Sequence
atgc intronic sequence ATGC exonic sequence...attttgtggggtgtcttgctaccagttacttttgtccatgtttgttttctggcactgaatgtgcaacagtgttgtttgaccaaatgttatttgtcttaagGCTCCCCAGAAGCACCAAAAGTATGTTGCTAATGTTCTTGGTCTTCCACAATCAAGAGTTGTTTGCAAGACTAAGCGTATTGGTGGTGGATTTGGTGGAA
Basic information
species | Oryza sativa |
transcript | LOC_Os03g31550.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g31550.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G050984_T01 (Zea mays), 3'ss of exon 2
attttgtggggtgtcttgctaccagttacttttgtccatgtttgttttctggcac----tgaatgtgcaacagtgttgtttgaccaaat-gttatttgtcttaagGCTCCCCAGAAGCACCAAAAGTATGTTGCTAATGTTCTTGGTCTTCCACAATCAAGAGTTGTTTGCAAGACTAAGCGTATTGGTGGTGGATTTGGTGGAA
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-ttctttt---tatgttgcttctggttgtttccatat-tatttgcattatactacctgtttagtctctgtcattgccaatttgtcatattgttctttatttttagGCTCCGCAGAAGCATCAGAAGTATGTTGCAAGTGTTCTTGGTCTTCCACAATCAAAAGTCGTTTGCAAGACTAAGCGTATTGGTGGTGGATTTGGTGGAA
upper sequence: LOC_Os03g31550.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA15G03870.1 (Glycine max), 3'ss of exon 6
-attttgtggggtgtcttgctaccagttacttttgtccatgtttgttttctggcactgaatgtgcaacagtgttgtttgaccaaatgttatttgtcttaagGCTCCCCAGAAGCACCAAAAGTATGTTGCTAATGTTCTTGGTCTTCCACAATCAAGAGTTGTTTGCAAGACTAAGCGTATTGGTGGTGGATTTGGTGGAA
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gaacccgtgtgtgtgagtgttagtgtttggcttgtattggcctaaatttatggcttgaaggaaataactgcattgtgaaaataa-cattgtgttgttgcagGCTCCTCAGAAGCACCAGAAATATGTTTCTCATGTTCTTGGCCTTCCCATGTCAAAGGTAGTTTGCAAAACAAAACGAGTTGGTGGTGGATTTGGGGGGA
upper sequence: LOC_Os03g31550.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G41520.1 (Glycine max), 3'ss of exon 7
attttgtg-gggtgtcttgctacca-gttacttttgtccatgtttgt-tttctggcactgaatgtgcaacagtgttgtttgaccaaatgttatttgtcttaagGCTCCCCAGAAGCACCAAAAGTATGTTGCTAATGTTCTTGGTCTTCCACAATCAAGAGTTGTTTGCAAGACTAAGCGTATTGGTGGTGGATTTGGTGGAA
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--tgtgtgtgagtgagtgagtgtagtgtttggcttgtattggcctaaatttatggcttgaaggaaataactgcattgtgaaaataa-cattgtgttattgcagGCTCCTCAGAAGCACCAGAAATATGTTTCCCATGTTCTTGGCCTTCCCATGTCAAAGGTAGTTTGCAAAACAAAGCGAATTGGTGGTGGATTTGGGGGGA
upper sequence: LOC_Os03g31550.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv06s0004g02030.t01 (Vitis vinifera), 3'ss of exon 6
attttgtggggtgtcttgctaccagttacttttgtccatgtttgttttctggcactgaatgtgcaacagtgttgtttgaccaaat-gttatttgtcttaagGCTCCCCAGAAGCACCAAAAGTATGTTGCTAATGTTCTTGGTCTTCCACAATCAAGAGTTGTTTGCAAGACTAAGCGTATTGGTGGTGGATTTGGTGGAA
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tatttgcctagaaatttattagcaatggatgccagtt-caactgctctgtggtggtcacagccttatttagaattttgacagatttgatctttatgtgcagTGTCCCCAGAAGCATCAGAAATATGTTTCTCATGTTCTTGGTCTTCCAATGTCAAAAGTAGTTTGCAAAACCAAGCGAATCGGTGGTGGATTTGGGGGGAMapped 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|58693457|gb|CK082144.1|CK082144EST: TATGGCCAGTTGATTCTGGAAATGAAATTCATATGATTTCATCTACCCAG GCTCCCCAGAAGCACCAAAAGTATGTTGCTAATGTTCTTGGTCTTCCACAA
genomic: TATGGCCAGTTGATTCTGGAAATGAAATTCATATGATTTCATCTACCCAGgtatgctatt ... ttgtcttaagGCTCCCCAGAAGCACCAAAAGTATGTTGCTAATGTTCTTGGTCTTCCACAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttctggcactgaatgtgcaacagtgttgtttgaccaaatgttatttgtcttaagGCTCCCCAGAAGCACCAAAAGTATGTTGCTAATGTTCTTGGTCTTCCACAATCAAGAGTTGTTTGCAAGACTAAGCGTATTGGTGGTGGATTTGGTGGAA
gtttgac putative branch site (score: 4)
tttgtctt putative PPT
aaatgttattt TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attttgtggggtgtcttgctaccagttacttttgtccatgtttgttttctggcactgaatgtgcaacagtgttgtttgaccaaatgttatttgtcttaagGCTCCCCAGAAGCACCAAAAGTATGTTGCTAATGTTCTTGGTCTTCCACAATCAAGAGTTGTTTGCAAGACTAAGCGTATTGGTGGTGGATTTGGTGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA