Sequence
atgc intronic sequence ATGC exonic sequenceAGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATGAAAACATTCCCAACCTTTTTAAGAAGATAAAGgtacattctattactcctcctctttcgtctatttgaactaatgcttgaattttttattttatttttcgtatcacccttcgactgtaaccttttttttttctcttttcgtcctatag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G01090.2 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G01090.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os05g45420.3 (Oryza sativa), 5'ss of exon 5
AGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATGAAAACATTCCCAACCTTTTTAAGAAGATAAAGgtacattctattactcctcctctttcgtctatttgaactaatgcttgaattttttattttatttttcgtatcacccttcgactgtaaccttttttttttctcttttcgtcctatag
||| ||||| ||||| |||||||| || || || |||||||| ||||| || |||||||||||||| || || |||||||||||||||||||| |||||||| || | | | | ||| | | |||| | || | |||| | | | | ||| | || |||| | |
AGTTGATGTGTGGAGTTGTGGTGTTATTCTTTATGCTCTTCTTTGTGGTACCCTTCCATTTGATGACGAGAATATTCCCAACCTTTTTAAGAAAATAAAGgt------tagcaaagatgtgatatatcctactgataaaggtgctg-----cctcatctccttttatatgttaaagtaaaactctgtccgttttgatgttctag------------
upper sequence: AT3G01090.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 5
AGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATGAAAACATTCCCAACCTTTTTAAGAAGATAAAGgt-acattctattactcctcctctttcgtctatttgaactaatgc-ttga-------attttt----tatttta-tttttcgtatcacccttcgactgtaaccttttttttttctcttttcgtcctatag
|| ||||| ||||||||||| ||||| || || ||||| || ||||| || ||||||||||||||||| || || |||||||| || || ||||||||||| | || ||| || | | | | |||| | |||| | || ||| | | ||||| ||| | || | | | ||| | | ||| || | ||
GGTTGATGTATGGAGCTGTGGAGTGATCCTTTATGCTCTCCTTTGTGGTACTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagatagatttatgtaggctagccagaccttgtaaactcttatgttgactagatggtccttaaaatatctaagtttttattattattctgtatatttgagtatttgacctgtttgtttggtgttccag
upper sequence: AT3G01090.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os08g37800.1 (Oryza sativa), 5'ss of exon 5
AGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATGAAAACATTCCCAACCTTTTTAAGAAGATAAAGgt-acattctattactcctcctctttcgtctatttgaacta--atgct---tgaat--ttttta------ttttatttttcgtatcacccttcgactgtaaccttttttttttctcttttcgtcctatag
|| ||||| ||||||||||| ||||| || || ||||| || ||||| || |||||||||||||| || || || |||||||| || || ||||||||||| | || ||| || | | | | |||| ||||| | || | ||| | ||||| ||| | || | | | ||| | || ||| || | ||
GGTTGATGTATGGAGCTGTGGAGTGATCCTTTATGCTCTCCTTTGTGGTACTCTTCCATTTGATGACGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagataaatttatgtaggctaaccagaccttataaactcttatgctgactagatggtccttaaaatatctaagtttttattattattctgtatatttgagtatttgacctgcttgtttggtgttccag
upper sequence: AT3G01090.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G077278_T01 (Zea mays), 5'ss of exon 5
AGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATGAAAACATTCCCAACCTTTTTAAGAAGATAAAGgtacattctattactcctcctctttcgtctatttgaactaatgcttgaattttttattttatttttcgtatcacccttcgactgtaaccttttttttttctcttttcgtcctatag
||| || |||||||||||||| || || || || |||||||| ||||| || || |||||||| ||||| || ||||| |||||||| ||||| |||||||| |||| | | ||| || |||| || | || ||| |||||||||||| ||| | | | | |||||| | | || | |
AGTTGACGTCTGGAGCTGTGGAGTTATTCTTTATGCTCTTCTTTGTGGCACTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtgag--ctataatctcagtgattt----tacctgaa--aaagattc--ctttatattttatttttaatatgctcaataaatt-----ctttttatatctaattgtag--------
upper sequence: AT3G01090.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G180704_T01 (Zea mays), 5'ss of exon 5
AGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATGAAAACATTCCCAACCTTTTTAAGAAGATAAAGgtacattctattactcctcctctttcgtctatttgaactaatgcttgaattttttattttatttttcgtatcacccttcgactgtaaccttttttttttctcttttcgtcctatag
||| ||||| ||||||||||| || || || || |||||| | ||||| || || ||||||||||| || ||||| || |||||||||||||| |||||||| | | || | | | ||| ||| | | ||| || || || | | | | | | ||||| | | ||||||||| | || |||
AGTTGATGTGTGGAGCTGTGGGGTTATTCTTTATGCTCTTTTATGTGGTACTCTGCCATTTGATGACGAGAACATACCAAACCTTTTTAAGAAAATAAAGgt------cagcaagtatctacggttttacattagaaatgttcattg----ttacatgttcctgctgatttagagcct-atctgtatctccctccttttctctt---gcactttag
upper sequence: AT3G01090.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G107867_T02 (Zea mays), 5'ss of exon 5
AGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATGAAAACATTCCCAACCTTTTTAAGAAGATAAAGgtacattctattactcctcctctttcgtctatttgaactaatgcttgaattttttattttatttttcgtatcacccttcgactgtaaccttttttttttctcttttcgtcctatag
|| ||||| ||||| ||||| ||||| || || |||||||| ||||| || ||||||||||||||||| || |||||||| || || || || || ||||| | || | | | | || || ||| | | | | || | | ||| || ||| || ||||
GGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATGAGAATATTCCCAATCTGTTCAAAAAAATTAAGgtgagaa-----agcacttatgtggaatacaaaccttgcaacaattagattctgttctggagttatg--accactctctatctg--gttttacggttttag---------------
upper sequence: AT3G01090.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA13G05700.1 (Glycine max), 5'ss of exon 5
AGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATGAAAACATTCCCAACCTTTTTAAGAAGATAAAGgtacattctattactcctcctctttcgtctatttgaactaatgcttgaattttttattttatttttcgtatcacccttcgactgtaaccttttttttttctcttttcgtcctatag
|||||||||||||||||||||||| || | || |||||||||||||| || ||||| ||||||||||||||||||||||| || || || || |||||||||| || | || | || |||| | | ||| ||| || || | |||| | || | | | || | | | || | || |
AGTAGATGTCTGGAGCTGTGGTGTAATTTTATATGCTCTTCTCTGTGGCACTCTTCCTTTTGATGATGAAAACATTCCCAATCTCTTCAAAAAAATAAAGgtac-------tatttttcttaatttaattattattatatttcctt---tttctttttatgggtttcaaaggactgatag--ttaaatttcctaccactgtcgtgtcaaatt----
upper sequence: AT3G01090.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA08G26180.1 (Glycine max), 5'ss of exon 5
AGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATGAAAACATTCCCAACCTTTTTAAGAAGATAAAGgtacattctattactcctcctctttcgtctatttgaactaatgcttgaattttttat-tttatttttcgtatcacccttcgactgtaaccttttttttttctcttttcgtcctatag
||| |||||||||||||||||||| || | || || ||||| ||||| || ||||| |||||||||||||||||||| || || || ||||| ||||||||| | || | | | | ||| | || || | | || | | || | | ||| | | | | || | || || | | | | |
AGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCGCTTCTTTGTGGCACTCTTCCTTTTGATGATGAAAACATTCCAAATCTCTTCAAGAAAATAAAGgtat-tgttaatgttaattttattt-atttaattaactgagtgatcagctgttgtctacatatatattaaaactgcccaggccttggacatatggctaattt---------------
upper sequence: AT3G01090.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA18G49770.1 (Glycine max), 5'ss of exon 6
AGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATGAAAACATTCCCAACCTTTTTAAGAAGATAAAGgtacattctatt-actcctcctctttcgtctatttgaactaatgcttgaattttttattttatttttcgtatcacccttcgac-tgtaaccttttttttttctcttttcgtcctatag
||| |||||||||||||||||||| || | || || ||||| ||||| || ||||| |||||||||||||| ||||| || || || ||||| ||||||||| | ||| | | | | || || |||| | | || | ||| | | | |||| ||| ||| |||| ||
AGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCCCTTCTTTGTGGCACCCTTCCTTTTGATGATGAAAATATTCCAAATCTCTTCAAGAAAATAAAGgtattgttaatttaattttatttatttaattaattgagtgatcggctgttgactacattcaaacatcc---caggccttggacatgtggataattttccagct---------------
upper sequence: AT3G01090.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 5'ss of exon 5
AGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATGAAAACATTCCCAACCTTTTTAAGAAGATAAAGgtacattctattactcctcctctttcgtctatttgaactaatgcttgaattttttattttatttttcgtatcacccttcgactgtaaccttttttttttctcttttcgtcctatag
|| ||||| |||||||| ||||| || | ||||||||||| ||||| || ||||||||||||||||||||||||||||||||||| ||||| ||||||||| ||||| | || | || | ||| | | ||| | ||| | | | | || | ||| | | |||||| |||| |||| || |
GGTGGATGTATGGAGCTGCGGTGTTATTTTGTACGCTCTTCTTTGTGGTACTCTTCCATTTGATGATGAAAACATTCCCAACCTTTTCAAGAAAATAAAGgtat-ttctaaatttacttcactaac-----ttttagcatgtgccag-----cttagctggatct--gcattgctcttt---tttgtccttttactttttatttttttgtttagaa
upper sequence: AT3G01090.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: EFJ16445 (Selaginella moellendorffii), 5'ss of exon 4
AGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATGAAAACATTCCCAACCTTTTTAAGAAGATAAAGgtacattctattactcctcctctttcgtctatttgaactaatgcttgaattttttattttatttttcgtatcacccttcgactgtaaccttttttttttctcttttcgtcctatag
|||||| || ||||||||||| |||||||| ||||| ||||||||||| | ||||| ||||| || ||||||||||| || || || ||||| || ||||| | || | | | | | ||| | ||| ||| |||| | || | || ||| ||
AGTAGACGTATGGAGCTGTGGGGTGATACTATACGCACTTCTCTGTGGCAGCCTTCCCTTTGACGACGAAAACATTCCAAATCTATTCAAGAAAATCAAGgtg-aatcagtca-------------gacaacaagaagt----cttaaatgttttttcttttcttgtttattcccag---------------------------------------
upper sequence: AT3G01090.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: EFJ17922 (Selaginella moellendorffii), 5'ss of exon 4
AGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATGAAAACATTCCCAACCTTTTTAAGAAGATAAAGgtacattctattactcctcctctttcgtctatttgaactaatgcttgaattttttattttatttttcgtatcacccttcgactgtaaccttttttttttctcttttcgtcctatag
|||||| || ||||||||||| |||||||| ||||| ||||||||||| | ||||| ||||| || ||||||||||| || || || ||||| || ||||| | || | | | | | | || ||| || |||| | |||||| |
AGTAGACGTATGGAGCTGTGGGGTGATACTATACGCACTTCTCTGTGGCAGCCTTCCCTTTGACGACGAAAACATTCCAAATCTATTCAAGAAAATCAAGgtg-aatcagtcagacaaca------agaagtcttaa---atgttttttttttcttgtttattcccag------------------------------------------------Mapped 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|86059932|gb|DR355689.1|DR355689EST: CGCTTCCATTTGATGATGAAAACATTCCCAACCTTTTTAAGAAGATAAAG GGAGGGATATACACATTACCTAGCCATTTATCTCCTGGTGCTAGAGATTTG
genomic: CGCTTCCATTTGATGATGAAAACATTCCCAACCTTTTTAAGAAGATAAAGgtacattcta ... cgtcctatagGGAGGGATATACACATTACCTAGCCATTTATCTCCTGGTGCTAGAGATTTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATGAAAACATTCCCAACCTTTTTAAGAAGATAAAGgtacattctattactcctcctctttcgtctatttgaactaatgcttgaattttttattttatttttcgtatcacccttcgactgtaaccttttttttttctcttttcgtcctatag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG