Sequence
atgc intronic sequence ATGC exonic sequenceGTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTTgtaagtatacaccttattcctttacagagacacttatttttcatttgtagaataaaagtaagtaaatatgtattccctcaaacactattggagaaacttt...
Basic information
species | Oryza sativa |
transcript | LOC_Os03g08070.2 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g08070.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA06G05890.1 (Glycine max), 5'ss of exon 5
GTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTTgtaagtat--acaccttattcctttacagagacacttatttttcatttgtagaataaaagtaag---taaatatgtattccctcaaacactattggagaaacttt
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GTCATGCTTCTTGGTTTCGTGCTTCTGGGACGTTCTCTGGAGGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTTgtaagttgcaatgtcgtgcacctctgtc-atctgataatattccagctaaataagatttgtataacctgattatttgctatctggagtcaaatataagatt----
upper sequence: LOC_Os03g08070.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA04G05900.2 (Glycine max), 5'ss of exon 4
-------GTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTTgtaagtatacaccttattc-ctttacagagacacttatttttcatttgtagaataaaagtaa-gtaaatatgtattccctcaaacactattggagaaacttt-
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CATGCAGGTCATGCTTCTTGGTTTTGTGCTTCTGGGACGTTCTCTGGAAGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTTgtaagttgcaatgtcatgcacctctttcatctgataatattcca---gcaaaataagatttctataacttggttatttgatatctggaatcaattgtgtttac
upper sequence: LOC_Os03g08070.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA04G05900.1 (Glycine max), 5'ss of exon 3
GTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTTgtaagtatacaccttattc-ctttacagagacacttatttttcatttgtagaataaaagtaa-gtaaatatgtattccctcaaacactattggagaaacttt-
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GTCATGCTTCTTGGTTTTGTGCTTCTGGGACGTTCTCTGGAAGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTTgtaagttgcaatgtcatgcacctctttcatctgataatattcca---gcaaaataagatttctataacttggttatttgatatctggaatcaattgtgtttac
upper sequence: LOC_Os03g08070.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv04s0008g01960.t01 (Vitis vinifera), 5'ss of exon 5
GTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTTgtaagta----tacaccttattcctttac-----agagacacttatttttcatttgtagaataaaagtaagtaaatatgtattccctcaaacactattggagaaacttt
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GTCATGCTTCTTGGTTTTGTGCTCCTTGGACGTTCTCTTGAAGAGAAGGCGAGGATCAGGGCATCTAGCGATATGAATAAACTTTTAgtaagttagattgcagtttatatgtgtaatacaaggaaatagacataatgcccacttgacttccttttgagtgaaattaagtttaatgatagttttctgt---------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|29622946|gb|CB627957.1|CB627957EST: TTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTT TCACTCTTATCACCTCAGTCAAGATTGGTCGTTACTTCCTCAAGTGACGAT
genomic: TTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTTgtaagtatac ... tctgttgcagTCACTCTTATCACCTCAGTCAAGATTGGTCGTTACTTCCTCAAGTGACGAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTTgtaagtatacaccttattcctttacagagacacttatttttcatttgtagaataaaagtaagtaaatatgtattccctcaaacactattggagaaacttt
- - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - AAGAAA