Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgtctttctggagcttttgacgcagtttaagaaacgggaaattgaagatagcctttgaattataagaaaatgtgttgtagactgcgttttactcttgtcacagtttcctatgaactctactctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G39080.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os03g14690.1 (Oryza sativa), 3'ss of exon 10
gtaagtgtctttctggagcttttgacgcagtttaagaaacgggaaattgaagatagcctttgaattataagaaaatgtgttgtagactgcgttttactcttgtcacagtttcctatgaactctactctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC
| | | | | ||| || || | || || || ||| || | || | | ||| |||| || | | ||| | ||| | ||||| ||||| ||||| || || ||||||||||| ||||| || || || ||| | || ||||| |||||||| |||||||| |||||||| |||
----------------aattagcattgactcctgaaaaatcaataa--agagcttgctgtttgtttgggccaaatggtttagttaggaactgctaact-ttgt----attacatctga---------tacagGATAGCCAAATATCAAGAAGCAAACCCTGGTGTATTCACTATTGTCACTTTTCCTTTCTTATTTGCTGTCATGTTTGGAGATTGGGGACATGGAATTTGC
upper sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G058910_T01 (Zea mays), 3'ss of exon 10
gtaagtgtctttctggagcttttgacgcagtttaagaaacgggaaattgaagatagcctttgaattataagaaaatgtgttgtagactgcgttttactcttgtcacagtttcctatgaactctactctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC
| | | ||| || | | ||| | ||||| | | | ||| |||| || | | | | || | | ||| | |||||| ||||||||||| ||||| ||||| || |||||||||||||| || ||||| ||| | || ||||| ||||||||||||||||| |||||||| |||
---------------------cttatatcttgtaaataaagaagtgtaattcatatcatttgaggtttgactcaatac--tgtaaggtggata--agtgctaatgatgtgttccatgtggt-------acagTGTAGCCAAGTATCAAGAAGCAAATCCTGGAGTATTCACCATTGTGACTTTCCCTTTCTTATTTGCTGTCATGTTTGGTGATTGGGGCCATGGAATTTGC
upper sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G104418_T01 (Zea mays), 3'ss of exon 1
gtaagtgtctttctggagcttttgacgcagtttaagaaacgggaaattgaagatagcctttgaattataagaaaatgtgttgtagactgcgttttactcttgtcacagtttcctatgaactctactctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC
||| | | || ||||| || |||| | | | | | | | ||| || || | || || | ||| ||| | | || | |||||| ||||| ||||| ||||| ||||| || ||||||||||| || || ||||| || || || || || ||||||||||||||||| ||||| || |||
----------------cttattttttgtaattaaagaagtgg--aattaatgtcatttgaggtttggctcaagactgtaaggtgga-taagtgttgatgctgt----gttccatgtgg---------tacagTGTAGCCAAATATCAAGAAGCAAATCCTGGAGTATTCACCATCGTGACTTTCCCTTTTCTATTTGCCGTCATGTTTGGTGATTGGGGCCATGGGATTTGC
upper sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA06G03040.1 (Glycine max), 3'ss of exon 10
gtaagtgtctttctggagcttttgacgcagtttaagaaacgggaaattgaagatagcctttgaattataagaaaatgtgttg-tagactgcgttttactcttgtcacagtttcctatgaactctactctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC
| | | |||| | | || | ||| | | | || || | ||| || |||| | | |||| | | ||| || |||| ||| | |||||||| |||||||| ||||| ||||||| ||| ||||| || || || |||||||| ||||| ||||||||||| ||||||||||| ||||||
--------------------actagtggattttatatccct---atttacaactagtttcttagttgcttcttgatttattgataatctgcctgtaactcaaataatcgtt-------aa---tacttgacagAATCGCCAAGTACCAGGAAGCAAATCCCGGTGTATACACAATTGTCACATTTCCATTCCTTTTTGCTGTGATGTTTGGTGACTGGGGGCATGGCATATGC
upper sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA04G03010.1 (Glycine max), 3'ss of exon 10
gtaagtgtctttctggagcttttgacgcagtttaagaaacgggaaattgaagatagcctttgaattataagaaaatgtgttg-tagactgcgttttactcttgtcacagtttcctatgaactctactctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC
| || || | ||| || | | | || | || || | ||| || ||| | |||| | | | | | |||| ||| | |||||||| |||||||| ||||| ||||||| ||| |||| || || || |||||||| || || ||||||||||| ||||||||||| ||||||
-----------------------ggtacaacttgtactagtggattttatatgttttcgtttagttgcttcttgatttattgataatctgtctgaaactcaaataatcgctac----------tacttgacagAATCGCCAAGTACCAGGAAGCAAATCCCGGTGTATACACAGTTGTCACGTTTCCATTCCTTTTTGCCGTAATGTTTGGTGACTGGGGGCATGGCATATGC
upper sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA11G12120.1 (Glycine max), 3'ss of exon 10
gtaagtgtctttctggagcttttgacgcagtttaagaaacgggaaattgaagatagcctttgaattataagaaaatgtgttgtagactgcgttttactcttgtcacagtttcctatgaactctactctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC
||| || || | | |||| || || || | || | | | | |||| | || | | | ||| || | ||| || || ||||||||||| || ||||| ||| | || | |||||||| || || ||||| ||||| |||||||||||||||||||||||||||||
------------------------------cctaacaatttaagaacttgtttcattatttgttttttacttttattttttatttgaaatatatcaatcttat-acttcaacttttatacta-acatttcagGGTTGCTAAGTATCAGGAGGCAAATCCTACTGTGTATACTGTAGTTACCTTTCCATTTCTTTTTGCTGTAATGTTTGGTGATTGGGGGCATGGAATATGT
upper sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA12G04330.1 (Glycine max), 3'ss of exon 10
gtaagtgtctttctggagcttttgacgcagtttaagaaacgggaaattgaagatagcctttgaattataagaaaatgtgttgtagactgcgttttactcttgtcacagtttcctatgaactctactctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC
| || || | |||||||| | ||| | ||| | || || || | | | | | |||| | || | | | | ||| | | ||| || || ||||||||||| || ||||| ||| | || | |||||||| || || ||||| ||||| ||||||||||||||||| |||||||||||
---------------ttattcttaac--aatttaagaacttgtt--ttgctattttttttttacttttat---------ttttgaaatatatc--aatcttat-actttaacttttatacta-atatttcagGGTTGCTAAGTATCAGGAGGCAAATCCGACTGTGTATACTGTAGTTACCTTTCCATTTCTTTTTGCTGTAATGTTTGGTGATTGGGGTCATGGAATATGT
upper sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv03s0038g00290.t01 (Vitis vinifera), 3'ss of exon 10
gtaagtgtctttctggagcttttgacgcagtttaagaaacgggaaattgaagatagcctttgaattataagaaaatgtgttgtagactgcgttttactcttgtcacagtttcctatgaactctactctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC
| | ||||| | || || | | || ||| ||| | ||| | |||| ||| | | | || | | | ||||| |||||||||||||| || || ||||| ||||||||||| |||||||| || || || ||||| ||||| ||||||||||||||||| |||||| |||||
----------------------tattttactttaacctatttgatttt-----cattttgctgatgatatcaaatta----acagaat-tgtttgcctcatactaaaattatgtgattccatttaattgcagGGTGGCCAAGTATCAAGAGGCAAATCCTGGTGTATTCACTATTGTTACATTTCCATTTCTTTTTGCTGTCATGTTTGGTGATTGGGGACATGGATTATGC
upper sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv18s0001g13410.t01 (Vitis vinifera), 3'ss of exon 10
gtaagtgtctttctggagcttttgacgcagtttaagaaacgggaaattgaagatagcctttgaattataagaaaatgtgttgtagactgcgttttactcttgtcacagtttcctatgaactctactctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC
|| | |||| | | | | ||| || | | |||| || || | | | | || | ||| | | ||| ||||||||||||||||||| ||||| ||||||| | ||| |||| ||||| |||||||| ||||| ||||||||||||||||| ||||||||||||
-------------------------------ttgttatttttcaaatggtattgccctatagaagtacttggctaaatgtt-taagtggcatcatccaatagtagagatcaactaattcaataatatttcagGGTGGCCAAGTATCAGGAAGTGAATCCTGGTGTATACGTGATTATTACATTCCCTTTCCTTTTTGCTGTAATGTTTGGTGATTGGGGCCATGGAATATGC
upper sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S296_62V6.1 (Physcomitrella patens), 3'ss of exon 9
gtaagtgtctttctggagcttttgacgcagtttaagaaacgggaaattgaagatagcc--tttgaattataagaaaatgtgttgtagactgcgttttactcttgtcaca-gtttcctatgaactctac-tctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC
||| |||| | | | | | | | |||| | || ||| | || ||| || | | | | |||| | | |||| || | ||||| | | | || | | || | | ||| |||| ||||||||| || ||||| ||| || ||||| | || || || ||||| |||||||||||||||||||| ||||| |||||||| |||
gtaggtgtggtgatcagtataattatgtcgag-gagaagctggtctgtgatttttgctatttttaactgtcaagcga----ttgtggtcatatttttgcttctttcacacggtactgatcatttaaacatgtacagAGTGGGGCGGTATCAGGAGGCAAATCCTGGTTGTTTTACCATAATAACATTTCCATTCCTGTTCGCTGTTATGTTTGGTGACTGGGGCCATGGAATCTGC
upper sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S107_75V6.1 (Physcomitrella patens), 3'ss of exon 9
gtaagtgtctttctggagcttttgacgcagtttaagaaacgggaaattgaagatagcc--tttgaatta-taagaaaatgtgttgtagactgcgttttactcttgtcacagtttcctatgaactct----actctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC
|||||||| | | | | ||| | | || ||| |||| ||| || ||| || | |||| | |||| | | || || |||| ||| || | | | | | |||||||||| |||||||||||| ||||| || || ||||| | || ||||| ||||| |||||||||||||||||||| ||||| |||||||| ||
gtaagtgtgcagatcaacgatattacgacgcgttgaaactgggttgttgatgatcgctgttttcaactgctaagggattgtggtaatggttgttttcctttctttcattcagttctgatcagatgttgtgaatatgcagTGTGGGACGGTATCAGGAAGCAAATCCTGGATGTTTTACCATAATAACTTTCCCTTTCCTATTCGCTGTTATGTTTGGTGACTGGGGACATGGAATCTGT
upper sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S6_159V6.1 (Physcomitrella patens), 3'ss of exon 9
gtaagtgtctttctggagcttttgacgcagt-ttaagaaacgggaaattgaa-gatagcc-tttgaatt--ataagaaaatgtgttgtagactgcgttttactcttgt---cacagtttcctatgaactct----actctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC
|| |||||| | | | | | |||||| | | | | ||| | || || ||||| || | | | ||| ||| ||| | |||| || | | | | | | | ||||||||| ||||||||| || ||||| || || || || || || ||||||||||| ||||||||||||||||||||||||||||| || || |||
gtcagtgtccatacacctatgtaactttggcatctagaaactgaattctatatgatgtctattccaagcggataaggaatctttgtaccgtgtgcttttcgttctcctatgcacaattgacaaggggttgttgaaaatgcgcagTGTGGGGCGGTATCAGGAGGCAAATCCTGGATGTTTTACTATCGTAACGTTCCCCTTCCTGTTCGCTGTTATGTTTGGTGATTGGGGGCACGGTATTTGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttgtagactgcgttttactcttgtcacagtttcctatgaactctactctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC
ctctactct CT-rich tract
ttttact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgtctttctggagcttttgacgcagtttaagaaacgggaaattgaagatagcctttgaattataagaaaatgtgttgtagactgcgttttactcttgtcacagtttcctatgaactctactctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA