Sequence
atgc intronic sequence ATGC exonic sequenceATTTGGACAGCCTATGAAAGTTAATTGGGCGTATGCAACTGGTCAAAGGGAAGATACATCAAgtaagttcttatgagcacggattgattgtcaaggactttctttttgttctttgagtgaggcatggtactgaatggttttggtttcatgaaatgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G54080.2 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G54080.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA16G01230.1 (Glycine max), 5'ss of exon 5
ATTTGGACAGCCTATGAAAGTTAATTGGGCGTATGCAACTGGTCAAAGGGAAGATACATCAAgtaagttcttatgagcacggattgattgtcaaggactttctttttgttctttgagtgaggcatggtactgaatggttttggtttcatgaaatgcag-------
|||||| |||||||| |||||||||||||| ||||| | |||||| || || ||||| ||| || ||||| || | | | ||| || | || | || | ||| | | ||| || | |||| |||
ATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCGAGTGGTCAGAGAGAGGATACGTCAGgttagttcagatttctg-agttaaaatgttaaataaattgatatttatgggccagtttgt--ttaaacttaaaaaaatcagtttagacaaacattaaaaaagc
upper sequence: AT1G54080.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA07G04640.1 (Glycine max), 5'ss of exon 5
ATTTGGACAGCCTATGAAAGTTAATTGGGCGTATGCAACTGGTCAAAGGGAAGATACATCAAgtaagttc----ttatgagc---acggattgat-tgtcaaggactttctttttgttctttgagtgaggcatggtactgaatggttttggtttcatgaaatgcag
|||||| |||||||| |||||||||||||| ||||| | |||||| || || ||||| ||| || ||||| || |||| | |||||| | | || | || | ||| |||||| || | | | || ||| ||| | ||||
ATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAGAGAGAGGATACGTCAGgttagttcacatttctgagttaaatatattgatatttttgggccattttgtttaaactttgaaaaagtgtt--ttttaaaaaatttattttttaagaaaaag--
upper sequence: AT1G54080.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 5'ss of exon 5
ATTTGGACAGCCTATGAAAGTTAATTGGGCGTATGCAACTGGTCAAAGGGAAGATACATCAAgtaagttcttatgagcacggattgattgtcaagg---actttctttttgttctttgagt-----gaggcatggtactgaatggttttggtttcatgaaat-gcag------------
||||| |||||||| |||||||||||||| ||||| | |||||||||||| || |||||| || ||| | | || | || ||| ||| | | || ||| | ||| ||| | | | | ||| | | | | | |
GTTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGAGGACACATCAGgttggtttctgt-agtttaattctatgcataagtttcactcttatgctgcaaactgattctatggagttttggcattcatcattgttgatgttgtattcttgtatgatgttgtgtag
upper sequence: AT1G54080.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S84_50V6.1 (Physcomitrella patens), 5'ss of exon 6
ATTTGGACAGCCTATGAAAGTTAATTGGGCGTATGCAACTGGTCAAAGGGAAGATACATCAAgtaagttcttatgagcacggattgattgtcaaggactttctttttgttctttgagtgaggcatg-gtactgaatggttttggtttcatgaaatgcag-----------------------
||||||||||||||| |||||||||||||| ||||||| || || || || ||||| || || || || | | | | | | ||| | || ||| | | || | || | || | | || | | |
ATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGAGGATACTACAGgtgttttatttttattttctagactatatttggcgcttctggtatggctgctgattaggaattgcatgatgtttagtatggactttagctattatttattttctatgttgcttgtaccagMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|125018538|gb|EL090807.1|EL090807EST: TATGAAAGTTAATTGGGCGTATGCAACTGGTCAAAGGGAAGATACATCAA GTCATTTCAACATTTTTGTTGGAGATCTTAGTCCAGAGGTTACTGATGCA
genomic: TATGAAAGTTAATTGGGCGTATGCAACTGGTCAAAGGGAAGATACATCAAgtaagttctt ... tgaaatgcagGTCATTTCAACATTTTTGTTGGAGATCTTAGTCCAGAGGTTACTGATGCA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATTTGGACAGCCTATGAAAGTTAATTGGGCGTATGCAACTGGTCAAAGGGAAGATACATCAAgtaagttcttatgagcacggattgattgtcaaggactttctttttgttctttgagtgaggcatggtactgaatggttttggtttcatgaaatgcag
- - - - - - - - - - - - - - - - - - - - - - - - GGAAGA