Sequence
atgc intronic sequence ATGC exonic sequencegtattgagttttacaatgctcttccatggaaacgttgaaccaattcttctatgtgatattttttattatttttgtgatagGTACTCTCTGTTGTTGGGATTCTTCAAGATGAAGTGGATCCAATGGTGTCTGTGATGAAAGTGGAGAAGGCTCCTTTGGAGTCATATGCTGACATTGGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G20140.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os07g49150.1 (Oryza sativa), 3'ss of exon 1
-----------------gtattgagttttacaat-gctcttccatggaaacgttgaaccaattcttctatgtgatattttttattatttttgtgat---agGTACTCTCTGTTGTTGGGATTCTTCAAGATGAAGTGGATCCAATGGTGTCTGTGATGAAAGTGGAGAAGGCTCCTTTGGAGTCATATGCTGACATTGGAG
| | ||| ||| | | |||||| | | | | |||| | | || | | || | | | |||| || ||||| || || ||| | ||||||||||| ||||| ||||| |||||||||||||||||||| ||||| |||| || |||||||||||||| |
tatcattttcttatgatcgaataagtgactcaaccgtacatccatgtggctagtaattttaatgctcta-gcaagcttgctcactaaatccctatttccagGTTCTGTCTGTGGTCGGAATTTTGCAAGATGAAGTTGATCCTATGGTTTCTGTGATGAAAGTGGAGAAAGCTCCGCTGGAATCCTATGCTGACATTGGTG
upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 3'ss of exon 1
-----------------------gtattgagttt--tacaatgctcttccatggaaacgttgaaccaattcttctatgtgatattttttattatttttgtgatagGTACTCTCTGTTGTTGGGATTCTTCAAGATGAAGTGGATCCAATGGTGTCTGTGATGAAAGTGGAGAAGGCTCCTTTGGAGTCATATGCTGACATTGGAG
|||| | || | |||||||| | ||| || | || ||| | || || || |||| |||||||| ||||| ||| | |||||||| || || || ||||| ||||| |||||||| || ||||| ||||||||||| ||||| ||||| || |
cttataaccaatagttggctctactattaaacttgctcttatgctcttttttac-----ttgtgagaagttttttataaccaaacttgataaatcatttcttcagGTTCTCTCTGTGGTTGGAATTTTGCAAGATGAGGTTGACCCTATGGTTTCTGTCATGAAAGTTGAAAAGGCACCTTTGGAGTCTTATGCGGACATCGGTG
upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 1
-----------gtattgagttttacaatgctc--ttccatggaaacgttgaaccaattcttctatgtgatattttttatt-------atttttgtgatagGTACTCTCTGTTGTTGGGATTCTTCAAGATGAAGTGGATCCAATGGTGTCTGTGATGAAAGTGGAGAAGGCTCCTTTGGAGTCATATGCTGACATTGGAG
| ||| || | ||| | || |||| || |||| | || || ||| | || || |||| |||||||| ||||| || | ||||||||||| ||||| ||||| |||||||||||||| ||||| || |||||||| || |||||||||||||| |
tgtgctcaataaccatttgttgtaaattgcacgctttagtggattgttttgaccatcaggagaggttcatcttgtttgctcactcaaatgttcacttcagGTTCTCTCTGTGGTTGGTATATTGCAAGATGAAGTTGATCCTATGGTATCTGTGATGAAAGTTGAGAAAGCGCCTTTGGAATCTTATGCTGACATTGGTG
upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 1
--------------gtattgagttttacaatgc-tcttccatggaaacgttgaacc--aattcttctatgtgatattttttatt---atttttgtgatagGTACTCTCTGTTGTTGGGATTCTTCAAGATGAAGTGGATCCAATGGTGTCTGTGATGAAAGTGGAGAAGGCTCCTTTGGAGTCATATGCTGACATTGGAG
| ||| | | | | || ||| | | | ||| ||| | | | | || || ||| ||||| || || || ||||| ||| | ||||| ||||| ||||| ||||| |||||||||||||| || ||||| ||||||||||| |||||||||||||| |
aaaatcaatgctgctcctcaagtgatgtactctgtgttttatgtacttccttgatttgaatgcttatttagtaaacagcttggccaaatgtttcccttagGTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCTGTGATGAAAGTTGAAAAGGCACCTTTGGAGTCTTATGCTGACATTGGTG
upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G095593_T01 (Zea mays), 3'ss of exon 1
--------------------gtattgagttttacaatgctcttccatggaaacgttgaaccaattcttctatgtgatattttttattatttttgtgatagGTACTCTCTGTTGTTGGGATTCTTCAAGATGAAGTGGATCCAATGGTGTCTGTGATGAAAGTGGAGAAGGCTCCTTTGGAGTCATATGCTGACATTGGAG
|| || | | || | | | | | | | |||| | | | | | | ||| |||| || ||||| ||||| || | ||||||||||| ||||| ||||| |||||||||||||| ||||| || |||||||| || |||||||||||||| |
tttgttgcattgcacatgcattagtggaccgtttacaactggtaggggatagcaagccagcttgttttctcactcaaacagtcaaatgtttactcttcagGTTCTTTCTGTAGTTGGTATATTGCAAGATGAAGTTGATCCTATGGTATCTGTGATGAAAGTTGAGAAAGCACCTTTGGAATCTTATGCTGACATTGGTG
upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 1
---------gtattgagttttacaatgctcttccatggaaacgttgaaccaattcttct------atgtgatattttttattat------ttttgtgatagGTACTCTCTGTTGTTGGGATTCTTCAAGATGAAGTGGATCCAATGGTGTCTGTGATGAAAGTGGAGAAGGCTCCTTTGGAGTCATATGCTGACATTGGAG
||||| | | | || | ||||| ||| |||| || || | ||||| || | | ||||| ||||||||||||||| |||||||||||||||| ||||||||||| ||||| ||||| || || ||||| |||||||| ||||||||||| ||||| |
attgtttttgtatttgaatcagttgtcacttcttgtgttca-gttgatatgattagatgcaggaaatgtaatgcttctcattatgtcttgttctttactagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTTATGAAGGTCGAAAAGGCCCCTTTGGAATCATATGCTGATATTGGTG
upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 1
----------------------gtattgagttttacaatgctcttccatggaaacgttgaaccaattcttctatgtgatattttttattatttttgtgatagGTACTCTCTGTTGTTGGGATTCTTCAAGATGAAGTGGATCCAATGGTGTCTGTGATGAAAGTGGAGAAGGCTCCTTTGGAGTCATATGCTGACATTGGAG
| | || ||| ||| | || | ||| | | | |||| || | |||| ||||| | |||| || |||||||||||| |||||||||||||||| ||||||||||| ||||| ||||| || |||||||||||| |||| || |||||||||||||| |
tattcttcagaaccataatatgatctcgaatttgacataattgttgttcatgtggatagaagctgacgatgca-atgat-ttatgtattttttttttatcagGTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTCATGAAGGTTGAGAAGGCTCCTCTGGAATCTTATGCTGACATTGGTG
upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA19G35510.1 (Glycine max), 3'ss of exon 1
-----------gtattgagttttacaatgctcttccatggaaacgt--tgaaccaattcttcta-tgtgatattttttattat------ttttgtgatagGTACTCTCTGTTGTTGGGATTCTTCAAGATGAAGTGGATCCAATGGTGTCTGTGATGAAAGTGGAGAAGGCTCCTTTGGAGTCATATGCTGACATTGGAG
||||| || | || || || | | ||| || || | ||| || || |||| || || | | |||| ||||||||||||||| |||||||||||||||| ||||||||||| ||||| ||||| || || ||||| |||||||| ||||||||||| ||||| |
taattgtttttgtattaagatcagtcatctctttttgtgcagttgatatgattagatgctggaaatgtaatgcttcttatcatgtatggttctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTTATGAAGGTTGAAAAGGCACCTTTGGAATCATATGCTGATATTGGTG
upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G04920.1 (Glycine max), 3'ss of exon 1
----------------gtattgagttttacaatgctcttccatggaaacgttgaaccaattctt-ctatgtgatattt---tttattatttttgtgatagGTACTCTCTGTTGTTGGGATTCTTCAAGATGAAGTGGATCCAATGGTGTCTGTGATGAAAGTGGAGAAGGCTCCTTTGGAGTCATATGCTGACATTGGAG
|| | || || | ||| || || || | || | || ||| | | | ||||| | |||| || |||||||||||| |||||||||||||||| ||||||||||| ||||| ||||| || ||||| |||||| |||| || |||||||||||||| |
cataattgttgttttcttaattgaattggtcatatattggtgtggttcacgtggttagatgctggccatataatgtttatgtatggtttttttttatcagGTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTTATGAAGGTCGAGAAAGCTCCTCTGGAATCTTATGCTGACATTGGTG
upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G27200.1 (Glycine max), 3'ss of exon 1
---------------gtattgagttttacaatgctcttccatggaaacgttgaaccaattcttctatgtgatattttttattat------ttttgtgatagGTACTCTCTGTTGTTGGGATTCTTCAAGATGAAGTGGATCCA---ATGGTGTCTGTGATGAAAGTGGAGAAGGCTCCTTTGGAGTCATATGCTGACATTGGAG
|| || | | | | | | ||| |||| | ||| | | ||| |||| | || | | |||| ||||||||||||||| |||||||||||||||| |||||| ||||| ||||| ||||| || || ||||| |||||||| ||||||| ||| ||||
ttatgaatgattttggttatggatgatttttctcaacttctcgtttttgttatttcaatcttattat-tagtctttcttatcacatatggttctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCATTAATGGTCTCTGTTATGAAGGTTGAAAAGGCACCTTTGGAATCATATGTTGATATTG---
upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 1
----------------------gtattgagttttacaatgctcttccatggaaa-cgttgaaccaattcttctatgtgatattttttattatttttgtgatagGTACTCTCTGTTGTTGGGATTCTTCAAGATGAAGTGGATCCAATGGTGTCTGTGATGAAAGTGGAGAAGGCTCCTTTGGAGTCATATGCTGACATTGGAG
|||| | || | ||| |||| | | | | | || | | | || ||| | | | | | |||| || ||||||||||| |||| ||||| ||||| |||||||||||||| || |||||||| ||||||||||| ||||| |||||||||||||| ||||
tctgttttatagttatgcattcttattcacattgaagatgtagttccttcaccatcatagtttcaggaggttcttatattactttgtgctgtctc---gtcagGTTCTTTCTGTTGTTGGTCTTCTCCAAGACGAAGTTGATCCAATGGTGTCCGTAATGAAAGTTGAGAAGGCTCCATTGGAATCATATGCTGACATAGGAG
upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------gtattgagttttacaatgctcttccatggaaacgttgaacca------attcttctatgtgatattttttattatttttgtgatagGTACTCTCTGTTGTTGGGATTCTTCAAGATGAAGTGGATCCAATGGTGTCTGTGATGAAAGTGGAGAAGGCTCCTTTGGAGTCATATGCTGACATTGGAG
|| || | || | | | | | | | || | | || | ||| || ||| | ||||| |||| || || ||||| || | || |||||||| ||||| |||||||| ||||| |||||||| || || |||||| | |||||||||||||||||||| |
aagttagagtaactgattagtcctggcggtcacgaacatggtttgagttatcaccagatcatgggaaacttgtccaaacgattttctttgtc----ttgtg-cagGTCCTTTCAGTTGTGGGATTGCTGCAAGATGACGTGGACCCAATGGTTTCTGTTATGAAAGTTGAAAAAGCTCCTCTAGAGTCATATGCTGACATTGGTG
upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S12_207V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------gtattgagttttacaatgctcttccatggaaac-gttgaaccaattcttctatgtgatattttttattatt--tttgtgatagGTACTCTCTGTTGTTGGGATTCTTCAAGATGAAGTGGATCCAATGGTGTCTGTGATGAAAGTGGAGAAGGCTCCTTTGGAGTCATATGCTGACATTGGAG
| | | ||| | || | || |||| | | | | | || | | || || | | || |||||| |||| || || || |||||| | || |||||||| ||||| || |||||||| ||||||||||| || || |||||| | ||||||||||| || || || |
gcaagcatcgaaacttttctcaactaaattt--ctatttttctctatggctattgatagagtagttgagtggaggcaaatgattcacttttggtttgtg-cagGTCCTTTCAGTGGTTGGGTTGCTGCAAGATGACGTGGACCCTATGGTGTCAGTGATGAAAGTTGAAAAAGCTCCTCTAGAGTCATATGCCGATATCGGTGMapped 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|86040345|gb|DR336100.1|DR336100EST: GATAAGGATCAGCTTGAACCTGGCTGCTCTATTTTTGATGCATAAACAAG GTACTCTCTGTTGT
genomic: GATAAGGATCAGCTTGAACCTGGCTGCTCTATTTT-GATGCATAA-CAAGgtattgagtt ... tttgtgatagGTACTCTCTGTTGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atggaaacgttgaaccaattcttctatgtgatattttttattatttttgtgatagGTACTCTCTGTTGTTGGGATTCTTCAAGATGAAGTGGATCCAATGGTGTCTGTGATGAAAGTGGAGAAGGCTCCTTTGGAGTCATATGCTGACATTGGAG
ttttttattattttt CT-rich tract
aattcttctatgtgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattgagttttacaatgctcttccatggaaacgttgaaccaattcttctatgtgatattttttattatttttgtgatagGTACTCTCTGTTGTTGGGATTCTTCAAGATGAAGTGGATCCAATGGTGTCTGTGATGAAAGTGGAGAAGGCTCCTTTGGAGTCATATGCTGACATTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG