Sequence
atgc intronic sequence ATGC exonic sequenceACTTTCCACCATGAGAGCTTTGGATAACTTAGGATTGGATGTTCAACAAGCGGTGATTAGCTGTTTCAATGGTTTTGCTTTGGATGTTTTCCGCGCTGAGgtaatatagttgttaagatgctatgctgatcactgattagtaaaactagcagtcaaagaatagttatttgagagaatgattagtatacaagtaacaacatgttttgtgtttctaatcag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G12860.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G12860.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os01g70310.2 (Oryza sativa), 5'ss of exon 3
ACTTTCCACCATGAGAGCTTTGGATAACTTAGGATTGGATGTTCAACAAGCGGTGATTAGCTGTTTCAATGGTTTTGCTTTGGATGTTTTCCGCGCTGAGgtaatatagttgttaagatgctatgctgatcactgattagtaaaactagcagtcaaagaatagtt-atttgagagaatgattagtatacaa---gtaacaacatgttttgtgtttctaatcag----
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GATGTCCACATTGAGGGCTCTCGACAGCCTTGGCCTCGGGATCGAGCAGGCGGTCATCAGCTGTTTCAATGGGTTTGCAATGGATGTTTTCCGCGCCGAGgtt-tgcattctccacatcataatatttttctcctccagctgagggttttttttcagttgtgttcgatctgatcctaccgttgttgttcactctcttaatgcttgctctgtacttctgttttgccag
upper sequence: AT1G12860.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA16G05390.1 (Glycine max), 5'ss of exon 3
ACTTTCCACCATGAGAGCTTTGGATAACTTAGGATTGGATGTTCAACAAGCGGTGATTAGCTGTTTCAATGGTTTTGCTTTGGATGTTTTCCGCGCTGAGgtaatatagttgttaagatgctatgctgatcactgattagtaaaactagcagtcaaagaatagttatttgagagaatgattagtatacaagtaacaacatgttttgtgtttctaatcag
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GCTTTCTACCATGAGGGCTTTGGATAACCTCGGATTGGATGTACAGCAGGCTGTTATTAGCTGTTTTAATGGCTTTGCTTTAGATGTGTTCAAAGCCGAGgtataattctctctcgtttgccaagct--tcact------tgaacatatctattattaacttgcttt--------accattatgatgcttgtcattgaactttatttggtcattag---
upper sequence: AT1G12860.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA19G27480.2 (Glycine max), 5'ss of exon 3
ACTTTCCACCATGAGAGCTTTGGATAACTTAGGATTGGATGTTCAACAAGCGGTGATTAGCTGTTTCAATGGTTTTGCTTTGGATGTTTTCCGCGCTGAGgtaatatagttgttaagatgctatgctgatcactgattagtaaaactagcagtcaaagaatagttatttgagagaatgattagtatacaagtaacaacatgttttgtgtttctaatcag
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GCTTTCTACCATGAAGGCTTTGGATAACCTCGGATTGGATGTACAGCAGGCTGTTATTAGCTGTTTTAATGGCTTTGCTTTAGATGTGTTCAAAGCTGAGgtataattctctctcctgtgccaagct--tcacc--tgaacatatctattattgatttgccttacttttattatgattctcgtcattgatgtt------tatttgggaat---------
upper sequence: AT1G12860.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA16G26290.1 (Glycine max), 5'ss of exon 3
ACTTTCCACCATGAGAGCTTTGGATAACTTAGGATTGGATGTTCAACAAGCGGTGATTAGCTGTTTCAATGGTTTTGCTTTGGATGTTTTCCGCGCTGAGgtaatatagttgttaagatgctatgctgatcactgattagtaaaactagcagtcaaagaatagttatttgagagaatgattagtatacaagtaacaacatgttttgtgtttctaatcag
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ACTTTCTACCATGAGGGCAATGGATAGCCTTGGATTGGATGTTCAGCAGGCCGTAATCAGTTGTTTCAATGGTTTTTCTTTAGATGTGTTTAGAGCTGAGgta-tgtagttttgtttatcctgtgccatgtttta--catcaatgtttccctttt-----tatttccttgctttat--attattgtgcttgccat----tgatttttgttcggg-----
upper sequence: AT1G12860.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv01s0244g00130.t01 (Vitis vinifera), 5'ss of exon 3
ACTTTCCACCATGAGAGCTTTGGATAACTTAGGATTGGATGTTCAACAAGCGGTGATTAGCTGTTTCAATGGTTTTGCTTTGGATGTTTTCCGCGCTGAGgtaatatagttgttaagatgctatgctgatcactgattagtaaaactagcagtcaaagaatagttatttgagagaatgattagtatacaagtaacaacatgttttgtgtttctaatcag
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GCTCTCTGCCATGAGGGCTTTGGATGGCCTTGGGCTAGACGTTCAACAGGCGGTCATCAGCTGTTTCAATGGGTTTGCTCTGGATATCTTCCAAGCTGAGgttagcttcct-tcaaaatcat------attactg-----tataatcatcaggccctgaacaat-acttaaaaacattttgacccttttttcaaaatttaaatcaattctccc------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|19798815|gb|AU230105.1|AU230105EST: C-GTGATTAGCTGTTTCAATGGTTTTGCTTT-GATGTTTTCCGCGCTGAG CAATGTCAAGAATACCATGACGTGTTACCTGAACAAATCAAAGCAGTGCTT
genomic: CGGTGATTAGCTGTTTCAATGGTTTTGCTTTGGATGTTTTCCGCGCTGAGgtaatatagt ... ttctaatcagCAATGTCAAGAAGACCATGACGTGTTACCTGAACAAATCAAAGCAGTGCTT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ACTTTCCACCATGAGAGCTTTGGATAACTTAGGATTGGATGTTCAACAAGCGGTGATTAGCTGTTTCAATGGTTTTGCTTTGGATGTTTTCCGCGCTGAGgtaatatagttgttaagatgctatgctgatcactgattagtaaaactagcagtcaaagaatagttatttgagagaatgattagtatacaagtaacaacatgttttgtgtttctaatcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT