Sequence
atgc intronic sequence ATGC exonic sequenceGTGAAAATCCATGGTCCTCATCCAACACCTCGAGCCGGTTGCAGTGGAGTTCTATGTGGAACTAAGTGGTACATTGCTGGCGGTGGAAGCAAGAAAAAACgtatgtttcaagctctcaacttatggaaatagaattggaaatgaggtctatttcagtttgtctctgagaaatcacactttcacaagaatggtttatcttgattatagcagtttgtaacaaaaaatatcgaattctcag
Basic information
species | Oryza sativa |
transcript | LOC_Os12g35350.1 |
intron # | 11 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g35350.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G174830_T01 (Zea mays), 5'ss of exon 11
GTGAAAATCCATGGTCCTCATCCAACACCTCGAGCCGGTTGCAGTGGAGTTCTATGTGGAACTAAGTGGTACATTGCTGGCGGTGGAAGCAAGAAAAAACgtatgtttcaagctctcaacttat--ggaaatagaattggaaatgaggtctatttcagtttgtctctgagaaatcacactttcacaagaatggtttatcttgattata--gcagtttgtaacaaaaaatatcgaattctcag
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GTGAAGACCCATGGTCCTCACCCATCACCTCGAGCTGGTTGCAGCGGAACTCTCTGTGGAACTAAGTGGTACATAGCTGGCGGCGCAAGCAAGAAAAAACgtaagtctcaagctctctctcaatttggaagatgagttggtgat-----ttatttcttaatg-----aagaatacatgtattgctaatgatgacc-atctagcttcttttgcaatttctaacaagaaa--tcaaattctcag
upper sequence: LOC_Os12g35350.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA15G10310.1 (Glycine max), 5'ss of exon 11
GTGAAAATCCATGGTCCTCATCCAACACCTCGAGCCGGTTGCAGTGGAGTTCTATGTGGAACTAAGTGGTACATTGCTGGCGGTGGAAGCAAGAAAAAACgtatg--tttcaagctctcaacttatggaaatagaattggaaatgaggtctatttcagtttgtctctgagaaatcacactttcacaagaatggtttatcttgattatagcagtttgtaacaaaaaatatcgaattctcag
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ATAAAAATACATGGTTTCCATCCATCACCAAGAGCTGGTTGCTGTGGTGTTTTATGTGGCACTAAATGGTATATTACAGGGGGTGGAAGCAAGAAAAAACgtatgctttttaaaggaggaagcttttttcgtaatattagagcata---ctatttatttatatct-tgtgaacttaaacttttacac------ttcagcttcagaaaaaa------------------------------
upper sequence: LOC_Os12g35350.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA13G28760.1 (Glycine max), 5'ss of exon 9
GTGAAAATCCATGGTCCTCATCCAACACCTCGAGCCGGTTGCAGTGGAGTTCTATGTGGAACTAAGTGGTACATTGCTGGCGGTGGAAGCAAGAAAAAACgtatgtttc--aagctctcaacttatggaaatagaattggaa-atgaggtctatttcagtttgtctctgagaaatcacactttcacaagaatggtttatcttgattatagcagtttgtaacaaaaaatatcgaattctcag
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ATAAAAATACGTGGTTTCCATCCATCACCAAGAGCTGGTTGCTGTGGTGTTTTATGTGGCACTAAATGGTATATTACAGGAGGTGGAAGCAAGAAAAAACgtatgtttttaaaggatgaagcatttattcgtaatattagagcatacattttatttctatctttt-----gaacttagacttttacac------ttcagcttcagaaaaaa------------------------------
upper sequence: LOC_Os12g35350.1 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv05s0020g01740.t01 (Vitis vinifera), 5'ss of exon 11
-GTGAAAATCCATGGTCCTCATCCAACACCTCGAGCCGGTTGCAGTGGAGTTCTATGTGGAACTAAGTGGTACATTGCTGGCGGTGGAAGCAAGAAAAAACgtatgtttcaagctctcaacttatggaaatagaattggaaatgaggtctatttcagtttgtctctgagaaatcacactttcacaagaatggtttatcttgattatagcagtttgtaacaaaaaatatcgaattctcag
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ATTAAGAAGAAACGAGGATT-TCCATCACCTAGAGCTGGTTGTTGTGGAGTTTTATGTGGAACTAAATGGTATATAGCAGGGGGTGGAAGCAGGAAAAAACgtatg-----agctagtagctaaaaagcaaaatgtttgaa-------cttttctaacttgtttttttcatttggaatatttgaaatgaaagcatatttacaagctcataact--------------------------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|300215852|gb|HO088478.1|HO088478EST: TCTATGTGGAACT-AGTGGTACATTGCTGGCGGTGGAAGCAAGAAAAAAC GGCATGCAGAAACCTGGGCTTTTGATGTTGTAGAATATAAGTGGTCGGTAT
genomic: TCTATGTGGAACTAAGTGGTACATTGCTGGCGGTGGAAGCAAGAAAAAACgtatgtttca ... gaattctcagGGCATGCAGAAACCTGGGCTTTTGATGTTGTAGAATATAAGTGGTCGGTAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTGAAAATCCATGGTCCTCATCCAACACCTCGAGCCGGTTGCAGTGGAGTTCTATGTGGAACTAAGTGGTACATTGCTGGCGGTGGAAGCAAGAAAAAACgtatgtttcaagctctcaacttatggaaatagaattggaaatgaggtctatttcagtttgtctctgagaaatcacactttcacaagaatggtttatcttgattatagcagtttgtaacaaaaaatatcgaattctcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA