Sequence
atgc intronic sequence ATGC exonic sequenceAGTAAACTCTGGGGCTCAATGTATACAAATATTTGATTCATGGGGTGGACAACTTCCACCTCATGTGTGGGAGCAGTGGTCAAAACCATATATCAAGCAGgtagcttacttttacttttctcggtcctgtttgcttccttaatccttatgactaatttcatgatgggtggctgctctaaggttaatcaggttggatctac...
Basic information
species | Oryza sativa |
transcript | LOC_Os01g43390.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g43390.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G024738_T02 (Zea mays), 5'ss of exon 3
AGTAAACTCTGGGGCTCAATGTATACAAATATTTGATTCATGGGGTGGACAACTTCCACCTCATGTGTGGGAGCAGTGGTCAAAACCATATATCAAGCAGgtagcttacttttacttttctcggtcctgtttgcttccttaatccttatgactaatttcatgatgggtggctgctctaaggttaatca--ggttggatctac--
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AGTTAACTCGGGGGCCCAGTGTATACAGATATTTGATTCATGGGGTGGACAGCTTCCACCTCATGTGTGGGAGCAGTGGTCAAAACCATATATCAAACAGgtgactcttccttacttttcttgctttcatgtattacc---aacttcatgg-tgttgctatgtatctgcactgtcttatggtataacactgatgacttccactg
upper sequence: LOC_Os01g43390.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G088533_T02 (Zea mays), 5'ss of exon 3
AGTAAACTCTGGGGCTCAATGTATACAAATATTTGATTCATGGGGTGGACAACTTCCACCTCATGTGTGGGAGCAGTGGTCAAAACCATATATCAAGCAGgtagcttacttttacttttctcggtcctgtttgcttccttaatccttatgactaatttcatgatgggtg---gctgctcta-aggttaatcaggttggatctac
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AGTTAACTCCGGGGCCTAGTGTATACAGATATTTGATTCATGGGGTGGACAACTTCCACCTCATGTGTGGGAGCAGTGGTCAAAACCATATATCAAAAAGgtgacttcct--tacttttcttgctttcatgtattaccaacttcatgattggcggtgctgctatgtatctgcactgtcttatagaacaacattgatggctcc--
upper sequence: LOC_Os01g43390.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G365644_T02 (Zea mays), 5'ss of exon 3
AGTAAACTCTGGGGCTCAATGTATACAAATATTTGATTCATGGGGTGGACAACTTCCACCTCATGTGTGGGAGCAGTGGTCAAAACCATATATCAAGCAGgtagcttacttttacttttctcggtcctgtttgcttccttaatccttatgactaatttcatgatgggtg---gctgctcta-aggttaatcaggttggatctac
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AGTTAACTCCGGGGCCCAGTGTATACAGATATTTGATTCATGGGGTGGACAACTTCCACCTCATGTGTGGGAGCAGTGGTCAAAACCATATATCAAAAAGgtgacttcct--tacttttcttgctttcatgtattaccaacttcatgattggcggtgctgctatgtatctgcactgtcttatagaacaacattgatggctcc--
upper sequence: LOC_Os01g43390.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G377609_T02 (Zea mays), 5'ss of exon 3
AGTAAACTCTGGGGCTCAATGTATACAAATATTTGATTCATGGGGTGGACAACTTCCACCTCATGTGTGGGAGCAGTGGTCAAAACCATATATCAAGCAGgtagcttacttttacttttctcg-gtcctgtttgcttccttaatccttatgactaatttcatgatgggtggctgctctaaggttaatcaggttggatctac-
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AGTTAACTCCGGGGCCCAGTGTATACAGATATTTGATTCATGGGGTGGACAACTTCCACCTCATGTGTGGGAGCAGTGGTCAAAACCATATATCAAAAAGgtgacttccttttcttgctttcatgtattaccaacttcatgattggcggtgctgctatgtatctgcactgtct--tatagaacaacattgatggctcccact
upper sequence: LOC_Os01g43390.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G025031_T01 (Zea mays), 5'ss of exon 1
AGTAAACTCTGGGGCTCAATGTATACAAATATTTGATTCATGGGGTGGACAACTTCCACCTCATGTGTGGGAGCAGTGGTCAAAACCATATATCAAGCAGgtagcttacttttacttttctcggtcctgtttgcttccttaatccttatgactaatttcatgatgggtggctgctctaaggttaatca--ggttggatctac--
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AGTTAACTCGGGGGCCCAGTGTATACAGATATTTGATTCATGGGGTGGACAGCTTCCACCTCATGTGTGGGAGCAGTGGTCAAAACCATATATCAAACAGgtgactcttccttacttttcttgctttcatgtattacc---aacttcatgg-tgttgctatgtatctgcactgtcttatggtataacactgatgactcccactg
upper sequence: LOC_Os01g43390.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA13G34500.1 (Glycine max), 5'ss of exon 4
AGTAAACTCTGGGGCTCAATGTATACAAATATTTGATTCATGGGGTGGACAACTTCCACCTCATGTGTGGGAGCAGTGGTCAAAACCATATATCAAGCAGgtagcttacttttacttttctcggtcctgt-ttgcttccttaatccttatgactaatttcatgatgggtggctgctctaaggttaatcaggttggatctac-
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AGTGGAGTCTGGGGCTCACTGCATACAAATATTTGATTCATGGGGTGGACAACTACCACCTGAAATGTGGGAATGCTGGTCAAAGTCATATATCAAAGAGgtaacagaaaaaaaaaatcctcatttctttcttgcctgatgaaattgtattttaatttttaaactttgcaatt--tggaattcttattattaagcctttgct
upper sequence: LOC_Os01g43390.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA12G35880.2 (Glycine max), 5'ss of exon 4
AGTAAACTCTGGGGCTCAATGTATACAAATATTTGATTCATGGGGTGGACAACTTCCACCTCATGTGTGGGAGCAGTGGTCAAAACCATATATCAAGCAGgtagcttacttttacttttctcggt-cctgtttgcttccttaatccttatgactaatttcatgatgggtggctgctctaaggttaatcaggttggatctac----
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AGTGGAGTCTGGGGCTCATTGCATACAAATATTTGATTCATGGGGTGGACAACTACCACCTGAAATGTGGGAACGCTGGTCAAAGCCTTATATCAAAGAGgtaacagaaaaaaaaatctccatttgcctgatgaaattgttttttaattttttaaacttcgcaatttggaattctt-----gttattaagccttcacttatgttaMapped 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|58695847|gb|CK084534.1|CK084534EST: AACTTCCACCTCATGTGTGGGAGCAGTGGTCAAAACCATATATCAAGCAG ATTGTGAATAAGATTAAGATTGAATGCCCCAATGTACCACTTGTTCTCTAT
genomic: AACTTCCACCTCATGTGTGGGAGCAGTGGTCAAAACCATATATCAAGCAGgtagcttact ... tcattggcagATTGTGAATAAGATTAAGATTGAATGCCCCAATGTACCACTTGTTCTCTAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGTAAACTCTGGGGCTCAATGTATACAAATATTTGATTCATGGGGTGGACAACTTCCACCTCATGTGTGGGAGCAGTGGTCAAAACCATATATCAAGCAGgtagcttacttttacttttctcggtcctgtttgcttccttaatccttatgactaatttcatgatgggtggctgctctaaggttaatcaggttggatctac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG