Sequence
atgc intronic sequence ATGC exonic sequencegtcagttaccaaatcaactcccataagcttcttactctgagcttcttttacctttgaaatttgcatatatccttcatcctctggtctgtattaatttattaatgctctatatattttaacaatacctctgacttttacatatccagGCTTTTCGCGCACAGAACATTGAAAGTGCAAAGTCAAGGCTCAGTATGTGTGCAGAAGACATCAGGGAAGAGTTGAAATCTAAAGAAGACAACCAAGAAC
Basic information
species | Oryza sativa |
transcript | LOC_Os02g55200.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g55200.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G049672_T01 (Zea mays), 3'ss of exon 3
gtcagttaccaaatcaactcccataagcttcttactctga----gcttcttttacctttgaaatttgcatatatccttcatcctctggtctgtattaatttatt---aatgct----ctatatattttaacaatacctctgacttttacatatccagGCTTTTCGCGCACAGAACATTGAAAGTGCAAAGTCAAGGCTCAGTATGTGTGCAGAAGACATCAGGGAAGAGTTGAAATCTAAAGAAGACAACCAAGAAC
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gtcagtaattaagttaactgcttta-gcctcttatgttgaaatagattcttgaacctgataaattttaata-actaatcattgtctattattcatggatttatttacaatattggtgttacaacttacaacaaggcct-taactgtt-tggctctagGCTTTTCGTGCCCGAAACATTGAAAGTGCAAAGTCAAGGCTCACTATGTGTGCAGACGACATCAGGGAGGAGTTAAAATCTTCAGAAGATAACTTAGACC
upper sequence: LOC_Os02g55200.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G101662_T01 (Zea mays), 3'ss of exon 3
gtcagttaccaaatcaactcccataagcttcttactctga----gcttcttttacctttgaaatttgcatatatccttcatcctctggtctgtattaatttattaatgctctatatattttaaca-atacctctgacttttacatatccagGCTTTTCGCGCACAGAACATTGAAAGTGCAAAGTCAAGGCTCAGTATGTGTGCAGAAGACATCAGGGAAGAGTTGAAATCTAAAGAAGACA-ACCAAGAAC--
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gtcaataactaagtaaattggtttc-gcctcttatgttgaaatagattcttgaacttgtaaaatttcaaca-actaatcattatatattattcattgatttatttacgatattgatattacaacttacaacaataactgttg-atctctagGCTTTTTGTGTCTAAAACATTGGAAGTGCAAAGTCAAGGCTCACTATGTGTGTAGACGATATCAAG---GAGTTAAAATGTTCAGAAGATAGACCTATGTTCA
upper sequence: LOC_Os02g55200.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G070276_T01 (Zea mays), 3'ss of exon 2
gtcagttaccaaatcaactcccataagcttcttactctga----gcttcttttacctttgaaatttgcatatatccttcatcctctggtctgtattaattt-attaatgctctatatattttaaca-atacctctgacttttacatatccagGCTTTTCGCGCACAGAACATTGAAAGTGCAAAGTCAAGGCTCAGTATGTGTGCAGAAGACATCAGGGAAGAGTTGAAATCTAAAGAAGACA-ACCAAGAAC----
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gtcaataactaagtaaattggttta-gcctcttatgttgaaaaagattcttgaacttgtaaaatttcaaca-actaatcattatatattattcattgattttatttacgatattgatattacaacttacaacaataactgttg-atctctagGCTTTTTGTGTCTAAGACATTGGAAGTGCAAAGTCAAGGCTCACTATGTGT--AGACGATATCAAG---GAGTTAAAATGTTCAGAAGATAGACCTATGTTCATAMapped 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|218487528|gb|FG948329.1|FG948329EST: AGGATGTCTCCATGGAGAGAGGAGCTTTTCTGGTCCAGCAAGCGATGAGG GCTTTTCGCGCACAGAACATTGAAAGTGCAAAGTCAAGGCTCAGTATGTGT
genomic: AGCATGTCTCCATGGAGAGAGGAGCTTTTCTGGTCCAGCAAGCGATGAGGgtcagttacc ... acatatccagGCTTTTCGCGCACAGAACATTGAAAGTGCAAAGTCAAGGCTCAGTATGTGT
EST:
gi|8956748|gb|BE230551.1|BE230551EST: AGCATGTCTCCATGGAGAGAGGAGCTTTTCTGGTCCAGCAAGCGATGAGG GCTTTTCGCGCACAGAACATTGAAAGTGCAAAGTCAAGGCTCAGTATGTGT
genomic: AGCATGTCTCCATGGAGAGAGGAGCTTTTCTGGTCCAGCAAGCGATGAGGgtcagttacc ... acatatccagGCTTTTCGCGCACAGAACATTGAAAGTGCAAAGTCAAGGCTCAGTATGTGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatttattaatgctctatatattttaacaatacctctgacttttacatatccagGCTTTTCGCGCACAGAACATTGAAAGTGCAAAGTCAAGGCTCAGTATGTGTGCAGAAGACATCAGGGAAGAGTTGAAATCTAAAGAAGACAACCAAGAAC
cttttac CT-rich tract
tattaatgctctatat 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 |
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gtcagttaccaaatcaactcccataagcttcttactctgagcttcttttacctttgaaatttgcatatatccttcatcctctggtctgtattaatttattaatgctctatatattttaacaatacctctgacttttacatatccagGCTTTTCGCGCACAGAACATTGAAAGTGCAAAGTCAAGGCTCAGTATGTGTGCAGAAGACATCAGGGAAGAGTTGAAATCTAAAGAAGACAACCAAGAAC
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