Sequence
atgc intronic sequence ATGC exonic sequencegtatgtgcttattacatatacttctctcgaacattcttgttattttataaagacttgtatggagagtgtgacaatatcacattctttttttcttcttttagGGAGCAAATGTTCCTTTGATTGTTAAATGGGCAGACACAGAAAAGGAAAGACAAGCTCGAAGACTTCTAAAAGTTCAATCTCATGTCTCCAGACTCGATC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G03457.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G03457.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os05g30980.1 (Oryza sativa), 3'ss of exon 5
--gtatgtgcttattacatatacttctctcgaacattcttgttattttataaagacttgtatggagagtgtgacaatatcacattctttttttcttcttttagGGAGCAAATGTTCCTTTGATTGTTAAATGGGCAGACACAGAAAAGGAAAGACAAGCTCGAAGACTTCTAAAAGTTCAATCTCATGTCTCCAGAC--TCGATC
| | |||| ||| | | | || |||| || | || | | | || | || | | | |||| || ||||| ||| ||| |||||| ||||||||||||| ||||| || ||||||||||||||||||| | | ||| | ||||| ||| || | || |
agccagctccttaagttgtattaatatattagctgtttcctttatgtt-tgaattttcaca-gttgattacatagatcttgatgtgccctgatctt-ttgtagGGTTCAAGTGTACCTTTGGTTGTTAAATGGGCTGACACTGAGAAGGAAAGACAAGCTCGAAAAGCACAAAAGGCTCAATTTCACCCATCTAATATGTCAA--
upper sequence: AT1G03457.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G128809_T01 (Zea mays), 3'ss of exon 6
gtatgtgcttattacatatacttctctcgaacattcttgttattttataaagacttgtatggagagtgtgacaatatcacatt-ctttttttcttcttttagGGAGCAAATGTTCCTTTGATTGTTAAATGGGCAGACACAGAAAAGGAAAGACAAGCTCGAAGACTTCTAAAAGTTCAATCTCATGTCTCCAGACTCGATC-
|| | | ||| ||| | || | | | | | | || | | || || | ||| | |||| ||| | || |||||| ||| |||||| ||| |||| |||||||| ||||| ||||||||||| |||||||||| | | |||| || || || |||| | || | |
-taatagatcattg-ataccttggccttgtatagttgtatgatatagattacttcagttctgaaatctcatgaatctaacatggcttggtcattttggttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGGCAAGCTCGAAAAGCGCAAAAATCTCCATTCCA-GTCTTCTAACATGTTGA
upper sequence: AT1G03457.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G177001_T01 (Zea mays), 3'ss of exon 5
gtatgtgcttattacatatacttctctcgaacattcttgttattttataaagacttgtatggagagtgtgacaa-tatcacattctttttttcttctt-ttagGGAGCAAATGTTCCTTTGATTGTTAAATGGGCAGACACAGAAAAGGAAAGACAAGCTCGAAGACTTCTAAAAGTTCAATCTCATGTCTCCAGACTCGATC-
|| | || ||| | | | | | | ||| | | | | || ||| ||| |||| | | |||| | | | || || |||||| ||| |||||| ||| |||| |||||||| ||||| ||||||||||| || ||||||| | | ||||| ||||| || |||| | || | |
--atatcattgatacct-tggtcttgtatgatattgatcacttcagttctgaaatttcatgaccagttacacaaatctaacatgccctggtcatttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGGCAGGCTCGAAAAGCACAAAAAGCTCAATTCCA-GTCTTCTAACATGTTGA
upper sequence: AT1G03457.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G17090.1 (Glycine max), 3'ss of exon 5
gtatgtgcttattacatatacttctctcgaacattcttgttattttataaagacttgtatggagagtgtgacaat----atcacattctt-tttttcttcttttagGGAGCAAATGTTCCTTTGATTGTTAAATGGGCAGACACAGAAAAGGAAAGACAAGCTCGAAGACTTCTAAAAGTTCAATCTCATGTCTCCAG-ACTCGATC
|| || | || | | | || | || || | |||| ||| ||||||| || || ||| |||||| | | |||| ||| |||||||||| |||||||||||||||| || ||||||||||||| ||||||||| || |||| || || | || || | | |
----ttgttttgcctgggtggttaatatgtttgctactcgtacatgatgaaaa-ttgtcaattaagt-tgacaattgcagtctgatgcttatttttccttctacagGGTTCAAGTGTTCCTTTGGTTGTTAAATGGGCAGATACTGAAAAGGAAAGACTAGCTCGAAGGGCTCAAAAAACACAGTCCCGAGTTTCTAATGCGCCGC-
upper sequence: AT1G03457.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G02700.3 (Glycine max), 3'ss of exon 4
gtatgtgcttat-tacatatacttctctcgaacattcttgttattttataaagacttgtatggagagtgtgacaatatcacattctttttttcttcttttagGGAGCAAATGTTCCTTTGATTGTTAAATGGGCAGACACAGAAAAGGAAAGACAAGCTCGAAGACTTCTAAAAGTTCAATCTCATGTCTCCAGACTCGATC
|| | || || | | | || | | | | | | || | | | || | | | |||| | | | ||||| ||||| |||| ||| |||||||||| |||| ||||||||||| || ||||||||||| | ||||||||| || ||||| || || || || || | | |
-tagctactcatacatgatgaaaattgtcaattaaattgctaactcaatgattatataaattcatacaattgcaatctgatggttatttttccttctac-agGGTTCAAGTGTTCCTTTGGTTGTCAAATGGGCAGATACTGAAAAGGAAAGGCTAGCTCGAAGGGCTCAAAAAGCACAGTCCCAAGTTTCTAACATGCCGC
upper sequence: AT1G03457.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G36650.2 (Glycine max), 3'ss of exon 5
gtatgtgcttattacatatacttctctcgaacattcttgtt----attttataaagacttgtatggagagtgtgacaatatcacattctttttttcttcttttagGGAGCAAATGTTCCTTTGATTGTTAAATGGGCAGACACAGAAAAGGAAAGACAAGCTCGAAGACTTCTAAAAGTTCAATCTCATGTCTCCAGACTCGATC
||||| | || |||| | | || | | || | | | || | | || ||| | |||||| | ||| | || ||||| | |||| ||| |||||| || |||| |||||||| || || |||||||||||||||||||||||| || |||| || || || | || | | |
-tatgtttct-ccactcatacatgacaaagtcactgatattgctaactcgacaagtatattaattcagatatttgcaatatgatatt--tgttgtcttccat-agGGTTCAAGTGTTCCCTTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGACAAGCTCGAAGAGCTCAGAAAGCACAGTCCCAAGCTTCTAATGTACCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataaagacttgtatggagagtgtgacaatatcacattctttttttcttcttttagGGAGCAAATGTTCCTTTGATTGTTAAATGGGCAGACACAGAAAAGGAAAGACAAGCTCGAAGACTTCTAAAAGTTCAATCTCATGTCTCCAGACTCGATC
tatcacattctttttt CT-rich tract
tttttttcttctttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtgcttattacatatacttctctcgaacattcttgttattttataaagacttgtatggagagtgtgacaatatcacattctttttttcttcttttagGGAGCAAATGTTCCTTTGATTGTTAAATGGGCAGACACAGAAAAGGAAAGACAAGCTCGAAGACTTCTAAAAGTTCAATCTCATGTCTCCAGACTCGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA