Sequence
atgc intronic sequence ATGC exonic sequenceGGAAGATTCCTTGAAGAAAAAGTGGAAGAAAATAGAAGAATTTGATGCTCGTAGATCAGAACTTGAGTGCATTTACAATGCTCTTCTGCGGGCCAATATGgttagtctggagcctttgtacttttccttactagctctttacttagttcgctattcaattttttaaagaaagttttagatatagacatgaatatagaaat...
Basic information
species | Oryza sativa |
transcript | LOC_Os09g21780.2 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g21780.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G055917_T02 (Zea mays), 5'ss of exon 5
GGAAGATTCCTTGAAGAAAAAGTGGAAGAAAATAGAAGAATTTGATGCTCGTAGATCAGAACTTGAGTGCATTTACAATGCTCTTCTGCGGGCCAATATGgttagt---ctggagcctttgtacttttccttactagctct-----ttacttagttcgctattcaattttttaaagaaagttttagatatagacatgaatatagaaat
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AGAAGATTCACTGAAGAAGAAATGGAAGAAAATCGAAGAATTTGACGCCCGTCGAACAGAGCTGGAGTGCATTTACAGTGCTCTTCAGCGGGCTAATATGgttagctagcttgcaatattgtgatcttttctttcaactctaggatttctctagtgcggcaatgagcttagtaatggatgt--caatagctgttttttattc------
upper sequence: LOC_Os09g21780.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G116196_T01 (Zea mays), 5'ss of exon 5
GGAAGATTCCTTGAAGAAAAAGTGGAAGAAAATAGAAGAATTTGATGCTCGTAGATCAGAACTTGAGTGCATTTACAATGCTCTTCTGCGGGCCAATATGgttagtc----tggagcctttgtacttttccttactagctctttacttagttcgctattcaattttttaaagaaagttt-tagatatagacatgaatatagaaat
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AGAAGATTCACTGAAGAAGAAGTGGAAGAAAATCGAAGAATTTGACGCCCGTCGATCAGAGCTGGAGTTCATTTACAGTGCTCTTCAGCGGGCCAATATGgttagctagcttgcaatattgtgactcttaaaaccttatgatttgtccggtacgggaatgagcttagtaatgaatgtcaatagctgtttttattcttgcc-----
upper sequence: LOC_Os09g21780.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA08G27740.1 (Glycine max), 5'ss of exon 5
GGAAGATTCCTTGAAGAAAAAGTGGAAGAAAATAGAAGAATTTGATGCTCGTAGATCAGAACTTGAGTGCATTTACAATGCTCTTCTGCGGGCCAATATGgt--tagtctggagcctttgtacttttccttactagctctttacttagttcgc-tatt--caattttttaaagaaagttttagatatagacatgaatatagaaat
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TGAAGATTCTCTAAAGAAAAAATGGAAAAAGATTGAAGAGTTTGATGCTCGTAGATCAGAACTTGAGACTATATATACGGCACTCCTTAAAGCAAACATGgtaatgttctgttatttcagta-tttcctgtactagtgaaatacaactgtggcatatttacagcttatccttgggaatggtaataccttgtttgaatccta----
upper sequence: LOC_Os09g21780.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA18G50960.1 (Glycine max), 5'ss of exon 5
-GGAAGATTCCTTGAAGAAAAAGTGGAAGAAAATAGAAGAATTTGATGCTCGTAGATCAGAACTTGAGTGCATTTACAATGCTCTTCTGCGGGCCAATATGgt--tagtctggagcctttgtacttttccttactagctctttacttagttcgctattcaattttttaaagaaagttttagatatagacatgaat-atagaaat---
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CTGAAGATTCTCTAAAGAAAAAATGGAAAAAGATTGAAGAGTTTGATGCTCGTAGATCAGAACTTGAGACTATATATATGGCACTCCTTAAAGCAAATATggtaatgttccgttatttcagta-tttcccgtattagtgaaataca------actgtggtatatttacagcttatccttgggaatggtgataccttgtttgaatcct
upper sequence: LOC_Os09g21780.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT5G38880.1 (Arabidopsis thaliana), 5'ss of exon 5
GGAAGATTCCTTGAAGAAAAAGTGGAAGAAAATAGAAGAATTTGATGCTCGTAGATCAGAACTTGAGTGCATTTACAATGCTCTTCTGCGGGCCAATATGgtta-gtctggagcctttgtacttttccttactagctctttacttagttcgctattcaattttttaaagaaagttttagatatagacatgaatatagaaat
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CGAAGATTCCTTGAAAAAGAAGTGGAAGAAAATTGAGGAATTTGATGCTCGCAGATCCGAACTTGAAACCATATATACAACTCTTCTCAAGGCCAACATGgtaatatcccaagtgattca--ttcattaaattgattaagtgataaataccatgagtaatactctgtatcatgaccttcctttttatatag----------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|66917271|gb|CX104119.1|CX104119EST: GTAGATCAGAACTTGAGTGCATTTACAATGCTCTTCTGCGGGCCAATATG GAGGCATCAACATTTTGGGAGCAACAGCCATTATCTGCAAGAGGATATGCG
genomic: GTAGATCAGAACTTGAGTGCATTTACAATGCTCTTCTGCGGGCCAATATGgttagtctgg ... ctatatatagGAGGCATCAACATTTTGGGAGCAACAGCCATTATCTGCAAGAGGATATGCG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGAAGATTCCTTGAAGAAAAAGTGGAAGAAAATAGAAGAATTTGATGCTCGTAGATCAGAACTTGAGTGCATTTACAATGCTCTTCTGCGGGCCAATATGgttagtctggagcctttgtacttttccttactagctctttacttagttcgctattcaattttttaaagaaagttttagatatagacatgaatatagaaat
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