Sequence
atgc intronic sequence ATGC exonic sequenceTGATGACAGTAAACTTCACGTCATTCACTACACTCTAGGCCCTCTTAAGCCTTGGGACTGGTGGACAGCATGGCTCGTGAAACCTGTTGATGCTTGGCATgtaggtcttcttcttcactatgatttttaggtttctattgagtgaatttctctaagtctgatttcaccgtgaacaattgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G18480.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G18480.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os02g41520.1 (Oryza sativa), 5'ss of exon 5
TGATGACAGTAAACTTCACGTCATTCACTACACTCTAGGCCCTCTTAAGCCTTGGGACTGGTGGACAGCATGGCTCGTGAAACCTGTTGATGCTTGGCATgtaggtcttcttcttcactatgatttt--taggtttctattgagtgaatttctctaagtctgatttcaccgtgaacaattgcag
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TGATGAGAAAGAACTTAGGGTCATTCACTACACACTTGGGCCTCTTAAGCCCTGGGACTGGTGGACTGCTTGGCTTGTTAAACCTGTGGCAGTATGGCAGgtaattaggtatttcttgtgtgattttagtgggatgtgaagtagcagaatggctcaa-tgaacttgtgttatccattgttgcag
upper sequence: AT5G18480.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA20G37000.1 (Glycine max), 5'ss of exon 5
TGATGACAGTAAACTTCACGTCATTCACTACACTCTAGGCCCTCTTAAGCCTTGGGACTGGTGGACAGCATGGCTCGTGAAACCTGTTGATGCTTGGCATgta----------ggtcttct-tcttcactatgatttttaggtttctattgagtgaatttctctaagtctgatttcaccgtgaacaattgcag-------------------------------------------------------------
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GGATGAGAACGAACTCCGTGTAATTCATTATACACTAGGCCCTCTTAAGCCTTGGGACTGGTGGACATCTTGGCTTGTGAAACCTGTTGATGTCTGGCAGgtatttgtgcattattattctattttagcaatatctcaaaaatttgtcttccagtaattttttaaaaggccatcttgct-tgagtagtcatgtgactaagttgaagtttgtgataaatgttaaataatttgcttttaccttgtttgtgctgcag
upper sequence: AT5G18480.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA10G30700.1 (Glycine max), 5'ss of exon 7
-TGATGACAGTAAACTTCACGTCATTCACTACACTCTAGGCCCTCTTAAGCCTTGGGACTGGTGGACAGCATGGCTCGTGAAACCTGTTGATGCTTGGCATgtaggtcttcttcttcactatgatttttaggtttctattgagtgaatttctctaagtctgatttcaccgtgaacaattgcag-
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TGGATGAGAATGAACTCCGTGTAATTCATTATACACTAGGTCCTCTTAAGCCTTGGGACTGGTGGACATCTTGGCTTGTGAAACCTGTTGATGTCTG-----CAGgtatt---------tgtgcaacttattatcctattttagcaatatctcaaaaacttgtcttccagtaattttttaaaag
upper sequence: AT5G18480.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA03G40980.1 (Glycine max), 5'ss of exon 5
TGATGACAGTAAACTTCACGTCATTCACTACACTCTAGGCCCTCTTAAGCCTTGGGACTGGTGGACAGCATGGCTCGTGAAACCTGTTGATGCTTGGCATgtaggtcttc--ttcttcactatgatttttaggtttctattga------gtgaatttctctaagtctgat-ttcaccgtga--acaattgcag--------------------------------------------------------------------------------
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AGATGAGAATGAACTCCGTGTGATTCACTATACACTGGGCCCCCTTAAGCCTTGGGACTGGTGGACGTCTTGGCTTTTGAAACCTGTTGATGTTTGGCAGgtacttccgcaactcatcatcctt-tttttggttttctattaatataaaaaaaaatggtctcatcctcatatttataaagaccacatttgcctaagtaaccatgttttcccagttgaagcttgttacaaaaagtatacttacttgtttgttcgaaccttggtgggatgtttag
upper sequence: AT5G18480.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA19G43630.1 (Glycine max), 5'ss of exon 5
TGATGACAGTAAACTTCACGTCATTCACTACACTCTAGGCCCTCTTAAGCCTTGGGACTGGTGGACAGCATGGCTCGTGAAACCTGTTGATGCTTGGCATgtaggtcttcttcttcactatgatttttaggtttctattgagtgaatttctctaagtctgatttcaccgtgaacaattgcag-----------------------------------------------------------------------------------------------
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AGATGAGAATGAACTCCGTGTGATTCACTATACACTGGGCCCCCTTAAGCCTTGGGACTGGTGGACGTCTTGGCTTTTGAAACCTGTTGATGTCTGGCAGgtacttttgcaact-cattatcctttttttggtcttct---attaatatcataaaaaatgttctcatcctca-tagttatagagaccacatttgtctaagtaactccatcttcccagttgaagcttgttacaaaaagtatactgacttgtttgttcgaaccttggtgatatgtttag
upper sequence: AT5G18480.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: EFJ37303 (Selaginella moellendorffii), 5'ss of exon 5
TGATGACAGTAAACTTCACGTCATTCACTACACTCTAGGCCCTCTTAAGCCTTGGGACTGGTGGACAGCATGGCTCGTGAAACCTGTTGATGCTTGGCATgtaggtcttcttcttcactatgatttttaggtttctattgagtgaatttctctaagtctgatttcaccgtgaacaattgcag
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TGATGGAAGCCAATTACGCGTTGTTCACTACACTCTCGGTCCTCTAAAACCTTGGGACTGGTGGACCGAGTGGCTTTTGAAGCCAGTCGATCTATGGCAGgtaatctggaaacgctcatctcatctaaaagtctgtaacttaagcctcttcgcag---------------------------
upper sequence: AT5G18480.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: EFJ27644 (Selaginella moellendorffii), 5'ss of exon 5
TGATGACAGTAAACTTCACGTCATTCACTACACTCTAGGCCCTCTTAAGCCTTGGGACTGGTGGACAGCATGGCTCGTGAAACCTGTTGATGCTTGGCATgtaggtcttcttcttcactatgatttttaggtttctattgagtgaatttctctaagtctgatttcaccgtgaacaattgcag
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TGATGGAAGCCAATTACGCGTTGTTCACTACACTCTCGGTCCTCTAAAACCTTGGGACTGGTGGACCGAGTGGCTTTTGAAGCCAGTCGATCTATGGCAGgtaatctggaaacgctcatctcatcttaaagtctgtaacttaagcctcttcgcag---------------------------Mapped 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|86060782|gb|DR356539.1|DR356539EST: CTTGGGACTGGTGGACAGCATGGCTCGTGAAACCTGTTGATGCTTGGCAT AGCATCAGGGTAAAGCTTGAGGAAACTCTTCCTGGAACTGGAGGTGGCAGT
genomic: CTTGGGACTGGTGGACAGCATGGCTCGTGAAACCTGTTGATGCTTGGCATgtaggtcttc ... acaattgcagAGCATTAGGGTAAAGCTTGAGGAAACTCTTCCTGGAACTGGAGGTGGTAGT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGATGACAGTAAACTTCACGTCATTCACTACACTCTAGGCCCTCTTAAGCCTTGGGACTGGTGGACAGCATGGCTCGTGAAACCTGTTGATGCTTGGCATgtaggtcttcttcttcactatgatttttaggtttctattgagtgaatttctctaagtctgatttcaccgtgaacaattgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA