Sequence
atgc intronic sequence ATGC exonic sequence...ttgttttctgtggatcactttatggcgacttgtgaagtatcatccattatcattgtttcataagcaacttagataaatgtttctttcattttcttgtcagATGCCAAATAGCAGTGCATCAGGAATGCTATGGCGCTAGACATGTTCGTGATTTCACCTCATGGGTCTGTAAAGCATGCGAGAGACCAGATATCAAGCGG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G27910.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G27910.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os01g46700.1 (Oryza sativa), 3'ss of exon 11
-ttgttttctgtggatcactttatggcgacttgtgaagtatcatccattatcattgtttcataagcaacttaga-taaatgtttctttca-ttttcttgt-cagATGCCAAATAGCAGTGCATCAGGAATGCTATGGCGCTAGACATGTTCGTGATTTCACCTCATGGGTCTGTAAAGCATGCGAGAGACCAGATATCAAGCGG
| ||| | | | || | || | || | | | |||||| | ||| | ||| | | || | || || | ||| || ||||||||| |||||||| ||||||||||||||||||| || | || ||||||||||||
gtagttaagtttttgttacgagaaatgtttttcttaactgtgaa-----atcattttgaaatacggaacaaactctgaacttgactaacaatattcacgttcagATGCCAGATAGCAGTTCATCAGGAATGCTATGGCGTGAGGGGAAAGCAAGACTTCACCTCATGG------------------------------------
upper sequence: AT4G27910.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA04G41500.1 (Glycine max), 3'ss of exon 12
ttgttttctgtggatcactttatggcgacttgtgaagtatcatccattatcattgtttcataa-gcaacttagataaatgtttctttcattttct-tgt--cagATGCCAAATAGCAGTGCATCAGGAATGCTATGGCGCTAGACATGTTCGTGATTTCACCTCATGGGTCTGTAAAGCATGCGAGAGACCAGATATCAAGCGG
| | | | | || | | | ||||| || || || | || | | | ||||| | ||| | | ||| |||||| ||||||||||| ||||| ||||||||||| || ||| |||| || ||||| || || ||||| |||||||| ||||| ||||| || |||||||||
--caatgttacagctttgtcattgatg-catatgaagctatattt-ttggggttactctatgttgtattgcaattaaatcacaaataaattatatatgttacagATGTCAAATAGCAGTTCATCAAGAATGCTATGGAGCAAGAAATGTCCGAGATTTTACATCTTGGGTTTGTAAAGCTTGCGAAAGACCTGACATCAAGCGG
upper sequence: AT4G27910.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA06G13330.1 (Glycine max), 3'ss of exon 12
--ttgttttctgtggatcactttatggcgacttgtgaagtatcatccattatcattgtttcataa-gcaacttagataaatgtttctttcattttcttgtcagATGCCAAATAGCAGTGCATCAGGAATGCTATGGCGCTAGACATGTTCGTGATTTCACCTCATGGGTCTGTAAAGCATGCGAGAGACCAGATATCAAGCGG
||||| | ||| || ||| || ||| | | | | | | | || |||| | | | | | || || | | |||||| ||||||||||| ||||| ||||||||||| || ||| |||| || ||||| || || ||||| ||||| || || || | ||| || |||||||||
cattgttacagctttgtca-ttgatgcagatgaagcaagatttttgtggttactctatgttgtattgcaattaaatcacaaataaattatatatgtta--cagATGTCAAATAGCAGTTCATCAAGAATGCTATGGAGCAAGAAATGTCCGAGATTTTACATCTTGGGTTTGTAAGGCTTGTGAAACACCTGACATCAAGCGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attatcattgtttcataagcaacttagataaatgtttctttcattttcttgtcagATGCCAAATAGCAGTGCATCAGGAATGCTATGGCGCTAGACATGTTCGTGATTTCACCTCATGGGTCTGTAAAGCATGCGAGAGACCAGATATCAAGCGG
tgtttctttcattttc CT-rich tract
ttagataaatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgttttctgtggatcactttatggcgacttgtgaagtatcatccattatcattgtttcataagcaacttagataaatgtttctttcattttcttgtcagATGCCAAATAGCAGTGCATCAGGAATGCTATGGCGCTAGACATGTTCGTGATTTCACCTCATGGGTCTGTAAAGCATGCGAGAGACCAGATATCAAGCGG
- - - - - - - - - - - - - - - - - - - -tcatcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagcaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agataaa