||| ||||||||||
atgctctgcaatctgaaaacctcaataaaagcaaattaattttcatcttgaaattgttaattgggaaatatttt--atttgtgg-gccttgtgatatttacagATTCTTGTAGCTACCCCTGGACGGCTAAAGGACCATATTGAGAATACAGCAGGATTTGCAACTCGTCTGATGGGTGTCAAAGTCCTTGTACTTGATGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtgatctttgtctctgtatatttttgaataataacatattttcacactctcagATTCTCGTGGCTACACCCGGAAGGCTCAAAGACCATATCGACAACACTTCTGGATTTGCAACAAGGTTGATGGGTGTGAAAGTCCTTGTGCTTGATGAAG
taataac putative branch site (score: 1)
ttttcac putative PPT
tctgtatatttttgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttttgcattatttgtcttccctgcagtcaaagtggctgcagagatggtgatctttgtctctgtatatttttgaataataacatattttcacactctcagATTCTCGTGGCTACACCCGGAAGGCTCAAAGACCATATCGACAACACTTCTGGATTTGCAACAAGGTTGATGGGTGTGAAAGTCCTTGTGCTTGATGAAG
- - - - - - - - - - - - -agtcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aataaca