Sequence
atgc intronic sequence ATGC exonic sequenceAGTAGATGTATGGAGTTGCGGAGTTATATTGTACGCTCTATTATGCGGTACTCTTCCTTTTGATGATGAAAACATTCCCAACCTTTTCAAGAAAATTAAGgtactgtacgttatactttgattcagctaaaagactcttcttaaatggattcatatgtatgtgaagtaacttatcaaggtgttttttttctctttag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G29160.2 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G29160.3 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os05g45420.3 (Oryza sativa), 5'ss of exon 5
AGTAGATGTATGGAGTTGCGGAGTTATATTGTACGCTCTATTATGCGGTACTCTTCCTTTTGATGATGAAAACATTCCCAACCTTTTCAAGAAAATTAAGgtactgtacgttatactttgattca--gctaaaagactcttcttaaatggattcatatgtatgtgaagtaacttatcaaggtgttttttttctctttag
||| ||||| |||||||| || ||||| | || ||||| | || ||||| ||||| |||||||| || || |||||||||||||| |||||||| ||||| | | | | | | | | |||| | || | | || |||||| | |||||| | | || |||| | |||
AGTTGATGTGTGGAGTTGTGGTGTTATTCTTTATGCTCTTCTTTGTGGTACCCTTCCATTTGATGACGAGAATATTCCCAACCTTTTTAAGAAAATAAAGgttagcaaagatgtgatatatcctactgataaaggtgctgcctcatctccttttatatgt---taaagtaa---aactctgtccgttttgatgttctag
upper sequence: AT3G29160.3 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G107867_T02 (Zea mays), 5'ss of exon 5
AGTAGATGTATGGAGTTGCGGAGTTATATTGTACGCTCTATTATGCGGTACTCTTCCTTTTGATGATGAAAACATTCCCAACCTTTTCAAGAAAATTAAGgtactgtacgttatactttgattcagctaaaagactcttcttaaatggattcatatgtatgtgaagtaacttatcaaggtgttttttttct-ctttag
|| |||||||||||||| || || || | || ||||| | || || |||||||| ||||||||||| || |||||||| || ||||| ||||||||||| | |||| | | || || || || | ||||| | | | | | || || | | |||| | |||||
GGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATGAGAATATTCCCAATCTGTTCAAAAAAATTAAGgtgagaaa----gcacttatgtggaa-tacaaaccttgcaacaattagattc-tgttctggagttatgaccactctctatctggttttacggttttag
upper sequence: AT3G29160.3 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G077278_T01 (Zea mays), 5'ss of exon 5
AGTAGATGTATGGAGTTGCGGAGTTATATTGTACGCTCTATTATGCGGTACTCTTCCTTTTGATGATGAAAACATTCCCAACCTTTTCAAGAAAATTAAGgtactgtacgttatactttgattcagct--aaaagactcttcttaaatggattcatatgtatgtgaagtaacttatcaaggtgttttttttctctttag
||| || || ||||| || |||||||| | || ||||| | || || ||||| || ||||| ||||| || ||||| ||||||||||||||||| ||||| || | | | || | || |||||| || | | | | ||| || |||| | ||| || | | || | | | | |||
AGTTGACGTCTGGAGCTGTGGAGTTATTCTTTATGCTCTTCTTTGTGGCACTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtgagctataatctcagtgattttacctgaaaaagattcctttatattttattttta-atatgctcaataaattct-----ttttatatctaattgtag
upper sequence: AT3G29160.3 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA13G05700.1 (Glycine max), 5'ss of exon 5
AGTAGATGTATGGAGTTGCGGAGTTATATTGTACGCTCTATTATGCGGTACTCTTCCTTTTGATGATGAAAACATTCCCAACCTTTTCAAGAAAATTAAGgtactgtacgttatactttgattcagctaaaagactcttcttaaatggattcatatgtatgtgaagtaacttatcaaggtgttttttttctctttag---------
||||||||| ||||| || || || || || || ||||| | || || |||||||||||||||||||||||||||||||| || ||||| ||||| |||||||| | | || ||| ||| | | | ||| || || |||| | | || ||| || ||| | | || | |
AGTAGATGTCTGGAGCTGTGGTGTAATTTTATATGCTCTTCTCTGTGGCACTCTTCCTTTTGATGATGAAAACATTCCCAATCTCTTCAAAAAAATAAAGgtactatttttcttaatttaattattattatatttcctttttc------tttttatgggtttcaaaggactgatagttaaatttcctaccactgtcgtgtcaaatt
upper sequence: AT3G29160.3 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA08G26180.1 (Glycine max), 5'ss of exon 5
AGTAGATGTATGGAGTTGCGGAGTTATATTGTACGCTCTATTATGCGGTACTCTTCCTTTTGATGATGAAAACATTCCCAACCTTTTCAAGAAAATTAAGgtactgtacgttatactttgattcagctaaaagactct-tcttaaatggattcatatgtatgtgaagtaacttatcaaggtgttttttttctctttag---
||| ||||| ||||| || || || || || || || || | || || ||||||||||||||||||||||||||||| || || ||||||||||| |||||| ||| | || ||| ||| | ||| ||| | | | | | || ||| | |||| | ||| || | | ||
AGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCGCTTCTTTGTGGCACTCTTCCTTTTGATGATGAAAACATTCCAAATCTCTTCAAGAAAATAAAGgtattgttaatgttaattttatttatttaattaactgagtgatcagctgttgtctacatatatattaaaact-gcccaggccttggacatatggctaattt
upper sequence: AT3G29160.3 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA18G49770.1 (Glycine max), 5'ss of exon 6
AGTAGATGTATGGAGTTGCGGAGTTATATTGTACGCTCTATTATGCGGTACTCTTCCTTTTGATGATGAAAACATTCCCAACCTTTTCAAGAAAATTAAGgtactgtacgttatactttg---attcagctaaaagactcttc-----ttaaatggattcatatgtatgtgaagtaacttatcaaggtgttttttttctctttag
||| ||||| ||||| || || || || || || || || | || || || |||||||||||||||||||| ||||| || || ||||||||||| |||||| ||| || | ||| ||| | ||| || | || || | | ||||| | | | | || | | ||||
AGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCCCTTCTTTGTGGCACCCTTCCTTTTGATGATGAAAATATTCCAAATCTCTTCAAGAAAATAAAGgtattgttaatttaattttatttatttaattaattgagtgatcggctgttgactacattcaaacatcccaggccttggacatgtggataattttccagct-----
upper sequence: AT3G29160.3 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 5'ss of exon 5
AGTAGATGTATGGAGTTGCGGAGTTATATTGTACGCTCTATTATGCGGTACTCTTCCTTTTGATGATGAAAACATTCCCAACCTTTTCAAGAAAATTAAGgtactgtacgttatactttgattcagctaa--aagactcttcttaaatggattcatatgtatgtgaagtaacttatcaaggtgttttttttctctttag--
|| ||||||||||| ||||| ||||| ||||||||||| | || ||||||||||| |||||||||||||||||||||||||||||||||||||| |||||| | | ||||| | | | | | | |||| ||||| || | | | | | | | | || ||||| | |||||
GGTGGATGTATGGAGCTGCGGTGTTATTTTGTACGCTCTTCTTTGTGGTACTCTTCCATTTGATGATGAAAACATTCCCAACCTTTTCAAGAAAATAAAGgtatttctaaatttacttcactaacttttagcatgtgccagcttagctggatctgcattgctcttttttgtccttttact-ttttatttttttgtttagaaMapped 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|124827681|gb|EH912547.1|EH912547EST: TTTTCAAGAAAATTAAG GGTGGGATTTACACTCTTCCAAGTTCATTTATACATCTGAGGCTAGAGACC
genomic: TTTTCAAGAAAATTAAGgtactgtacg ... ttctctttagGGTGGGATTTACACTCTTCCAAG-TCATTTAT-CATCTGAGGCTAGAGACC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGTAGATGTATGGAGTTGCGGAGTTATATTGTACGCTCTATTATGCGGTACTCTTCCTTTTGATGATGAAAACATTCCCAACCTTTTCAAGAAAATTAAGgtactgtacgttatactttgattcagctaaaagactcttcttaaatggattcatatgtatgtgaagtaacttatcaaggtgttttttttctctttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA