Sequence
atgc intronic sequence ATGC exonic sequencegttcggcttggattatctgtgtttaatcttagtatgtttacgtagaattaaatctagtagataacaagagaaaacctttttgttaaatgccgttaagGTTTTGGATCCTCTAAGAGCTATGGTTGCCGGTTCTCCTCTTGAAGATGCTCGTCATCTTGCTCAACGTTACAGCCGCATGAGACAAGAAGCAGAGACAC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G18060.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G18060.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os07g32460.1 (Oryza sativa), 3'ss of exon 4
gttcggcttggattatctgtgttta--atcttagtatgttta-cgtagaattaaatct--agtagataacaagagaaaacctttttgttaaatgccgttaagGTTTTGGATCCTCTAAGAGCTATGGTTGCCGGTTCTCCTCTTGAAGATGCTCGTCATCTTGCTCAACGTTACAGCCGCATGAGACAAGAAGCAGAGACAC
| | ||| |||| | | || | ||| || | || | | ||| || | | || | | | || | | | || || || | | ||||| | || ||||||| ||| || |||| || |||||||||||| |||||| |||||||| ||||| |||||||| ||||| |||| |
--tagccttcaattaaagatctctagaaatttaagatctgtagtattgcattggtccttcaatgtattttacaaatatacttccatttattttgaatttcagACTATAGATCCATTGAGGGCTATGGCTGCAGGCGCTCCCCTGGAAGATGCTCGTGGTCTTGCACAACGTTATAGCCGGATGAGACATGAAGCTGAGATCC
upper sequence: AT4G18060.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G29700.2 (Glycine max), 3'ss of exon 4
---gttcgg----cttggattatctgtgtttaatcttagtatgtttacgtagaattaaatctagtagataacaagagaaaacctttttgttaaatgccgttaagGTTTTGGATCCTCTAAGAGCTATGGTTGCCGGTTCTCCTCTTGAAGATGCTCGTCATCTTGCTCAACGTTACAGCCGCATGAGACAAGAAGCAGAGACAC
|| || || | | | |||| ||| ||| | | || |||||| || || || || || | | ||| | | |||| ||||||||| | ||| ||| | ||| |||| | || |||||||| |||||||||||||| || || || |||||||||||||||||| |||
gacatttggaatcctaaagggaggtcaatgtaat-ttattatttgcat-tatctttaaatgtataaggaaagaaacatgaatccaatagtttcaatt--tccagGTATTGGATCCTTTGAGACAAATGATCAATGGTGTTCCTTTGGAGGATGCTCGCCATCTTGCTCAACGATATAGTCGGATGAGACAAGAAGCAGAGGCAC
upper sequence: AT4G18060.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G12810.1 (Glycine max), 3'ss of exon 4
---gttcgg----cttggattatctgtgtttaatcttagtatgtttacgtagaattaaatctagtagataacaagagaaaacctttttgttaaatgccgttaagGTTTTGGATCCTCTAAGAGCTATGGTTGCCGGTTCTCCTCTTGAAGATGCTCGTCATCTTGCTCAACGTTACAGCCGCATGAGACAAGAAGCAGAGACAC
|| || ||| | | | | |||| ||| ||| | || ||| || || || | || || || | | ||| | | |||| ||||||||| | ||| ||| | ||| |||| | || |||||||| |||||||||||||| || || || |||||||||||||||||| |||
gacatttggaatccttaagggagatctatgtaat-ttattattcgcat-tatctttacatgtataaggggagaaaagtgaatccaatggtttcaatt--tccagGTATTGGATCCTTTGAGACAAATGATCAATGGTGTTCCTTTGGAGGATGCTCGCCATCTTGCTCAACGATATAGTCGGATGAGACAAGAAGCAGAGGCAC
upper sequence: AT4G18060.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv10s0003g02590.t01 (Vitis vinifera), 3'ss of exon 4
gttcggcttgga---ttatctgtgttt-aatcttagtatgtttacgtagaattaaatctagtagataacaagagaaaacctttttgtt---aaatgccgttaagGTTTTGGATCCTCTAAGAGCTATGGTTGCCGGTTCTCCTCTTGAAGATGCTCGTCATCTTGCTCAACGTTACAGCCGCATGAGACAAGAAGCAGAGACAC
||| | | || ||||| || ||| || || | || || || || | | | | | | | |||||||| | || || || |||| |||||| | ||||| ||||| | ||| ||||| | |||||||| |||||||| ||||||||||| ||||| |||||||| ||||| |||||||
-ttctaaaggaacctttttctgttttccaatttttgt-taactaattaagatagaagc-attgattcctcaaacattttttttttgtttttatatatt-ttcagATTTTAGATCCTTTGAGAGCAATGGTCACTGGTGCTCCTTTGGAAGATGCCCGTCATCTAGCTCAACGTTATAGCCGAATGAGACATGAAGCTGAGACACMapped 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|86058789|gb|DR354546.1|DR354546EST: AACATGTAGACAAAGAACAAGAAGACTTCAACAAGCTTTTGGCTTCTCAG GTTTTGGATCCTCTAAGAGCTATGGTTGCCGGTTCTCCTCTTGAAGATGCT
genomic: AACATGTAGACAAAGAACAAGAAGACTTCAACAAGCTTTTGGCTTCTCAGgttcggcttg ... tgccgttaagGTTTTGGATCCTCTAAGAGCTATGGTTGCCGGTTCTCCTCTTGAAGATGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagaattaaatctagtagataacaagagaaaacctttttgttaaatgccgttaagGTTTTGGATCCTCTAAGAGCTATGGTTGCCGGTTCTCCTCTTGAAGATGCTCGTCATCTTGCTCAACGTTACAGCCGCATGAGACAAGAAGCAGAGACAC
agataac putative branch site (score: 3)
tttttgttaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcggcttggattatctgtgtttaatcttagtatgtttacgtagaattaaatctagtagataacaagagaaaacctttttgttaaatgccgttaagGTTTTGGATCCTCTAAGAGCTATGGTTGCCGGTTCTCCTCTTGAAGATGCTCGTCATCTTGCTCAACGTTACAGCCGCATGAGACAAGAAGCAGAGACAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC