Sequence
atgc intronic sequence ATGC exonic sequence...aacctacctatctgaagctggttaccaacctcataaacttgatttggatggatgaccctatgtccttaatctgtttccttttcttgtttgatgccatcagGTGAAGGTTGCGACGAGGAAGATCTATGACCCGCTGGAGGAGGACGCCTTCCGGCCGATCCTCCACCACTACGACGGCCCCAAGTTCAGGCTGGAGCTCA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g36950.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g36950.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G071154_T01 (Zea mays), 3'ss of exon 3
aacctacctatctgaagctggttaccaacctcataaacttgatttggatgg-atgaccctatgtccttaatctgtttccttttcttgtttgatgccat-cagGTGAAGGTTGCGACGAGGAAGATCTATGACCCGCTGGAGGAGGACGCCTTCCGGCCGATCCTCCACCACTACGACGGCCCCAAGTTCAGGCTGGAGCTCA
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-gaggatctggtcgcaggctccaagtgcgaccatctagatgctgtagctgctgcatttcctcgttattgacgcatggtgcttgcg-atgtgatgtgctgcagGTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTCCGCCCCATCCTGCACCACTACGACGGGCCCAAGTTCCGGCTCGAGCTCT
upper sequence: LOC_Os01g36950.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AC207342.3_FGT008 (Zea mays), 3'ss of exon 3
------aacctacctatctgaagctggttaccaacctcataaacttgatttggatggatgaccctatgtccttaatctgtttccttttcttgtttgatgccatcagGTGAAGGTTGCGACGAGGAAGATCTATGACCCGCTGGAGGAGGACGCCTTCCGGCCGATCCTCCACCACTACGACGGCCCCAAGTTCAGGCTGGAGCTCA
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tgtagcatgttgtttcatcgcatctaggcctctagggagtatctagtactcgtagttgttaccc-aagtggtga---cgcatgcatgatgtttgtgatgt--gcagGTGCGAGTGGCAACGCGGAAGATCTACGATCCACTGGAGGAGGACGCCTTCCGCCCCATCCTTCACCACTACGACGGGCCCAAGTTTCGGCTCGAGCTCT
upper sequence: LOC_Os01g36950.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv02s0025g01720.t01 (Vitis vinifera), 3'ss of exon 3
----aacctacctatctgaagctggttaccaacctcataaacttgatttggatggatgaccctatgtccttaatctgtttccttttcttgtttgatgccatcagGTGAAGGTTGCGACGAGGAAGATCTATGACCCGCTGGAGGAGGACGCCTTCCGGCCGATCCTCCACCACTACGACGGCCCCAAGTTCAGGCTGGAGCTCA
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gaagaaattccccatacccatctgctta--atctagatgatggtccatttaataaaaggtcatactgaattggggtttaccattctgtggttttgtg--aatagGTGCGGGTGGTCACCAGGAAAATCTGTGAGCCAATGGAAGAGGATTCATTCAGGCCGGTCCTCCATCACTATGACGGCCCCAAGTTCCGCCTGGAGCTGA
upper sequence: LOC_Os01g36950.2 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ24245 (Selaginella moellendorffii), 3'ss of exon 3
aacctacctatctgaagctggttaccaacctcataaacttgatttggatggatgaccctatgtccttaatctgtttccttttcttgtttgatgccat-cagGTGAAGGTTGCGACGAGGAAGATCTATGACCCGCTGGAGGAGGACGCCTTCCGGCCGATCCTCCACCACTACGACGGCCCCAAGTTCAGGCTGGAGCTCA
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-----gtttgtctctcgttttctaggagaatagaaagctttttcttgttcttgagctgcaagagctacaaaggaaaacccatc----gtgatcccatacagGTAAGAACGAGAGTGCGAAAGGCCTGTAAAGCTCTGGAGGAGGATGCGTTTCGGCCCATACTCCATCACTACGACGGCCCAAAGTTTCGCTTGCAGCTCTMapped 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|9884513|gb|BE607346.1|BE607346EST: CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAG GTGAAGGTTGCGACGAGGAAGATCTATGACCCGCTGGAGGAGGACGCCTTC
genomic: CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAGgtaccattga ... atgccatcagGTGAAGGTTGCGACGAGGAAGATCTATGACCCGCTGGAGGAGGACGCCTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggatggatgaccctatgtccttaatctgtttccttttcttgtttgatgccatcagGTGAAGGTTGCGACGAGGAAGATCTATGACCCGCTGGAGGAGGACGCCTTCCGGCCGATCCTCCACCACTACGACGGCCCCAAGTTCAGGCTGGAGCTCA
ttaatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aacctacctatctgaagctggttaccaacctcataaacttgatttggatggatgaccctatgtccttaatctgtttccttttcttgtttgatgccatcagGTGAAGGTTGCGACGAGGAAGATCTATGACCCGCTGGAGGAGGACGCCTTCCGGCCGATCCTCCACCACTACGACGGCCCCAAGTTCAGGCTGGAGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- cctacct
- - - - - -ctgaagc
- - - - - - - - - - - - - - - -cataaac
- - - - - - - - - - - - - - - - - - - - - - - -atggatg