Sequence
atgc intronic sequence ATGC exonic sequenceCCCAATCTTGGGCCTGGCGTTTATCTTGGAGCTGTTGAAAGAGCAACTTCTTTCATCACAGATGACGTTTGGTATGGAATCTATGCTGGAACAAACCCAGgtagagcagttacaaattagctggtcagggctttatctacaattgtttgtctatttaaaaacaatgtcttaagtaacattaaaagacacttcaactcact...
Basic information
species | Oryza sativa |
transcript | LOC_Os04g52479.3 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g52479.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G102346_T01 (Zea mays), 5'ss of exon 4
CCCAATCTTGGGCCTGGCGTTTATCTTGGAGCTGTTGAAAGAGCAACTTCTTTCATCACAGATGACGTTTGGTATGGAATCTATGCTGGAACAAACCCAGgtagagcagttacaaattagctggtcagggcttta--tctacaattgtttgtctatttaaaaacaatgtc--ttaagta-acattaaaagacacttcaactcact
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CCCAACCTTGGGCCTGGTGTTTATCTTGGAGCTGTCGAAAGGGCAACATCTTTCATCACAGATGATGTTTGGTATGGAATCTATGCTGGAACAAACCCAGgtagagcagttataaattatgcggttaatataggagattaagtattacttgcagctttaattgcttggttatttatctatatatttaaattttcatgaga-----
upper sequence: LOC_Os04g52479.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G033724_T02 (Zea mays), 5'ss of exon 4
CCCAATCTTGGGCCTGGCGTTTATCTTGGAGCTGTTGAAAGAGCAACTTCTTTCATCACAGATGACGTTTGGTATGGAATCTATGCTGGAACAAACCCAGgtagagcagttacaaattagctggtcagggctttatctacaattgtttgtctatt-taaaaacaatgtcttaagtaacattaaaagacacttcaactcact-----
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CCCAACCTTGGGCCTGGTGTTTATCTTGGAGCTGTCGAAAGGGCAACATCTTTTATCACGGATGATGTTTGGTATGGAATCTATGCTGGAACAAACCCAGgtagaggagttataagttatgtggttaa-----tataggaaattaagtattacctgcagctttagttgcttggataattttctgt-atatttaatttctcaggtga
upper sequence: LOC_Os04g52479.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA08G18300.1 (Glycine max), 5'ss of exon 4
CCCAATCTTGGGCCTGGCGTTTATCTTGGAGCTGTTGAAAGAGCAACTTCTTTCATCACAGATGACGTTTGGTATGGAATCTATGCTGGAACAAACCCAGgtagagcag--ttacaaat-tagctggtcagg--gctttatctacaattgtttgtctatttaaaaacaat-gtcttaagtaacattaaaagacacttcaactcact-------
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CCCACTTTGGGGCCTGGGGTTTATCTTGGTGCAGTAGAGAGAGCAACTTCATTTATAACGGATGAGCTTTGGTATGGCATATTTGCTGGAATAAACCCAGgtaacataaatttaggagtctaattgatttacttgggttacttgcattttgttccccacgcatgctccttagtcctcgct--cgtcatgagtcatgatgtgtttcttgtgcag
upper sequence: LOC_Os04g52479.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA07G34800.1 (Glycine max), 5'ss of exon 4
CCCAATCTTGGGCCTGGCGTTTATCTTGGAGCTGTTGAAAGAGCAACTTCTTTCATCACAGATGACGTTTGGTATGGAATCTATGCTGGAACAAACCCAGgtagagcagttaca------aattagctggtcagggctttatctacaattgtttgtctat-ttaaaaacaatgtcttaagtaacattaaaagacacttcaactcact
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CCCAGCCTTGGACCTGGTGTGTATCTTGGTGCAGTTGAGAGAGCAACATCATTTATTACTGATGATCTTTGGTACGGAATTTTTGCAGGAACAAACCCAGgtaatgtggttctagttctcagtcaacaaccagaagttctcagtcgagcaatttgccaatcttaaaatttggggtctaacttgcctttaatgcaaaataa-------
upper sequence: LOC_Os04g52479.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA15G40700.1 (Glycine max), 5'ss of exon 4
CCCAATCTTGGGCCTGGCGTTTATCTTGGAGCTGTTGAAAGAGCAACTTCTTTCATCACAGATGACGTTTGGTATGGAATCTATGCTGGAACAAACCCAGgtagagcagttacaaa---ttagctggtcagg--gctttatctacaattgtttgtctatttaaaaacaatgtcttaagtaacattaaaagacacttcaactcact-
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CCGACTTTGGGGCCTGGGGTTTATCTTGGTGCAGTAGAAAGAGCAACTTCATTTATAACGGATGAGCTTTGGTATGGTATATTTGCTGGAATAAACCCAGgtaacataattttaggagtctgattgatttaattgggttacttgcattttgttccccatgcatactc-----cttaggtagtgtttggttac-tttcatcttgggt
upper sequence: LOC_Os04g52479.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA20G02500.1 (Glycine max), 5'ss of exon 3
CCCAATCTTGGGCCTGGCGTTTATCTTGGAGCTGTTGAAAGAGCAACTTCTTTCATCACAGATGACGTTTGGTATGGAATCTATGCTGGAACAAACCCAGgtagagcagttaca------aattagctggtcagggcttt--atctacaattgtttgtctatttaaaaacaatgtcttaagtaacattaaaagacacttcaactcact
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CCCAGCCTTGGACCCGGTGTGTACCTTGGTGCAGTTGAGAGAGCAACATCATTTATTACTGATGATCTTTGGTATGGAATTTTTGCAGGAACAAACCCAGgtaatgtggttctagttctcagtcaacaactagaagttctcagccaggagctatttgttaatcttaaatctggggtctaacttgcctttaatgcaaaata--------
upper sequence: LOC_Os04g52479.3 (Oryza sativa), 5'ss of exon 3
lower sequence: AT5G45030.1 (Arabidopsis thaliana), 5'ss of exon 4
CCCAATCTTGGGCCTGGCGTTTATCTTGGAGCTGTTGAAAGAGCAACTTCTTTCATCACAGATGACGTTTGGTATGGAATCTATGCTGGAACAAACCCAGgtagagcagttacaaattagctggtcagggctttatctacaattgtttgtc-tatttaaaaacaatgtcttaagtaacattaaaagacacttcaactcact
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CCTAGCCTCGGACCCGGAGTCTACTTAGGTGCAGTGGAAAGAGCAACTTCATTCATTACCGATGACCTTTGGTATGGCATTTTCGCTGGAACTAACCCAGgtagcctagtaacaatgtatagagttaactctg-atgtataatggcgtagcacgattttaattatcggtttctctctttctgcag----------------
upper sequence: LOC_Os04g52479.3 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv01s0011g01870.t01 (Vitis vinifera), 5'ss of exon 5
CCCAATCTTGGGCCTGGCGTTTATCTTGGAGCTGTTGAAAGAGCAACTTCTTTCATCACAGATGACGTTTGGTATGGAATCTATGCTGGAACAAACCCAGgtagagcagttacaaatta-----gctggtcagggctttatctacaattgtttgtctatttaaa-aacaatgtcttaagtaacattaaaagacacttcaactcact
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CCCAGCCTTGGACCTGGGGTGTATCTGGGTGCAGTGGAGAGGGCAACATCCTTCATCACAGATGATCTTTGGTATGGCATCTTTGCCGGAACAAACCCAGgtaatgtagttccaaattgtaagtattgttttgtatctactctgtcaacacttctcattgtgagcaagcgagttctgagtg-catgaatcattcatctagc-----
upper sequence: LOC_Os04g52479.3 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv19s0027g00520.t01 (Vitis vinifera), 5'ss of exon 3
CCCAATCTTGGGCCTGGCGTTTATCTTGGAGCTGTTGAAAGAGCAACTTCTTTCATCACAGATGACGTTTGGTATGGAATCTATGCTGGAACAAACCCAGgtagagcagttacaaattagctggtcagggctttatctaca-attgtttgtctatttaa-aaacaatgtcttaagtaacattaaaagacacttcaactcact
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CCAACACTTGGACCTGGGGTATATCTTGGTGCAGTGGAGAGGGCTACTTCATTCATCACAGATGATCTTTGGTTTGGCATCTTTGCTGGAATAAACCCAGgtaatgtatttccaatttgtgtggctagttatcatgacatatgtggcttctagagatgataaactacacttttacacttttattatgagtgctcatgtga--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|2428270|gb|C72733.1|C72733EST: TTTCATCACAGATGACGTTTGGTATGGAATCTATGCTGGAACAAACCCAG AGACATTTGTACGAGCTGACGGTGCATTTATCCCATTTGCTGATGACTTTG
genomic: TTTCATCACAGATGACGTTTGGTATGGAATCTATGCTGGAACAAACCCAGgtagagcagt ... ggatttgcagAGACATTTGTACGAGCTGACGGTGCATTTATCCCATTTGCTGATGACTTTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CCCAATCTTGGGCCTGGCGTTTATCTTGGAGCTGTTGAAAGAGCAACTTCTTTCATCACAGATGACGTTTGGTATGGAATCTATGCTGGAACAAACCCAGgtagagcagttacaaattagctggtcagggctttatctacaattgtttgtctatttaaaaacaatgtcttaagtaacattaaaagacacttcaactcact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA