Sequence
atgc intronic sequence ATGC exonic sequencegtacttgtctttttaatgattcttctgtcttttactcggatttatcatagatgactaacttccctttttaatgattcagCAACAATATTTGCATATGGACAAACAAGCAGTGGAAAGACATATACCATGAGAGGAGTAACGGAGAAAGCTGTCAATGATATTTACAATCACATAATTAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G18370.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G18370.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g33040.1 (Oryza sativa), 3'ss of exon 3
gtacttgtctttttaatgattcttctgtcttttactcg--gatttatcataga----tgactaacttccctttttaatgattcagCAACAATATTTGCATATGGACAAACAAGCAGTGGAAAGACATATACCATGAGAGGAGTAACGGAGAAAGCTGTCAATGATATTTACAATCACATAATTAA
||| | || | | | | | | || | | ||| | || | | | | | || | || | | |||| || || ||||| ||||| ||||| |||||||| ||||||| ||||||||||| || || |||| ||||| |||||||| |||| |||||| ||
gtaaattaattctcactcagtagtttgaataaagttgaatgatcctttatctactctttattctttaccttcctttgttttgcagCCACCATTTTTGCCTATGGTCAAACCAGCAGTGGTAAGACATTCACCATGAGAGGCGTCACAGAGAGTGCTGTAAATGATATATACAGGCACATAGAAAA
upper sequence: AT1G18370.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G10790.1 (Glycine max), 3'ss of exon 2
--------------------------gtacttgtctttttaatgattcttctgtcttttactcgg-atttatcatagatgactaacttccctttttaatgatt-cagCAACAATATTTGCATATGGACAAACAAGCAGTGGAAAGACATATACCATGAGAGGAGTAACGGAGAAAGCTGTCAATGATATTTACAATCACATAATTAA
|| | ||| | |||||| | || ||| |||| || || || | || | | ||| | ||| |||| ||| | ||||| ||||||||||| ||||||||||||||||| || ||||||||| |||| ||||| |||||||||||||| ||| | || || || ||
gtactgtttcagatatttgtatctttgttttaaccttccttatgatttgtgacactgttaaggaccatttgcattacataacca--ttgcatgcttattcattgcagCTACAGTTTTTGCTTATGGACAAACTAGCAGTGGAAAGACATACACAATGAGAGGAATAACAGAGAAGGCTGTCAATGATATCTACGAGCATATTATGAA
upper sequence: AT1G18370.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G31270.1 (Glycine max), 3'ss of exon 2
----------------------------gtacttgtctttttaatgattcttctgtcttttactcggatttatcat-agatgactaacttccctttttaatgatt-cagCAACAATATTTGCATATGGACAAACAAGCAGTGGAAAGACATATACCATGAGAGGAGTAACGGAGAAAGCTGTCAATGATATTTACAATCACATAATTAA
|| | || |||||| | || ||| | ||| | || || ||| | | ||| | ||| |||| ||| | ||||| ||||||||||| ||||||||||||||||| || ||||||||| |||| ||||| |||||| ||||||| ||||| || || || ||
gtactgcttcagatatttgtgtatctttgtcttaacctcccatatgatttgtggccctgttagggactctctgcattacataacc--cttgcatacttatttattgcagCTACAGTTTTTGCTTATGGACAAACTAGCAGTGGAAAGACATACACAATGAGAGGAATAACAGAGAAGGCTGTCTATGATATCTACAAGCATATTATGAA
upper sequence: AT1G18370.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv17s0000g03290.t01 (Vitis vinifera), 3'ss of exon 2
----------------------------gtacttgtctttttaatgattc-ttctgtcttttactcggatttatcatagatgactaacttccctttttaatgattcagCAACAATATTTGCATATGGACAAACAAGCAGTGGAAAGACATATACCATGAGAGGAGTAACGGAGAAAGCTGTCAATGATATTTACAATCACATAATTAA
|| | ||| |||||| || ||| | | | || || || || ||| || ||| | | ||||||| |||||||||||||| ||||| |||||||| ||||| || || ||||||||| |||| ||||||||||| |||||||| || || || ||||| ||
gtagtgaacatctgtatattatctgtctgttaatatctctttaatagtttattcaattataagcatatatccatgctaaat--ctacttttatcccttatttttacagCAACTATATTTGCATATGGGCAAACCAGCAGTGGGAAGACTTACACAATGAGAGGAATAACAGAGAAAGCTGTTAATGATATCTATAAGCATATAATAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgtcttttactcggatttatcatagatgactaacttccctttttaatgattcagCAACAATATTTGCATATGGACAAACAAGCAGTGGAAAGACATATACCATGAGAGGAGTAACGGAGAAAGCTGTCAATGATATTTACAATCACATAATTAA
cttccctttttaat CT-rich tract
tttttaatgattca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttgtctttttaatgattcttctgtcttttactcggatttatcatagatgactaacttccctttttaatgattcagCAACAATATTTGCATATGGACAAACAAGCAGTGGAAAGACATATACCATGAGAGGAGTAACGGAGAAAGCTGTCAATGATATTTACAATCACATAATTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG