Sequence
atgc intronic sequence ATGC exonic sequenceCGTCTGGTTTGGACAGCTCTTCGTCTCTGCTTTTACTTCGTGCACTACGGCGGGAAGCTCTTGAAGGTGTGAACATCTCTATGGTGGTTCATCAACCCAGgtaaggttgtttgctctttttctccacaactttatatgcaccactcactcatgcaactttatgctgagtttattttcttttgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os06g51460.2 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g51460.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G166889_T01 (Zea mays), 5'ss of exon 9
CGTCTGGTTTGGACAGCTCTTCGTCTCTGCTTTTACTTCGTGCACTACGGCGGGAAGCTCTTGAAGGTGTGAACATCTCTATGGTGGTTCATCAACCCAGgtaaggttgtttgc---------tctttttctccacaactt-tatatgcacca--ctcactcatgcaactttatgctga--gtttattttcttttgcag
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CATCAGGCCTGGACAGCGCCTCGTCCTTGCTTTTACTTCGTGCCCTACGCAGGGAAGCTCTCGAGGGTGTCAACATCTCTATGGTCGTCCATCAGCCCAGgtt-gtttatttgcattgcagattcatcttcttgcttgcttgtatttgtatgatgctggtttat-cagctatatataactcgagtggttttacttgcag
upper sequence: LOC_Os06g51460.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA20G32210.1 (Glycine max), 5'ss of exon 10
CGTCTGGTTTGGACAGCTCTTCGTCTCTGCTTTTACTTCGTGCACTACGGCGGGAAGCTCTTGAAGGTGTGAACATCTCTATGGTGGTTCATCAACCCAGgtaaggttgtttgc----tctttttctccacaactttatatgcaccactcactcatgcaactttatgctgagt-ttattttcttttgcag----------
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CATCTGGCTTGGACAGTGCATCATCTCAGCTCCTTCTAAGAGCACTAAGACGCGAAGCTCTTGAGGGAGTGAACATTTGCATGGTGGTTCACCAACCCAGgtaaactttaatcccatgtctgcatcattggaatattgcttgcctcattggtctttgttttttctttccggccaccatttactgtactagaattttattt
upper sequence: LOC_Os06g51460.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA02G21570.1 (Glycine max), 5'ss of exon 8
CGTCTGGTTTGGACAGCTCTTCGTCTCTGCTTTTACTTCGTGCACTACGGCGGGAAGCTCTTGAAGGTGTGAACATCTCTATGGTGGTTCATCAACCCAGgtaaggtt-gtttgctctttttctccacaacttt-atatgcaccac-tcactcatg-------caactttatgctgagtttattttcttttgcag-----
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CGTCTGGGTTGGACAGTGCATCATCTCAACTCCTTCTTAGAGCACTAAGACGTGAAGCTCTTGAAGGAGTGAACATTTGCATGGTGGTTCACCAACCCAGgtgactctcaattccatgtcttctacatcatggagatatggctagcctcatttatgattatattatttttcagttgattttatatatttttttaatataa
upper sequence: LOC_Os06g51460.2 (Oryza sativa), 5'ss of exon 9
lower sequence: AT2G37010.1 (Arabidopsis thaliana), 5'ss of exon 9
CGTCTGGTTTGGACAGCTCTTCGTCTCTGCTTTTACTTCGTGCACTACGGCGGGAAGCTCTTGAAGGTGTGAACATCTCTATGGTGGTTCATCAACCCAGgtaaggttgtttgctcttt----ttctccacaactttatatgcaccactcactcatgcaactttatgctgagtttattttcttttgcag
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CTACAGGTTTAGATAGTGCATCTTCACAATTACTTCTTAGAGCACTTCGACGTGAAGCACTTGAAGGTGTTAACATTTGTATGGTCGTCCATCAACCCAGgtatg-ttatctcctccatgaattatgttacaattttatgttaagaaatactttttgc---ttaataattggttttttcctcttattagMapped 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|33664907|gb|CF295874.1|CF295874EST: TGAAGGAGTAGAA-ATCTCTATGGTGGTTCATCAACCCAG CTATACATTGTATAAGATGTTTGATGATTTGATACTTCTCGCGAAAGGTGG
genomic: TGAAGGTGT-GAACATCTCTATGGTGGTTCATCAACCCAGgtaaggttgt ... tcttttgcagCTATACATTGTATAAGATGTTTGATGATTTGATACTTCTCGCGAAAGGTGG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CGTCTGGTTTGGACAGCTCTTCGTCTCTGCTTTTACTTCGTGCACTACGGCGGGAAGCTCTTGAAGGTGTGAACATCTCTATGGTGGTTCATCAACCCAGgtaaggttgtttgctctttttctccacaactttatatgcaccactcactcatgcaactttatgctgagtttattttcttttgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG