Sequence
atgc intronic sequence ATGC exonic sequencegtaaaagttattctctatcaatataaggtgcaagtcgctaaatgcttctactgtcagctaattcttgtgtggttcttatgtagGCTTACATTGAGAAAGAAGATGGTAAGAAATTGAAGCAAAAGCAACGGGAGAGAATGCAACCAAAAATGGGAAAGATGGACATTGACTACCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G21660.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G21660.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g58090.1 (Oryza sativa), 3'ss of exon 6
-----------------gtaaaagttattctctatcaatataaggtgcaagt---cgctaaatgcttc----tactgtcagctaattcttgtgtggttcttatgtagGCTTACATTGAGAAAGAAGATGGTAAGAAATTGAAGCAAAAGCAACGGGAGAGAATGCAACCAAAAATGGGAAAGATGGACATTGACTACCAG
| | | | | | | | | | || | || ||| | || | | ||| | | || || | |||| || |||||||| || ||| |||| || ||||| |||||||| |||||| | ||||||||||||||||| |||||||| || || || |||
gtaacttgattatctcgattcttttaggcttttcttgggacatgataccagcttactttaggagctgtgtggtgctcgaattttatttaaatttctttttttttcagGCATATATTGAGAAGGAGGATAGTAAAAAGTTGAAACAAAAGCAGCGGGAGCGTATGCAACCAAAAATGGGCAAGATGGATATAGATTATCAG
upper sequence: AT4G21660.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA15G07760.1 (Glycine max), 3'ss of exon 6
-----gtaaaagttattctctatcaatataaggtgcaagtcg-----ctaaatg-cttctactgtca-----gctaattcttgtgtggt-tcttatgtagGCTTACATTGAGAAAGAAGATGGTAAGAAATTGAAGCAAAAGCAACGGGAGAGAATGCAACCAAAAATGGGAAAGATGGACATTGACTACCAG
| ||| ||| || || | | || | |||||| |||| || ||||| | | || | ||| ||| ||||||| ||||||||||| ||| ||||||| |||| ||||||||| ||||| | ||||||||||||||||| || ||||| || || || |||
agaagtttttcgttgctctttacacatgtgtcttttaattaatttacctaaataatttctgtagttgctgtttttaattgtcatatgttatctcatgcagGCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAG
upper sequence: AT4G21660.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 6
----------------gtaaaagttattctctatcaatataaggtgc--aagtcgctaaatgcttctactgtcagctaattcttgtgtggt-tcttatgtagGCTTACATTGAGAAAGAAGATGGTAAGAAATTGAAGCAAAAGCAACGGGAGAGAATGCAACCAAAAATGGGAAAGATGGACATTGACTACCAG
|| | || | ||| | ||| ||| | | || || | || |||| ||||| | | || | ||| ||| ||||||| ||||||||||| ||| ||||||| |||| ||||||||| ||||| | ||||||||||||||||| || ||||| || || || |||
aagttttctgtgctctttacatgtgtgtgtcttttaat-taatttacctaaatcattgc-tgtagtcgctgttttttaattgtcatatgttgtctcatgcagGCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAG
upper sequence: AT4G21660.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G25110.2 (Glycine max), 3'ss of exon 6
---------------gtaaaagttattctctatcaata--taaggtgcaagtcgctaaatgcttcta--ctgtcagctaattcttgtgtggttcttatgtagGCTTACATTGAGAAAGAAGATGGTAAGAAATTGAAGCAAAAGCAACGGGAGAGAATGCAACCAAAAATGGGAAAGATGGACATTGACTACCAG
||| ||| ||| | | || | | || | || ||||||| ||| ||| | || ||| ||| |||| ||| ||||||| |||||||||||||| |||| || |||||||||||||| | || | ||||||||||||||||| || ||||| ||||| || |||
ctttctctttgcaatgtatgtgtttgtcttttcaagtagttttattacattactgtacttgcttcttacctgccaggttat-cttctgtt-ttctcatgcagGCTTATATTGAGAAAGAAGACAGTAAAAAGCTGAAGCAAAAGCAAAGAGAACGCATGCAACCAAAAATGGGGAAAATGGATATTGATTATCAG
upper sequence: AT4G21660.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S98_7V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------gtaaa-agttattctctatcaatataaggtgca----agtcgctaaatgcttctactgtcagctaattcttgtgtggttc---ttatgtagGCTTACATTGAGAAAGAAGATGGTAAGAAATTGAAGCAAAAGCAACGGGAGAGAATGCAACCAAAAATGGGAAAGATGGACATTGACTACCAG
||| | | | || ||| || ||| |||| ||| || | ||| | | | || | || | ||| |||||||||||||||| ||||| | ||||| | ||||||||||| |||||| |||||| || || ||||||||||||||||| || || |||
tgagatcaatcgtactcaatcagaacttagtgatacaatttgctccgtagtcatgtcatg-ttatgtcatcaattgaatattttatgctatgggctat-cagGCTTACATTGAGAAGGAAGACAGCAAGAAGCTCAAGCAAAAGCAGAGGGAGAAAATGCAGCCTAAGATGGGAAAGATGGACATCGATTATCAGMapped 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|124728292|gb|EH819694.1|EH819694EST: CTGATTTCATTGCTGCAACCGGAATTGAGAAGATTAGACAG GCTTACATTGAGAAAGAAGATGGTAAGAAATTG
genomic: CTGATTTCATTGCTGCAACCGGAATTGAGAAGATTAGACAGgtaaaagtta ... tcttatgtagGCTTACATTGAGAAAGAAGATGGTAAGAAATTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcaagtcgctaaatgcttctactgtcagctaattcttgtgtggttcttatgtagGCTTACATTGAGAAAGAAGATGGTAAGAAATTGAAGCAAAAGCAACGGGAGAGAATGCAACCAAAAATGGGAAAGATGGACATTGACTACCAG
agctaat putative branch site (score: 3)
ttcttat putative PPT
taattctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaagttattctctatcaatataaggtgcaagtcgctaaatgcttctactgtcagctaattcttgtgtggttcttatgtagGCTTACATTGAGAAAGAAGATGGTAAGAAATTGAAGCAAAAGCAACGGGAGAGAATGCAACCAAAAATGGGAAAGATGGACATTGACTACCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA