Sequence
atgc intronic sequence ATGC exonic sequencegtaaaatgcaattctctattttcttttttgcaaaagttgtctgattcacatattatgacaccacaacctgaggttaaaacggattattgctttctttgctgcagTATACTCCTGCCATTGATATATGGAGCATAGGATGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAGAATGTGGTGCACCAATTGG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G18040.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g45620.1 (Oryza sativa), 3'ss of exon 3
gtaaaatgcaattctctattttcttttttgcaaaagttgtctgattcacatattatgacaccacaacctgaggttaaaacggatta----ttgctttctttgctgcagTATACTCCTGCCATTGATATATGGAGCATAGGATGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAGAATGTGGTGCACCAATTGG
|||| || |||| | | || | || | || ||| || | | || || | | | || | | ||| ||||||| |||||||| |||||||| |||||| | || || |||||||| |||||||| | || |||||| | |||||||| ||||||||||| || |||||||
-----atgccatgctcttgaactatcgatacata---tgcttagcataccaatttggataatttcaaatgcacttgcaccatactaaactcaaatgtgttttttgcagTACACTCCTGCAATTGATATTTGGAGCGTCGGTTGTATATTTGCTGAAATGCTTATGGGAAAGCCACTTTTTCCTGGAAAGAATGTGGTACATCAATTGG
upper sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os05g50120.1 (Oryza sativa), 3'ss of exon 4
---------------------------------------------------------gtaaaatgcaattctctattttcttttttgcaaaagttgtctgattcacatattat----gacaccacaacctgaggttaaaacg-gattattgctttctt------tgctgcagTATACTCCTGCCATTGATATATGGAGCATAGGATGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAGAATGTGGTGCACCAATTGG
|| | | | || | | ||| | || | | || | | || || | |||| | | |||| | | | |||| | ||| | | ||||||| || ||||| |||||||| ||||| ||||||| ||||||||||| |||| || || |||||| | ||||| ||||| ||||| ||||| |||||||
gtaagggaatttccatttaacatggtgatggctatattattttttcttccaacattgttatattactatgatatgtttggatcaatgtagcaacagtgttttgagaatgttctcttagacattgtcgcattaggtgatatcttgatttatattttgtcattggcttttgcagTACACCCCTGCAATTGATATTTGGAGTGTAGGATGTATATTTGCAGAGCTGCTTACAGGAAAGCCACTCTTTCCAGGGAAAAATGTTGTGCATCAATTGG
upper sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G062761_T02 (Zea mays), 3'ss of exon 4
---gtaaaatgcaattctctattttcttttttgcaaaagttgtctgattcacatattatgacaccacaacctgaggttaaaacggattattgctttctttgctgcagTATACTCCTGCCATTGATATATGGAGCATAGGATGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAGAATGTGGTGCACCAATTGG
| || | | || | | |||| | | || || ||| ||| | | | | ||||| | || | | || || | ||||||| ||||||||||||||||| |||||| |||| || |||||||| ||| ||||||| ||||||||| | ||||| ||||||||||| ||||| || ||||
tacttgaacagtgtgtacatagtgtggagtttgatgtatcagcttgttttacaaatttt---atagaatcacaaggtt----ctgaatctggcattaacttttgcagTACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTTGCTGAATTGCTCACAGGGAAGCCACTCTTTCCAGGGAAGAATGTTGTGCATCAGTTGG
upper sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G375975_T01 (Zea mays), 3'ss of exon 3
---------------gtaaaatgcaattctctatt--ttcttttttgcaaaagttgtctgattcacatattatgacaccacaacctgaggttaaa---acggattattgctttctttgctgcagTATACTCCTGCCATTGATATATGGAGCATAGGATGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAGAATGTGGTGCACCAATTGG
| ||| | |||| | |||| |||| | | | | || | ||||||| | | | | || || ||| ||| ||| |||||||||||||||| |||||||| |||||| |||| || |||||||| |||||||| | |||||||| | |||||||| ||||||||||| || ||| |||
gtcggatagttttcacccggacacaact-tctactagctcttcattgctatatggttttttactgtttaagagtacaccacttcattttgctgaatttacaacttaacacttaattt--tgcagTATACTCCTGCGATTGATATCTGGAGCCTAGGTTGTATATTTGCTGAAATGCTTATAGGGAAGCCTCTCTTTCCTGGCAAGAATGTGGTACATCAACTGG
upper sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G05700.1 (Glycine max), 3'ss of exon 4
gtaaaatgcaattctctattttcttttttgcaaaagttg--tctgattcacatattatgaca----ccacaacctgaggttaaaacggatt-----attgctttctttgctgcagTATACTCCTGCCATTGATATATGGAGCATAGGATGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAGAATGTGGTGCACCAATTGG
|||| | | | | | || | | ||| | |||| | | ||| | | | ||| ||| | | | | | ||| |||| || ||||||| ||||| || |||||||| |||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||||||||||||
gtaagtttcttcttttttttaacatcttttcttgggttgaatataatttaagcaattgaacatacttggtgtattgaaatatgcatgtaattttaaatttatttcctttttgcagTACACTCCAGCAATTGATATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAAAATGTTGTGCACCAATTGG
upper sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G30790.1 (Glycine max), 3'ss of exon 4
gtaaaatgcaattctctattttcttttttgcaaaagttgtctgattcacata--ttatgacaccacaacctgaggttaaaacggattattg---ctttctttgctgcagTATACTCCTGCCATTGATATATGGAGCATAGGATGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAGAATGTGGTGCACCAATTGG
| || || || | | | ||| ||||| | | | | | | | | || | | | | | || | | |||||||||| ||||| |||||||| |||||||| ||||||||||||||||||||||||| ||||||||||||||||||||| || ||||| |||||||||||||
---------cctcttcaatcctcctctaccgggattgtgtatgatttatgaagttgaatatatttaagtattgcactagtgtgtaatttcaaatccttgtcttttgcagTATACGCCTGCAATTGATATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG
upper sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G33980.1 (Glycine max), 3'ss of exon 4
gtaaaatgcaattctct------attttctt---ttttgcaaaagttgtctgattca-catattatgacaccacaacctgaggttaaaacggattattgctttctttgctgcagTATACTCCTGCCATTGATATATGGAGCATAGGATGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAGAATGTGGTGCACCAATTGG
|||| | | |||| | |||||||| || | | || | ||| | ||| | ||| | | | | | || ||| |||| || ||||||| || ||||| |||||||| |||||||| || ||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||||||||||||
gtaagcttcttttcttttaacatattttcttgggttctatataatataagcaattgaacatgct-tgatatattgaattatgcatgcaattttaaatttatttcctttttgcagTACACCCCTGCAATTGATATTTGGAGCATTGGGTGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAAAATGTTGTGCACCAATTGG
upper sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G11470.1 (Glycine max), 3'ss of exon 4
gtaaaatgcaattctctattttcttttttgcaaaagttgtctga---ttcacatattatgacaccacaacctgaggttaaaacggattattgctttctttgctgcagTATACTCCTGCCATTGATATATGGAGCATAGGATGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAGAATGTGGTGCACCAATTGG
| |||| ||| | | ||| | | | | ||| | | ||||| | || | | | | | | || | | |||||||||| || || ||||| || |||||||| ||||||||||||||||||||||||| ||||||||||||||||||||| || ||||| |||||||||||||
---ctcttcaatcctcctctaccaggattgtgtatgatttatgaagttgaatatatttaagtattgcagtacgtgtacgatttcaaat----ccttgtcttttgcagTATACCCCCGCAATTGACATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG
upper sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv01s0011g04920.t01 (Vitis vinifera), 3'ss of exon 4
gtaaaatgcaattctctattttcttttttgcaaaagttgtctgattcacatattatgacaccacaacctgaggttaaaacggat-tattgctttc--tttgctgcagTATACTCCTGCCATTGATATATGGAGCATAGGATGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAGAATGTGGTGCACCAATTGG
|| || | | | ||| | || ||| || | | ||| ||| | | || | || |||| | | | | || ||||| | | ||||||| || ||||| |||||||| |||||||||||||| |||||||| |||||||| ||||| ||||| ||||||||||| || |||||||| || |||||||
gttttatactaatatctgtgttatttatttcga---ttgaactgatcatacaccataatccc----tctgaaatggtacagtttctaaagcttttcatcttttgcagTACACCCCTGCTATTGATATTTGGAGCATAGGATGTATATTTGCGGAAATGCTTACTGGAAAGCCCTTGTTTCCTGGTAAAAATGTGGTCCAGCAATTGG
upper sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 4
-gtaaaatgcaattctctattttcttttttgcaaaagttgtctg-attcacatattatgacaccacaacctgaggttaaaacggattattgctttctttgctgcagTATACTCCTGCCATTGATATATGGAGCATAGGATGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAGAATGTGGTGCACCAATTGG
| ||| ||| | | | | ||| |||| || || | | | | |||| | || | | | || | | | | || || ||||| |||||||| |||||||| |||||||||||||||||||||||||||||||| || || || || ||||||| ||||| ||||| |||||||| ||||
cttttgatgaaata-tgacctctttggtttataaaatttaagtggagttatgttttattaaactatatatcaaatttcttaaaaccttctccattttt-----cagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG
upper sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S80_71V6.2 (Physcomitrella patens), 3'ss of exon 4
gtaaaatgcaattctctattttcttttttgcaa----aagttgtctgattcacat-attat-gacaccacaacct---------gaggttaaaacggattattgctttctttgctgcagTATACTCCTGCCATTGATATATGGAGCATAGGATGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAGAATGTGGTGCACCAATTGG
|| | ||| | | || || | | || | || | ||| || || |||| | | ||| | | | |||| |||||| | | | ||||||||||||||||||| || ||||| ||||| ||||| || |||||||| ||| || | ||||| ||||| | |||||||| |||||||| || || ||| |||
gtgagcagcactagtacccttcgttctattgaactttatgtactgtgacgcaaattgttattaagaacacgttttttgtgtggtgtgactaaataagattat-gttacttgtgctgcagTATACTCCTGCGATCGATATCTGGAGTATAGGCTGTATATTTGCGGAAGTGTTGACTGGAAAGCCGCTTTTTCCTGGAAAGAATGTCGTTCATCAACTGG
upper sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 4
gtaaaatgcaattctctattttcttttttgcaaaagttgtctgattcacatattat--gacaccaca-acctgaggttaaaacgga----------ttattgctttctttgctgcagTATACTCCTGCCATTGATATATGGAGCATAGGATGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAGAATGTGGTGCACCAATTGG
|||| | | | | || | | | | || | | |||| |||| | | ||| | || | | | || |||| | | ||| | |||||||||||||| || ||||| ||||| ||||| || |||||||| ||| || | || || |||||| | || |||||||||||||| || || || |||
gtaacac-tagtgcgct-ctcgttcagtggaggtcgtggaccatgacacaagttattgggtagaacatatttgtgagtgattttgaataagtgttgttatgtcccttttttttacagTATACTCCTGCGATCGATATCTGGAGTATAGGCTGTATATTTGCGGAAGTGTTGACCGGAAAGCCACTTTTCCCTGGGAAGAATGTTGTTCATCAGCTGG
upper sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ26549 (Selaginella moellendorffii), 3'ss of exon 4
gtaaaatgcaattctctattttcttttttgcaaaagttgtctgattcacatattatgacaccacaacctgaggttaaaacggattattgctttctttgctgcagTATACTCCTGCCATTGATATATGGAGCATAGGATGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAGAATGTGGTGCACCAATTGG
|| | || | | | || ||| | || | |||| ||||||||||||| || || || ||||||||||| || ||||||||||| || | ||||| |||||||| |||||||||| ||||| || || || | |
-------------------------------------------------gtaagaggatattggttcatttttttctgacgc-caagtgatctcttgtatgcagTATACTCCAGCAATCGACATATGGAGCATTGGTTGCATATTTGCTGAGACAATCACTCGGAAGCCACTGTTTCCTGGAAAGAACGTTACTCATCAGCTCGMapped 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|163976858|gb|ES086288.1|ES086288EST: GATGGTACCGTGCGCCAGAACTTTGTGGCTCTTTCTTCTCCAAA TATACTCCTGCCATTGATATATGGAGCATAGGATGCATATT
genomic: GATGGTACCGTGCGCCAGAACTTTGTGGCTCTTTCTTCTCCAAAgtaaaatgca ... tttgctgcagTATACTCCTGCCATTGATATATGGAGCATAGGATGCATATT
EST:
gi|164028430|gb|ES106285.1|ES106285EST: GATGGTACCGTTGCGCCAGAACTTTGTGGCTCTTTCTTCTCCAAA TATACTCCTGCCATTGATATATGGAGCATAGGATGCATATT
genomic: GATGGTACCG-TGCGCCAGAACTTTGTGGCTCTTTCTTCTCCAAAgtaaaatgca ... tttgctgcagTATACTCCTGCCATTGATATATGGAGCATAGGATGCATATT
EST:
gi|124952886|gb|EL028121.1|EL028121EST: CTTTGTGGCTCTTTCTTCTCCAAA TATACTCCTGCCATTGATATATGGAGCATAGGATGCATATTTGCAGAAATG
genomic: CTTTGTGGCTCTTTCTTCTCCAAAgtaaaatgca ... tttgctgcagTATACTCCTGCCATTGATATATGGAGCATAGGATGCATATTTGCAGAAATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atattatgacaccacaacctgaggttaaaacggattattgctttctttgctgcagTATACTCCTGCCATTGATATATGGAGCATAGGATGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAGAATGTGGTGCACCAATTGG
ttattgctttcttt CT-rich tract
ttaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaatgcaattctctattttcttttttgcaaaagttgtctgattcacatattatgacaccacaacctgaggttaaaacggattattgctttctttgctgcagTATACTCCTGCCATTGATATATGGAGCATAGGATGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAGAATGTGGTGCACCAATTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA