Sequence
atgc intronic sequence ATGC exonic sequence...tacccatttaatacctctttagtttccctaaatgtaaagcgttgtatttcttccttcgtacacacttttctgaccttaggtttcattgttagtatttcagGCTGTTCTAGAGAAGCTCAGTTACATGCTCATTGGGAGGCATGATATTGAGAAATTGATGCGGCTTGATGCGGCGAGTGCTTGTTTACCATCTACGCTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G10380.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G10380.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA20G32370.1 (Glycine max), 3'ss of exon 18
--tacccatttaa-tacctctttagtttccctaaatgtaaagcgttgtat-ttcttccttcgtacacacttttctgaccttaggtttcattgttagtatttcagGCTGTTCTAGAGAAGCTCAGTTACATGCTCATTGGGAGGCATGATATTGAGAAATTGATGCGGCTTGATGCGGCGAGTGCTTGTTTACCATCTACGCTTG
| |||||| || || | || | || | || | ||||| | |||| | | || ||| | |||| || || || | | |||| ||||||||||| ||||||| ||||| ||||| |||||||||||||||||||||||||||||| || |||| | | ||||| | |||||| | |||||
ctcaagcatttaggtaacttgatcattgacatatctatatattgttgtttactcttgcatggtgcactatcttctaacatt----tttgtcaattatattacagGCTGTTCTTGAGAAGCAGAGTTATATGCTTATTGGGAGGCATGATATTGAGAAATTGATGAGGATTGACCCCTCAAGTGCATATTTACCGAATCTGCTTG
upper sequence: AT3G10380.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA10G35190.2 (Glycine max), 3'ss of exon 15
tacccatttaa-tacctctttagtttccctaaatgtaaagcgttgtat-ttcttccttcgtacacacttttctgaccttaggt-ttcattgttagtatttcagGCTGTTCTAGAGAAGCTCAGTTACATGCTCATTGGGAGGCATGATATTGAGAAATTGATGCGGCTTGATGCGGCGAGTGCTTGTTTACCATCTACGCTTG
|||||| || | || | || | || | ||||| | |||| | | || | | | || | | || | | |||| ||||||||||| ||||||| ||||| ||||| ||||||||||||||||||||||| |||||| || |||| | | ||||| | |||||| | |||||
---gcatttaggtaagctgatcattggcatatctatatatagttgtttactcttgcatggtggccttcgctatcttctaacatgtttgtcaattatattgcagGCTGTTCTTGAGAAGCAGAGTTATATGCTTATTGGGAGGCATGATATTGAGAAGTTGATGAGGATTGACCCCTCAAGTGCATATTTACCGAATCTGCTTG
upper sequence: AT3G10380.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: Vv13s0019g04770.t01 (Vitis vinifera), 3'ss of exon 16
tacccatttaatacctctttagtttccctaaatgtaaagcgttgtatttcttccttcgtacacacttttctgaccttaggtttcattgttagtatttcagGCTGTTCTAGAGAAGCTCAGTTACATGCTCATTGGGAGGCATGATATTGAGAAATTGATGCGGCTTGATGCGGCGAGTGCTTGTTTACCATCTACGCTTG
|| |||| || | | || | || | | ||| | | |||| ||| ||| || || | |||||||| ||||| ||||||| ||||| ||||| |||||||||||||||||||||||||||||||| |||| | || ||||| ||||||||| | | |||
ggtgtatgacatacatcaacaataaattcttgcatacttccaattaccttataattcattcgtttttttggtttcttttttttttttttttttttttcagGCAGTTCTTGAGAAGCAGAGTTATATGCTAATTGGGAGGCATGATATTGAGAAATTGATGCGATGTGATCCAGCTAGTGCATGTTTACCAAATCCATTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttcttccttcgtacacacttttctgaccttaggtttcattgttagtatttcagGCTGTTCTAGAGAAGCTCAGTTACATGCTCATTGGGAGGCATGATATTGAGAAATTGATGCGGCTTGATGCGGCGAGTGCTTGTTTACCATCTACGCTTG
ttctgac putative branch site (score: 2)
ttagtattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tacccatttaatacctctttagtttccctaaatgtaaagcgttgtatttcttccttcgtacacacttttctgaccttaggtttcattgttagtatttcagGCTGTTCTAGAGAAGCTCAGTTACATGCTCATTGGGAGGCATGATATTGAGAAATTGATGCGGCTTGATGCGGCGAGTGCTTGTTTACCATCTACGCTTG
- - - - - - -cctcttt
- - - - - - - - - - - - -ccctaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tacacac