Sequence
atgc intronic sequence ATGC exonic sequencegtattcaacaagaaccatattcttctgttatgtaaaatgttatgtgtctagattttgactcagctatccgttgcatgcttttcagGGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G08850.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os11g01872.1 (Oryza sativa), 3'ss of exon 7
gtattcaacaagaaccat-attcttctgttatgtaaaatgttatgtgtctagattttgactcagctatccgttgcatgcttttcagGGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAG
||| | | | |||||| | || | | | | || | || | | | | ||| | ||| ||||||||||||||||||||||| || ||||| |||||| ||||||| ||| | || || || | ||||||| |||
gtaattgatggcactagccattctttttatagtttagctacctcttctccattttct---ttaatt-tcctaaatttcaattttagGGATGCATGGGACATGGCTGCAGAGATCTGCCTTTCTAAGCTTCCTCAATTAATTGCTGATCCTAATGCAGAGTTTCAG
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os12g01922.1 (Oryza sativa), 3'ss of exon 8
gtattcaacaagaaccatattcttctgttatgtaaaatgttatgtgtctagattttgactcagctatccgttgcatgcttttcagGGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAG
||| | | | || | | | |||| | | ||| ||||| || | ||| | ||| ||||||||||||||||||||||| || ||||| |||||| ||||||| ||| | || || || | ||||||| |||
gtaattgatg-gcactagccattctttttatagtttagctacctcttctgcatttt--ctttaatttcctaaattttaattttagGGATGCATGGGACATGGCTGCAGAGATCTGCCTTTCTAAGCTTCCTCAATTAATTGCTGATCCTAATGCAGAGTTTCAG
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G048067_T02 (Zea mays), 3'ss of exon 8
gtattcaacaagaaccatattcttctgttatgtaaaatgttatgtgtctagattttgactcagctatccgttgcatgcttttcagGGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAG
||| ||| || | | || | || | || | | ||| | || | || |||| | |||||||||||||||||||||||||||| || || ||||| ||||||| || | || || |||| ||||||| |||
gtaactaacctgacttgttctttttt-ttgcattaactaccttttgtgtgatttgtaacat-gctaaa-----------tctcagGGATGCATGGGACATGGCTGCTGAGATTTGCCTTTCCAAGCTTCCTCAGTTAATTGCTGATCCAAATGCAGAGTTTCAG
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 8
gtatt--caacaagaaccatattcttctgttatgtaaaatgttatgtgtctagattttgact-cagct-at-ccgttgcatgcttttcagGGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAG
||||| | | | | | | || | ||| || ||| | |||||| | ||| | || || ||| | ||||||||||||||||||||||||||| |||| || ||||| ||||| | ||| ||| || | | || || |||
gtattgttggtgattatttttatgatatttttttctaaacgtgttgt---caaattttgtcaacagtttatgtttttatctgcactgcagGGATGCATGGGACATGGCTGCTGAGCTCTGCCTCTCTCAACTTCCGTCTTTAGTTGAGGATCCTAATGCTGAATTTCAG
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA18G44210.1 (Glycine max), 3'ss of exon 8
gtattcaacaagaaccatattcttctgttatgtaaaatgttatgtgtctagattttgact-cagctatccgttgcat--gcttttcagGGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAG
||||| || | || | | | | | ||| | | ||||| | ||| | || || || | ||||||||||||||||||||||||||| |||| || ||||| ||||| | ||| ||| || | | || || |||
gtattgttggtgattattgttatgataatttttttctaaacgtgttgccaacttttgtcaacagtttatgtttttatccgcactgcagGGATGCATGGGACATGGCTGCTGAGCTCTGCCTCTCTCAACTTCCATCTTTAGTTGAGGATCCTAATTCTGAATTTCAG
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 8
gtattcaacaagaaccatattcttctg-ttatgtaaaatgttatgtgtctagattttgactcagctatccgt-tgcatgcttttcagGGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAG
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gtacctactggaaatactagataagtaattttgttaagtgttcaataatccatttgtctcataatgtgccatgcatgtgtgctatagGGATGCATGGGACATGGCTGCTGAAATCTGCCTTTCTCAGCTTAAGTCATTGGTTGATGATCCCAATGCAGAGTTTCAG
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S199_73V6.1 (Physcomitrella patens), 3'ss of exon 8
--------------------------------------------------------------------------------------------gtattcaa--caagaaccatattct--tctgttatgtaaa-------atgttatgtgtctagattttgactca------gctatccgttgcatgctttt-cagGGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAG
|| || | | ||| || | || | | | || || | | | | || || || | | || || ||||||| |||| |||||||||| |||||||||||||| |||||||| ||| | || | | || || |||| | ||||| |||
gtacgcttgttctctcatactttcttgcttcctccttttcattcccccttttcttgaaatatattttcctctttacctctctcggtctttttgtgtttaggttatgaagaatttcctaatttataatacgaatgaaattgcttcgtctacccgaatcttctctgatagaacacattctgtgtgttgcttttgcagGCATGCATGGGATATGGCTGCTGAAATTTGTCTTTCACAGTTGCCTGCATTGGTGGATGATCCAAATGCTGAGTTTCAG
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S124_156V6.1 (Physcomitrella patens), 3'ss of exon 8
----------gtattcaacaagaaccatattcttctgttatgtaaaatgttatgtgtctagattt--tgactcagctatccgttgcatgctttt----cagGGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAG
| | || | ||| || | || | || | | | ||| ||| | | | ||| ||| |||| |||| | |||||||| |||||||||||||| |||||||| ||||| || | | | ||| |||| | || || ||
ttccttcattgaagcatcttgaaaatgtcatctaatgcaacagaataccttttccaccaaattttcctgatgta-ccacattttgtatgtttttttcgcagGCACGCATGGGATATGGCTGCTGAAATTTGTCTTTCGCAGCTGCCTGCATTGCTAGAGGATCCAACTATTGAATTTCATMapped 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|116411083|gb|EG453675.1|EG453675EST: AATCCAATATCTCACCCTATGCTGCCTCCTACGCATCAACATCATATGTG GGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACT
genomic: AATCCAATATCTCACCCTATGCTGCCTCCTACGCATCAACATCATATGTGgtattcaaca ... tgcttttcagGGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACT
EST:
gi|116411080|gb|EG453672.1|EG453672EST: AATCCAATATCTCACCCTATGCTGCCTCCTACGCATCAACATCATATGTG GGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACT
genomic: AATCCAATATCTCACCCTATGCTGCCTCCTACGCATCAACATCATATGTGgtattcaaca ... tgcttttcagGGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtaaaatgttatgtgtctagattttgactcagctatccgttgcatgcttttcagGGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAG
ttttgac putative branch site (score: 3)
tgcttttc putative PPT
aatgttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattcaacaagaaccatattcttctgttatgtaaaatgttatgtgtctagattttgactcagctatccgttgcatgcttttcagGGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT