Sequence
atgc intronic sequence ATGC exonic sequencegtaaagagaactcgacaagaagtatatgtacattttttcatgcacactatagagacatgtgctgtgccctttagatccttacacaagcaattggtcaaagatgttaattttgatgttctcagGTATGTAGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAGCGATGACATTTGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGAC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G22780.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G22780.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 12
gtaaagagaactcgacaagaagtatatgtacattttttcatgcacactatagagacatgtgctgtgccctttagatccttacacaagca-attggtcaaagatgttaattttgatgttctcagGTATGTAGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAGCGATGACATTTGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGAC
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-------------gtcacgccatatttcagtaca-----aaaaatacccttgatatttgatcagaacttattgttgattta-atatgtacactgat--atcatgccatcccttttatac--agGTATGTTGACGTGATTCTTCAATTAATTGACAAGGCCGGAGATTTTGTTAGCGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGAC
upper sequence: AT5G22780.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 12
gtaaagagaactcgacaagaagtatatgtacattttttcatgcacactatagagacatgtgctgtgccctttagatcct--tacacaagcaat-tggtcaaagatgttaattttgatgttct---cagGTATGTAGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAGCGATGACATTTGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGAC
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------------------------tcaccccatatttcagtacaaa----aaattcccttgatatcttgatcagaacttattgttgatgtaatatgtatactgatatcatgtcatcccttttatacagGTATGTTGATGTGATTCTTCAATTAATTGACAAGGCCGGTGATTTTGTCAGTGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGAC
upper sequence: AT5G22780.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 12
gtaaagagaactcgacaagaagtatatgtacattttttcatgcacactatagagacatgtgctgtgccctttagatccttacacaagcaattggtcaaagatgttaattttgatgttctcagGTATGTAGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAGCGATGACATTTGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGAC
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------gtgctttcattggaaggttggaagcaattgtt---gcctgttgaagcaacaaga-------tcttctactgtttatatatgttgtca--tgtattcttcaattgtcatg----cagGTATGTGGACGTGATCCTACAGTTGATTGACAAGGCAGGAGATTTTGTCAGTGATGACATATGGTTTCGTGTTGTGCAGTTTGTTACAAACAATGAAGAC
upper sequence: AT5G22780.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: EFJ34224 (Selaginella moellendorffii), 3'ss of exon 12
gtaaagagaactcgacaagaagtatatgtacattttttcatgcacactatagagacatgtgctgtgccctttagatccttacacaagcaattggtcaaagatgttaattttgatgttctcagGTATGTAGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAGCGATGACATTTGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGAC
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----------------------------------------------------------gtattgatatctgaagaaatctctcc---ctgttgctaataaggaattgttttggc-----tagGTACGTGGATGTTATCTTACAGCTTATTGAGAAGGCTGGAGATTTCGTTAGCGATGACATTTGGTACAGAGTAGTCCAATTTGTGACAAACAATGATGATMapped 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|301501394|gb|HO206934.1|HO206934EST: AGAAGTTTGCTCCTGATCTTTCATG GTATGTAGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAG
genomic: AGAAGTTTGCTCCTGATCTTTCATGgtaaagagaa ... atgttctcagGTATGTAGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctttagatccttacacaagcaattggtcaaagatgttaattttgatgttctcagGTATGTAGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAGCGATGACATTTGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGAC
tgttctc CT-rich tract
aaagatgttaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagagaactcgacaagaagtatatgtacattttttcatgcacactatagagacatgtgctgtgccctttagatccttacacaagcaattggtcaaagatgttaattttgatgttctcagGTATGTAGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAGCGATGACATTTGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA