Sequence
atgc intronic sequence ATGC exonic sequence...tgatcttaagcaattgcatgaagcactggtggtccagtatgctttagcggtaccatggctttaaaactacatttaacttggagttatgctgctgttgcagAAATGGTGATGCGTATGCTGGGGAGTATTTTGCAGACAAGATGCATGGTTTTGGAGTGTATCACTTTGCGAACGGGCATAAGTATGAAGGAGCTTGGCAC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G35170.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G35170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA17G15940.1 (Glycine max), 3'ss of exon 1
-tgatcttaagcaattg---catgaagcactggtggtccagtatgctttagcggtaccatggctttaaaactacatttaacttggagttatgctgctgttgcagAAATGGTGATGCGTATGCTGGGGAGTATTTTGCAGACAAGATGCATGGTTTTGGAGTGTATCACTTTGCGAACGGGCATAAGTATGAAGGAGCTTGGCAC
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ttacaaaagaacaattgtgacgggaaggtttgattttttaacaaatacgaaaagtatctc--ttttgagtgggtctttacacttattttatgtatcc--tgcagAAATGGGGACATATATGCTGGTGAATATTTTGCAGACAAGATGCATGGTTTTGGAGTGTATCAATTTCAGAATGGTCATCGGTATGAGGGGGCATGGCAT
upper sequence: AT2G35170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G05640.1 (Glycine max), 3'ss of exon 3
--tgatcttaagcaattgcat--gaagcactggtggtccagtatgctttagcggtaccatggctttaaaactacatttaacttggagttatgctgctgttgcagAAATGGTGATGCGTATGCTGGGGAGTATTTTGCAGACAAGATGCATGGTTTTGGAGTGTATCACTTTGCGAACGGGCATAAGTATGAAGGAGCTTGGCAC
| | |||||| | | | | | | | | ||| | ||| | |||| | ||||| | ||||||||||| || |||||||| || ||||||||||||||||||||||||||||||||
attacaaaagaacaattgtgatgggaaggtttatttttgaacaaatacaaaaagtatctc--ttttgagtgggtctttacaattattttatgta--tactgcagAAATGGGGACATATATGCTGGTGAATATTTTGCAGACAAGATGCATGGTTTTGGAGT-------------------------------------------
upper sequence: AT2G35170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv02s0012g00090.t01 (Vitis vinifera), 3'ss of exon 3
tgatcttaagcaattgcatgaagcactggtggtccagtatgctttagcggtaccatggctttaaaactacatttaacttggagtta--tgctgc----tgttgcagAAATGGTGATGCGTATGCTGGGGAGTATTTTGCAGACAAGATGCATGGTTTTGGAGTGTATCACTTTGCGAACGGGCATAAGTATGAAGGAGCTTGGCAC
| ||| || | ||| | || | | || || | | | | ||| | | || | || || || | | ||| | | |||||||||| || ||||||||| || |||||||| |||||||||||||||||||| || || | ||||| || || ||| || || ||||| |||
-ttttgtaatatatgttctccagcttttgtaatata-ta-gcagaaatgatgacttgggtgttaatgttttcttttctctgaccaagtttctgtaatatatagCAGAAATGGCGACATGTATGCTGGAGAATATTTTGCTGACAAGATGCATGGTTTTGGGGTATACCGATTTGCAAATGGACATCGATACGAGGGAGCCTGG---
upper sequence: AT2G35170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ10395 (Selaginella moellendorffii), 3'ss of exon 1
tgatcttaagcaattgcatgaagcactggtggtccagtatgctttagcggtaccatggctttaaaactacatttaacttggagttatgctgctgttgcagAAATGGTGATGCGTATGCTGGGGAGTATTTTGCAGACAAGATGCATGGTTTTGGAGTGTATCACTTTGCGAACGGGCATAAGTATGAAGGAGCTTGGCAC
||| |||| | || || | ||| | | | ||| | || ||| |||| ||| || |||||| | || ||||| ||||| || || |||||||||||||| | |||||| || ||||||||||||||||| ||| || || || ||||||
------------------------------------gtaagcttgatcgt--ccgag-----aaagtttcttccaacctttcttttggct-ttgttccagGAACGGTGATACTTACGCTGGCGAGTACTTCGCCGACAAGATGCATGGCTATGGAGTCTACCACTTTGCGAACGGGCACTTGTACGAGGGTGCCTGGCAC
upper sequence: AT2G35170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ19700 (Selaginella moellendorffii), 3'ss of exon 1
tgatcttaagcaattgcatgaagcactggtggtccagtatgctttagcggtaccatggctttaaaactacatttaacttggagttatgctgctgttgcagAAATGGTGATGCGTATGCTGGGGAGTATTTTGCAGACAAGATGCATGGTTTTGGAGTGTATCACTTTGCGAACGGGCATAAGTATGAAGGAGCTTGGCAC
||| |||| | || || | ||| | | | ||| | || || |||| ||| || |||||| | || ||||| ||||| || || |||||||||||||| | |||||| || ||||||||||||||||| ||| || || || ||||||
------------------------------------gtaagcttgatcgt--ccgag-----aaagtttcctccaaccttttcttttggctttgttccagGAACGGTGATACTTACGCTGGCGAGTACTTCGCCGACAAGATGCATGGCTATGGAGTCTACCACTTTGCGAACGGGCACTTGTACGAGGGTGCCTGGCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agcggtaccatggctttaaaactacatttaacttggagttatgctgctgttgcagAAATGGTGATGCGTATGCTGGGGAGTATTTTGCAGACAAGATGCATGGTTTTGGAGTGTATCACTTTGCGAACGGGCATAAGTATGAAGGAGCTTGGCAC
atttaac putative branch site (score: 3)
tttaaaactacattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgatcttaagcaattgcatgaagcactggtggtccagtatgctttagcggtaccatggctttaaaactacatttaacttggagttatgctgctgttgcagAAATGGTGATGCGTATGCTGGGGAGTATTTTGCAGACAAGATGCATGGTTTTGGAGTGTATCACTTTGCGAACGGGCATAAGTATGAAGGAGCTTGGCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - -aagcaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaacta