Sequence
atgc intronic sequence ATGC exonic sequencegtataaaatgagttttaacactatttctaaatcttttgtaaccattttctatatgttaatgaggtgttttgtgtgttgattagGGACACGATATCCTAATGGCGACAATGCTGAATGGAGCAGCGATTATGGATGGTGCTTTACTAATCATTGCTGCGAATGAGACATGTCCACAACCACAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G18720.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G18720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G117900_T02 (Zea mays), 3'ss of exon 5
-------------------gtataaaatgagttttaacactatttctaaatcttttgtaaccattttctatatgttaatgaggtgttttgtgtgttgattagGGACACGATATCCTAATGGCGACAATGCTGAATGGAGCAGCGATTATGGATGGTGCTTTACTAATCATTGCTGCGAATGAGACATGTCCACAACCACAAA
| | | || ||| | | | | || | | | || | | | |||||| | | |||| ||||||||||| || || ||||| |||||||| |||||||| || || |||||||| ||| | || | || || || ||||| | |||||||| || || |
aaaatggttatcttaatttctttgacatttcatttgatattgatc--aattatgatatagaaaataattgtatgtttcaacaatacctatctccttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCTCTTCTTTTGATCGCAGCAAATGAAAGTTGTCCACAGCCTCAGA
upper sequence: AT2G18720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G107654_T01 (Zea mays), 3'ss of exon 5
gtataaa-atgagttttaaca----ctatttc--taaatcttt-tgtaaccattttctatatgttaatgaggtgttt---------tgtgtgttgattagGGACACGATATCCTAATGGCGACAATGCTGAATGGAGCAGCGATTATGGATGGTGCTTTACTAATCATTGCTGCGAATGAGACATGTCCACAACCACAAA
| |||| | |||| |||| |||| || | ||| || | | | | |||| ||||| | | |||| ||||||||||| || || ||||| |||||||| |||||||| || || |||||||| ||| | || | || || || ||||| | |||||||| || || |
gaataattgtatgtttcaacaacacctatctccttgaatagagatgaatttgtctaacaggaaataattgtatgtttaacaatacctattccttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCTCTTCTTTTGATCGCAGCAAATGAAAGTTGTCCACAGCCCCAGA
upper sequence: AT2G18720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G40750.1 (Glycine max), 3'ss of exon 5
gtataaa-atgagttttaacactatttctaaatcttttg-taaccattttctatatgttaatg---aggtgttttgtgtgttgatt--------------agGGACACGATATCCTAATGGCGACAATGCTGAATGGAGCAGCGATTATGGATGGTGCTTTACTAATCATTGCTGCGAATGAGACATGTCCACAACCACAAA
|||| | || || | | | | ||||||| || | ||||| | | | || | ||| | | ||| || | | ||||||| ||||| || ||||| |||||||| ||||||||||| || |||||||| ||||| ||| |||||||||| ||||| | || |||||||||||||
--ataattacaggtcttcaatcaaatgctaaatcattgaacatatattttttttgttttgacatctgtgtgatatttgtttttacttttccaatttctgcagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCTTTGCTACTCATTGCTGCCAATGAAAGCTGCCCACAACCACAAA
upper sequence: AT2G18720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G18240.1 (Glycine max), 3'ss of exon 5
----------gtataaaatgagttttaacac-----tatttctaaatcttttgt--aaccattttctatatgttaatgaggtgttttgtgtgttgattagGGACACGATATCCTAATGGCGACAATGCTGAATGGAGCAGCGATTATGGATGGTGCTTTACTAATCATTGCTGCGAATGAGACATGTCCACAACCACAAA
||| | |||| | | || || | ||| | || | || |||| | |||| || |||||||| ||||| || ||||| |||||||| ||||||||||| || |||||||| || || ||| |||| ||||| ||||| | || |||||||||||||
ttccatatttttatgagtatcctttttataagcaggtaattacaggtctccaatcaaatgctaaatcatttgtttgtttttacttttccaatttctgtagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCGTTGCTACTCATAGCTGCTAATGAAAGCTGCCCACAACCACAAA
upper sequence: AT2G18720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv13s0074g00310.t01 (Vitis vinifera), 3'ss of exon 5
gtataaaatgagttttaacactat---ttctaaatcttttgtaaccattttctatatgttaatgaggtgttttgtgtgttgatt----------------agGGACACGATATCCTAATGGCGACAATGCTGAATGGAGCAGCGATTATGGATGGTGCTTTACTAATCATTGCTGCGAATGAGACATGTCCACAACCACAAA
|| | | | ||||| | | | | ||| | | | || | | | | | || |||| ||| || || |||| || ||||| || ||||| |||||||| ||||||||||| ||||||||||| || ||||| | || ||||| || || | |||||||| || ||||
ctaaagacttgactttaaggttctggatgtccaggcttatatgcctggttg--agagtccagtaaagttttttatgtttttctttttcatttttcaatctagGGTCATGATATTCTCATGGCTACAATGCTTAATGGAGCAGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAACGAAAGCTGTCCACAGCCGCAAA
upper sequence: AT2G18720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv10s0042g01220.t01 (Vitis vinifera), 3'ss of exon 4
--------gtataaaat---gagttttaacact---atttctaaatcttttgt--aaccattttctatatgttaatgaggtgttttgtgtgttgat-tagGGACACGATATCCTAATGGCGACAATGCTGAATGGAGCAGCGATTATGGATGGTGCTTTACTAATCATTGCTGCGAATGAGACATGTCCACAACCACAAA
| ||| || | | | | | || || ||| ||| | ||||| | | | | | | ||| | | || ||||| || ||||| || ||||| |||||||| |||||||| || ||||||||||| || ||||| | || ||||| ||||| | |||||||| || ||||
gaaggtggctttaagattctggatgtccaggcctaaatgcctgggtctactgtctagtgattttttttttatgtttttcttttttcatcttcccatctagGGGCATGATATTCTCATGGCTACAATGCTTAATGGAGCGGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAATGAAAGCTGTCCACAGCCGCAAA
upper sequence: AT2G18720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S207_94V6.1 (Physcomitrella patens), 3'ss of exon 4
------------------gtataaaatgagttttaacactatttctaaatcttttgtaaccattttctatatgttaatgaggtgttt-tgtgtgttgattagGGACACGATATCCTAATGGCGACAATGCTGAATGGAGCAGCGATTATGGATGGTGCTTTACTAATCATTGCTGCGAATGAGACATGTCCACAACCACAAA
||| |||| | | | | | | ||| |||| || | | ||| ||||| ||| |||| ||||||||||||| || ||||| || ||||| |||||||| || |||||||||||||||||||| | ||||| ||||||| || || || || ||||
aattcgactacacacatcacttaatctgagggcttatgggaagcggtactttcgtgttcttgtttttaatccgg-attgaaatgtttgtgtttgtttgc-agGGACACGATATTCTCATGGCTACTATGCTTAATGGAGCTGCTATTATGGATGGTGCTTTACTTTTGATTGCCAGCAATGAGAGTTGCCCCCAGCCCCAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatcttttgtaaccattttctatatgttaatgaggtgttttgtgtgttgattagGGACACGATATCCTAATGGCGACAATGCTGAATGGAGCAGCGATTATGGATGGTGCTTTACTAATCATTGCTGCGAATGAGACATGTCCACAACCACAAA
attttctatatgttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataaaatgagttttaacactatttctaaatcttttgtaaccattttctatatgttaatgaggtgttttgtgtgttgattagGGACACGATATCCTAATGGCGACAATGCTGAATGGAGCAGCGATTATGGATGGTGCTTTACTAATCATTGCTGCGAATGAGACATGTCCACAACCACAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC