Sequence
atgc intronic sequence ATGC exonic sequencegtaagtcatcaccttattggttccaccatttactttcgaccaaaattataacttttaaagtgggaatctaagaatgcttcttcagCTATTATGAAGCTCTAGGAAATATGGACATGAGCCTGCACTCAATGGAAGTTGTGAATAGGCTCACAACTGCAGTTGAACTTCCCAAGGACTTCATACGG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G18420.3 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G18420.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os12g09610.1 (Oryza sativa), 3'ss of exon 8
gtaagtcatcaccttattggttccaccatttactttcgaccaaaattataacttttaaagtgggaatctaagaatg--cttcttcagCTATTATGAAGCTCTAGGAAATATGGACATGAGCCTGCACTCAATGGAAGTTGTGAATAGGCTCACAACTGCAGTTGAACTTCCCAAGGACTTCATACGG
||| ||| ||| | | | | || || | | | || | | || | | | | | | | ||| ||||| || | || | ||| | ||||||| ||||||||||| || ||||||||||| || ||||| || ||||| || ||||| || | || || | |
gtatgtctgtttcttttctttgctagtcaatatgatcaccaacacttttttttaatatattttaattgtgacccttttctttttcagTTACTTAGATGTTCTTGTGCATATGGAGATGAGCCTGCATTCTATGGAAGTTGTAAACAGGCTTACTACTGCTGTAGAACTCCCGACAGAGTTTGTCCAT
upper sequence: AT5G18420.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os11g13694.1 (Oryza sativa), 3'ss of exon 9
-----------------gtaagtcatcaccttattggttccaccatttactt-tcgaccaaaattata-acttttaaagtgggaatc-taagaatgcttctt---cagCTATTATGAAGCTCTAGGAAATATGGACATGAGCCTGCACTCAATGGAAGTTGTGAATAGGCTCACAACTGCAGTTGAACTTCCCAAGGACTTCATACGG
|| | || || || | | ||||| | || | || | ||| || || | || | | | ||||| ||| || | ||| ||| | | ||||| |||||||| || |||||||||||||| || |||||||| || ||||| || || || | ||||| |
gtatgtagattagccttgtcgtttattctattgttttcttatttaattactaatttactatgtttctctactcacaacgtcttactcacatgcctttttctttgacagTTACTTTGATATTCTTGTGCACATGGAAATGAGCCTACATTCAATGGAAGTTGTAAACAGGCTCACTACAGCAGTAGATCTACCACCAGGATTCATTCAT
upper sequence: AT5G18420.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G133757_T01 (Zea mays), 3'ss of exon 9
----gtaagtca-tcaccttattggttccaccatt-tactttcgaccaaaattataactttta-aagtgggaatctaagaatgcttctt-------cagCTATTATGAAGCTCTAGGAAATATGGACATGAGCCTGCACTCAATGGAAGTTGTGAATAGGCTCACAACTGCAGTTGAACTTCCCAAGGACTTCATACGG
| | | | || ||| | | || | ||| | | | | || | | | || | | ||| | | ||| || | ||| ||| | | ||||||| |||||| |||| ||||||||||| || || |||||||| |||||||| | | || | || | |
gtacacatactagccttttcatctgttttatctttatccttgtaattattgtgcttttttctgcatgccagatttcacacttgccttattgttcaacagATACTTTGATGCTATTGTCCATATGGATATGAGCTTGCATTCAATGGAAGTAGTAAACAGGCTCACTACTGCAGTAGTTTTACCACCAGGATTTGTTCAC
upper sequence: AT5G18420.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G011575_T02 (Zea mays), 3'ss of exon 9
------------------------------------------------------------------------gtaagtcatcaccttattggttccaccattt------actttcgaccaaaattataacttttaaagtgggaatctaaga-atgcttcttcagCTATTATGAAGCTCTAGGAAATATGGACATGAGCCTGCACTCAATGGAAGTTGTGAATAGGCTCACAACTGCAGTTGAACTTCCCAAGGACTTCATACGG
| ||| | ||| | | || |||| | | | | | || | | | | | | | | || ||| ||| || | ||| ||| | | ||||||| |||||| |||| ||||||||||| || ||| ||||||| |||||||| | | || | || | |
gtatgcatacttagccttttcatttgttttatctttatccttgtaattattgtgcttttttctctttgagacaaaggtcgggagctttcaattccgactattttaaaaaattattgtgcttttttctgcatgtcatatttcacacttgccttattgttcgacagGTACTTTGATGCTATTGTTCATATGGATATGAGCTTGCATTCAATGGAAGTAGTAAATCGGCTCACTACTGCAGTAGTTTTACCACCAGGATTTGTTCAT
upper sequence: AT5G18420.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G098815_T03 (Zea mays), 3'ss of exon 9
gtaagtcatcaccttattggttccaccatttactttcgaccaaaattataacttttaaagtgggaatctaagaatgcttcttc-----agCTATTATGAAGCTCTAGGAAATATGGACATGAGCCTGCACTCAATGGAAGTTGTGAATAGGCTCACAACTGCAGTTGAACTTCCCAAGGACTTCATACGG
|| ||| | | |||||||| | || | || | ||| | | | ||| | ||| || || | ||| | ||| | | ||||| |||||| |||| || |||||||||||||| || ||||| ||||| ||||| ||||| | || || | |
gtgtgtctctgctct--tggttccatgttctattatcatatatgcagccttcttcctgccctttatttgatcgatgatccttttttgtagTTACTTTGATGTTCTTGTGCACATGGAAATGAGCTTGCATTCTATGGAAGTTGTGAACAGACTCACTACTGCCGTTGACCTTCCAACAGAATTTGTCCAT
upper sequence: AT5G18420.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA10G00610.3 (Glycine max), 3'ss of exon 9
----------gtaagtcatcaccttattggt--tccaccatttactttcgaccaaaattataacttttaaagtgggaatctaagaatgcttc--ttcagCTATTATGAAGCTCTAGGAAATATGGACATGAGCCTGCACTCAATGGAAGTTGTGAATAGGCTCACAACTGCAGTTGAACTTCCCAAGGACTTCATACGG
| || | |||| || | | | ||| || | | ||| | ||| | || | || | | ||| || | || || | |||||||||||||| || || ||||||||||||||||| ||||| ||||| ||||||||||| || | ||||| |
gtatgcatttttcctctattatattatctgtgctttagtacatacattgccctatcgctattattttctttatttctatttgcttatttatggatacagATACTTCACAGTACTTGTCAATATGGACATGAGTCTACATTCAATGGAAGTTGTGAACAGGCTTACAACAGCAGTTGAACTACCGTCTCAATTCATTCAC
upper sequence: AT5G18420.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA02G00750.2 (Glycine max), 3'ss of exon 9
----------gtaagtcatcaccttattggt--tccaccatttactttcgaccaaaattataacttttaaagtgggaatctaagaatgcttc--ttcagCTATTATGAAGCTCTAGGAAATATGGACATGAGCCTGCACTCAATGGAAGTTGTGAATAGGCTCACAACTGCAGTTGAACTTCCCAAGGACTTCATACGG
| || | |||| || || | | ||| || | | ||| | ||| | || | || | | ||| || | | || || | |||||||||||||| || || ||||||||||||||||| ||||| ||||| || |||||||| || | ||||| |
gtatgcattcttcctctattatattatctgtgctctagtacatacattaccctatcgctattattttctttatttctatttgcttatttatggatacagATACTTTACAGTACTTGTCAATATGGACATGAGTCTACATTCAATGGAAGTTGTGAACAGGCTGACAACAGCTGTTGAACTACCATCTCAATTCATTCAC
upper sequence: AT5G18420.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv07s0130g00310.t01 (Vitis vinifera), 3'ss of exon 9
------------------------------------------gtaagtcatcaccttattggttccaccatttactttcgaccaaaattataacttttaaagtgggaatctaagaatgcttcttcagCTATTATGAAGCTCTAGGAAATATGGACATGAGCCTGCACTCAATGGAAGTTGTGAATAGGCTCACAACTGCAGTTGAACTTCCCAAGGACTTCATACGG
|| | || | | | | | || | |||| || | |||| | ||| || || || || | || ||| | | ||||||||||||||| || ||||||||||| || || ||||| || || || ||||||||||||| || || |||
gtatgtttttgtcatgttgatttacctttcttgctttattactgaaatgataagcatcccagcactttaatct-ttttcttttttttttctgtatttttgctttcctttcttttt-tgtcaatttagGTACTTCAGAGTTCTTGTCAGTATGGACATGAGCCTACATTCAATGGAAGTCGTTAACAGGCTTACTACAGCGGTTGAACTTCCCACCGAATTTGTACAC
upper sequence: AT5G18420.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ16277 (Selaginella moellendorffii), 3'ss of exon 4
gtaagtcatcaccttattggttccaccatttactttcgaccaaaattataacttttaaagtgggaatctaagaatgcttcttcagCTATTATGAAGCTCTAGGAAATATGGACATGAGCCTGCACTCAATGGAAGTTGTGAATAGGCTCACAACTGCAGTTGAACTTCCCAAGGACTTCATACGG
| ||| | | | |||| || | | | | || | |||| ||| |||| | || || | || |||||||||||||||||||| |||||||| || ||| | || ||||| || || | | || || | || |
-------------------------gtaagtacgtctg-tggagattacaagctgtttatctcgcttcg------gtttctacagGTATTTCAACGCGCTTGTAAGCATGGACATGAGCCTGCACTCCATGGAAGTCGTCAATCGCCTGACAACGGCCGTGCAGATCCCTGTCGAATATATCCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactttcgaccaaaattataacttttaaagtgggaatctaagaatgcttcttcagCTATTATGAAGCTCTAGGAAATATGGACATGAGCCTGCACTCAATGGAAGTTGTGAATAGGCTCACAACTGCAGTTGAACTTCCCAAGGACTTCATACGG
ttataac putative branch site (score: 2)
tgcttcttc putative PPT
aaaattataactttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtcatcaccttattggttccaccatttactttcgaccaaaattataacttttaaagtgggaatctaagaatgcttcttcagCTATTATGAAGCTCTAGGAAATATGGACATGAGCCTGCACTCAATGGAAGTTGTGAATAGGCTCACAACTGCAGTTGAACTTCCCAAGGACTTCATACGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG