Sequence
atgc intronic sequence ATGC exonic sequenceACTCTCTCTGCAGCCTTGATGGTTGGGGCTAAGTTTGATGGTGCAGATATGACTGAAGTTGTTATGTCAAAAGCTTATGCTGTAGAAGCAAGCTTTAAAGgtatatagacttaaatcttgaaatttgaaagcatatggtaaaattatggaccaaaatgttaattaatgttttagtgtgaattcttttctag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G53490.3 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G53490.3 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os10g35810.1 (Oryza sativa), 5'ss of exon 2
ACTCTCTCTGCAGCCTTGATGGTTGGGGCTAAGTTTGATGGTGCAGATATGACTGAAGTTGTTATGTCAAAAGCTTATGCTGTAGAAGCAAGCTTTAAAGgtatatagacttaaatcttgaaatttgaaagcatatggt------------aaaattatggacc---aaaatgttaa---------ttaatgttttagtgtgaattcttttctag
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TCTCTAGCTGCAGCCTTGATGTCCGATTCAAAGTTTGATGGGGCCGACATGTCTGAAGTTGTGATGTCCAAAGCTTATGCTGTGGGGGCAAGCTTCAAAGgtaaactaactcaccttctgtcattcatcacactattgctgcattatttccaaaatcatgtacctttgaattgataaacagaacactagatgcttatatctcaattgttttcag-
upper sequence: AT5G53490.3 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA06G13640.1 (Glycine max), 5'ss of exon 3
ACTCTCTCTGCAGCCTTGATGGTTGGGGCTAAGTTTGATGGTGCAGATATGACTGAAGTTGTTATGTCAAAAGCTTATGCTGTAGAAGCAAGCTTTAAAGgtatatagacttaaatcttg-aaatttga--aagcatatggtaaaattatggaccaa--aatgttaattaatgttttagtgtgaattcttttctag-----
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TCCCTGTCTGCTGCACTCATGTCAGATGCTAAGTTTGATGGAGCTGATATGACAGAAGTTGTAATGTCAAAGGCTTATGCTGCTGGTGCCAGCTTTAAAGgta-acagtttttacttgtgcaaaatcaactaaatgttagattagtttgtcacttcgtcagcctttatagatgacaaattttaagttttccaacaatctta
upper sequence: AT5G53490.3 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA04G41210.1 (Glycine max), 5'ss of exon 3
ACTCTCTCTGCAGCCTTGATGGTTGGGGCTAAGTTTGATGGTGCAGATATGACTGAAGTTGTTATGTCAAAAGCTTATGCTGTAGAAGCAAGCTTTAAAGgtatatagacttaaatcttgaaatttga--aagcatatggtaaaattatggaccaa--aatgttaattaatgttttagtgtgaattcttttctag-----
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TCCCTGTCTGCTGCACTCATGTCAGATGCCAAGTTTGATGGAGCTGATATGACAGAAGTTGTAATGTCAAAGGCTTATGCTGTTGGTGCCAGCTTCAAGGgtaacaatatttacttgtgcaaaatcaactaaatgttagattagtttgtatcttcatcagcctttataaaggaaaaaattcaagtttttcaacaatctta
upper sequence: AT5G53490.3 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv16s0098g01540.t01 (Vitis vinifera), 5'ss of exon 3
ACTCTCTCTGCAGCCTTGATGGTTGGGGCTAAGTTTGATGGTGCAGATATGACTGAAGTTGTTATGTCAAAAGCTTATGCTGTAGAAGCAAGCTTTAAAGgtatatagacttaaatcttgaaatttgaaagcatatggt---aaaattatggaccaaaatgttaattaatgttttagtgtgaattcttttctag------
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TCTCTTGCAGCAGCACTCATGTCAGAAGCTAAGTTTGATGGTGCAGACATGTCCGAGGTAGTGATGTCAAAGGCTTATGCCGTTGGAGCCAGCTTCAAAGgtaagtaggttgattttttgccttctctgactaatttgcttgaatatttcatagtcctcatttcataatcttcttggaatgagtcttagtagacttgaagMapped 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|125311989|gb|EL326074.1|EL326074EST: GACTGAAGTTGTTATGTCAAAAGCTTATGCTGTAGAAGCAAGCTTTAAAG GGGTGAATTTC
genomic: GACTGAAGTTGTTATGTCAAAAGCTTATGCTGTAGAAGCAAGCTTTAAAGgtatatagac ... tcttttctagGGGTGAATTTC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ACTCTCTCTGCAGCCTTGATGGTTGGGGCTAAGTTTGATGGTGCAGATATGACTGAAGTTGTTATGTCAAAAGCTTATGCTGTAGAAGCAAGCTTTAAAGgtatatagacttaaatcttgaaatttgaaagcatatggtaaaattatggaccaaaatgttaattaatgttttagtgtgaattcttttctag
- - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT