Sequence
atgc intronic sequence ATGC exonic sequenceGCACTGGGCGCTCCTGGCAGGGCTGCTCTGTGGGTTTGGCAATGGGTTCCAGTTCATGGGTGGGCAGGCTGCTGGATATGCAGCTGCTGATGCTGTCCAGgtgatcctctccttaggttcatatcagctctgcaatgtttgctgcattttacctgcatttcagctgtaatacaactaaaactcatggtgttcatgatatggtgtgatcag
Basic information
species | Oryza sativa |
transcript | LOC_Os12g31890.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g31890.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA02G12970.2 (Glycine max), 5'ss of exon 7
GCACTGGGCGCTCCTGGCAGGGCTGCTCTGTGGGTTTGGCAATGGGTTCCAGTTCATGGGTGGGCAGGCTGCTGGATATGCAGCTGCTGATGCTGTCCAGgtgatcctctccttaggttcatatcagctctgcaatgtttgctgcattttacctgcatttcagctgtaatacaactaaaactcatggtgttcatgatatggtgtgatcag
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AGTCTGGGCCATGTTGGCTGGTTTGCTTTGTGGGTTTGGGAATGGTCTCCAATTTATGGGTGGTCAAGCTGCAGGATATGCAGCAGCAGATGCAGTCCAGgttag--ttttatta--cttcgattagaaaaagaat-ttaatttgaatgcactaacattgtaatggttgtttacatcggctatttaatgggtaaaatatgtttat-----
upper sequence: LOC_Os12g31890.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT1G26440.1 (Arabidopsis thaliana), 5'ss of exon 6
GCACTGGGCGCTCCTGGCAGGGCTGCTCTGTGGGTTTGGCAATGGGTTCCAGTTCATGGGTGGGCAGGCTGCTGGATATGCAGCTGCTGATGCTGTCCAGgtgatcctctc-cttaggttcatatcagctctgcaatgtttgctgcat-tttacctgcatttcagctgtaatacaactaaaactcatggtgttcatgatatggtgtgatcag
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AGGTTGGGCACTTGCAGCTGGATTGTTATGTGGGTTTGGTAACGGTCTTCAGTTCATGGGTGGACAAGCTGCAGGATATGCAGCCTCAGATGCTGTTCAGgtcacacaaacacttataatcctaaa----ctagaacgtttctttgatctttgcttgcgttttagtgattct-tgattggtattcttg---tacag----------------
upper sequence: LOC_Os12g31890.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT2G03590.1 (Arabidopsis thaliana), 5'ss of exon 5
GCACTGGGCGCTCCTGGCAGGGCTGCTCTGTGGGTTTGGCAATGGGTTCCAGTTCATGGGTGGGCAGGCTGCTGGATATGCAGCTGCTGATGCTGTCCAGgtgatcctctccttaggttcatatcagctctgcaatgtttgctgcattttacctgcatttca-gctgtaatacaactaaaactcatggtgttcatgatatggtgtgatcag
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AGGCTGGTCTTTCTTGGCTGGATTTCTATGTGGATTTGGCAATGGTCTTCAGTTCATGGGTGGTCAAGCCGCAGGCTATGCAGCTGCAGACGCTGTTCAGgt-----ttagacaataaacaaatcctctgttccatgatttaagagtgaaatatgttttacttattatgatttgaatatgtttcag-------------------------
upper sequence: LOC_Os12g31890.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv01s0011g00530.t01 (Vitis vinifera), 5'ss of exon 6
GCACTGGGCGCTCCTGGCAGGGCTGCTCTGTGGGTTTGGCAATGGGTTCCAGTTCATGGGTGGGCAGGCTGCTGGATATGCAGCTGCTGATGCTGTCCAGgtgatcctctccttag-gttcatatcagc-----tctgca-atgtttgctg-cat-----------tttacctgcatttcagctgtaatacaactaaaactcatggtgttcatga------tatggtgtgatcag
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AGGCTGGGCCTTTTTAGCTGGGCTCCTCTGTGGGTTCGGGAACGGTCTCCAGTTCATGGGAGGCCAAGCTGCAGGATATGCAGCAGCTGATGCAGTTCAGgtgagtttaagcacagcatacatattgacaaacacatacacatagaggcaatcataaatcggggtgtttgtgtgtgttttc-ctgcaatccaatcagaatgtgctgatcatttgaacttttcatggtaacatcag
upper sequence: LOC_Os12g31890.1 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ12276 (Selaginella moellendorffii), 5'ss of exon 5
GCACTGGGCGCTCCTGGCAGGGCTGCTCTGTGGGTTTGGCAATGGGTTCCAGTTCATGGGTGGGCAGGCTGCTGGATATGCAGCTGCTGATGCTGTCCAGgtgatcctctccttaggttcatatcagctctgcaatgtttgctgcattttacctgcatttcagctgtaatacaactaaaactcatggtgttcatgatatggtgtgatcag
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GCCGTGGGCATTGCTCGCAGGACTCTTGTGTGGCTTTGGAAACGGGCTCCAGTTCATGGGAGGCCAAGCTGCTGGTTACGCTGCTGCCGACGCTGTCCAGgta----------tggatcgaagtttcttcttcg-tctttgatg-gttttgttctttctccag-----------------------------------------------
upper sequence: LOC_Os12g31890.1 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ08167 (Selaginella moellendorffii), 5'ss of exon 5
GCACTGGGCGCTCCTGGCAGGGCTGCTCTGTGGGTTTGGCAATGGGTTCCAGTTCATGGGTGGGCAGGCTGCTGGATATGCAGCTGCTGATGCTGTCCAGgtgatcctctccttaggttcatatcagctctgcaatgtttgctgcattttacctgcatttcagctgtaatacaactaaaactcatggtgttcatgatatggtgtgatcag
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GCCGTGGGCATTGCTCGCAGGACTCTTGTGTGGCTTTGGAAACGGGCTCCAGTTCATGGGAGGCCAAGCTGCTGGTTACGCTGCTGCCGACGCTGTCCAGgtatggatcg----aagtttctccttcgtctttgatggttttgttctttctccag-------------------------------------------------------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|112786166|gb|EE592193.1|EE592193EST: AGTTCATGGGTGGGCAGGCTGCTGGATATGCAGCTGCTGATGCTGTCCAG GCACTGCCTCTTGTCAGTACATTCTGGGGAGTCATCCTCTTTGGCGAGTAC
genomic: AGTTCATGGGTGGGCAGGCTGCTGGATATGCAGCTGCTGATGCTGTCCAGgtgatcctct ... gtgtgatcagGCACTGCCTCTTGTCAGTACATTCTGGGGAGTCATCCTCTTTGGCGAGTAC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCACTGGGCGCTCCTGGCAGGGCTGCTCTGTGGGTTTGGCAATGGGTTCCAGTTCATGGGTGGGCAGGCTGCTGGATATGCAGCTGCTGATGCTGTCCAGgtgatcctctccttaggttcatatcagctctgcaatgtttgctgcattttacctgcatttcagctgtaatacaactaaaactcatggtgttcatgatatggtgtgatcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG