Sequence
atgc intronic sequence ATGC exonic sequencegtaagcatttccaaaaatcttgtcagaattatccataagtactctagaccaagaacctaaatgtttagtttttgactattgagcagGCGAAGGATTTGCACTAATTTCTGGCACAAGCATGGCTGCACCACACATTGCGGGTATTGCTGCTCTGGTGAAACAGAAGCATCCTCAATGGAGTCCAGC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G30020.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G30020.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os06g48650.2 (Oryza sativa), 3'ss of exon 8
----------------------------------------------------------------------------gtaagcatttccaaaaatcttgtcagaattatccataagtactctagaccaaga--------acctaa---atgtttagtttttgactattga----gcagGCGAAGGATTTGCACTAATTTCTGGCACAAGCATGGCTGCACCACACATTGCGGGTATTGCTGCTCTGGTGAAACAGAAGCATCCTCAATGGAGTCCAGC
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gtaagctttgctgtacttttatatcccttgaagcatacaaagctttttaagcatgttatggttgcattgaaattttccttgcatgtttgattgttctatgtgg-taattcatatggacgtttgtcaatcatgtggcttacctaaaatatatttctcttgtggcaatgcatattccagGGGAAGGATTTGCAATGGTTTCTGGAACTAGTATGGCTGCACCACATATTGCTGGTATCGCGGCACTAATAAAACAGAAGAACCCCAAGTGGAGTCCCTC
upper sequence: AT4G30020.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA17G06740.1 (Glycine max), 3'ss of exon 8
---gtaagcattt--ccaaaaat-cttgtcagaattatccataagtact--ctagaccaagaacctaaatgtttagtttttgactat------tgagcagGCGAAGGATTTGCACTAATTTCTGGCACAAGCATGGCTGCACCACACATTGCGGGTATTGCTGCTCTGGTGAAACAGAAGCATCCTCAATGGAGTCCAGC
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agaataattgcttgattaaggacgcgagggaggaaggtagaagaaaacttactaatatatttacataattgattcattttaagctattttgcttgtgcagGTGAAGCGTTTGCCATGATATCTGGAACCAGCATGGCTGCACCACATATAGCTGGAATTGCTGCTCTTATAAAGCAGAAGCATCCTCATTGGAGCCCTGC
upper sequence: AT4G30020.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA13G00580.1 (Glycine max), 3'ss of exon 8
------------------gtaagcatttccaaaaatcttgtcagaa-ttatccataagtactctagaccaagaacctaaatgtttagtttttgactattgagcagGCGAAGGATTTGCACTAATTTCTGGCACAAGCATGGCTGCACCACACATTGCGGGTATTGCTGCTCTGGTGAAACAGAAGCATCCTCAATGGAGTCCAGC
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gaataattgcatgattaaggagggagggacaaaggtagaagaaaaacttactgatatgttatatagttgattcattttaag---cagttttttgct--tgtgcagGTGAGGGGTTTGCCATGATATCTGGAACTAGCATGGCTGCACCACATATAGCTGGAATTGCTGCTCTCATAAAGCAGAAGCATCCTCATTGGAGCCCTGC
upper sequence: AT4G30020.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA15G17830.1 (Glycine max), 3'ss of exon 8
--gtaagcat-----ttccaaaa-------atcttgtcagaattatc--cat--aagtactctagaccaagaacctaaatgtttagtttttgactattgagcagGCGAAGGATTTGCACTAATTTCTGGCACAAGCATGGCTGCACCACACATTGCGGGTATTGCTGCTCTGGTGAAACAGAAGCATCCTCAATGGAGTCCAGC
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gaataagcacggaacttatagaagaaaaacacttgataaaagatatcatcatcaaaatactatagaatttga-tttatttaagcagtttttgc---ttgagcagGAGAGGGGTTTGCAATGATATCTGGGACTAGTATGGCTGCACCACATATAGCTGGAATTGCTGCTCTGATAAAGCAGAAACATCCACATTGGAGCCCTGCMapped 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|164228338|gb|EL986311.1|EL986311EST: GACGAGGCTAACTATATCG GCGAAGGATTTGCACTAATTTCTGGCACAAGCATGGCTGCACCACACATTG
genomic: GACGAGGCTAACTATATCGgtaagcattt ... tattgagcagGCGAAGGATTTGCACTAATTTCTGGCACAAGCATGGCTGCACCACACATTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccataagtactctagaccaagaacctaaatgtttagtttttgactattgagcagGCGAAGGATTTGCACTAATTTCTGGCACAAGCATGGCTGCACCACACATTGCGGGTATTGCTGCTCTGGTGAAACAGAAGCATCCTCAATGGAGTCCAGC
ttttgac putative branch site (score: 3)
taaatgtttagttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcatttccaaaaatcttgtcagaattatccataagtactctagaccaagaacctaaatgtttagtttttgactattgagcagGCGAAGGATTTGCACTAATTTCTGGCACAAGCATGGCTGCACCACACATTGCGGGTATTGCTGCTCTGGTGAAACAGAAGCATCCTCAATGGAGTCCAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC