Sequence
atgc intronic sequence ATGC exonic sequenceGTGAGGAGGGAGAGGATCAGTGAGAGGATGAGGATGCTGCAAGCACTGGTCCCTGGTTGTGACAAGgtaaaaaataagttggttactatttaactattacatgctctagttcaattctttcctctcatttttatttttgagagtaattattgttgagttgtacagttgtagtgacatcttgctaatgcatggctctaactttgataagaaacaactgtgcttttcttcag
Basic information
species | Oryza sativa |
transcript | LOC_Os08g42470.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g42470.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G145579_T02 (Zea mays), 5'ss of exon 3
GTGAGGAGGGAGAGGATCAGTGAGAGGATGAGGATGCTGCAAGCACTGGTCCCTGGTTGTGACAAGgtaaaaaataagttggttactatttaactattacatgctctagttca-attctttcctctcatttttatttttgagagtaattattgttgagttgtacagttgtagtgacatcttgctaatgcatggctctaactttgataagaaacaactgtgcttttcttcag
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GTGAGGAGAGAGAGGATCAGCGAGAGGATGAGGATGCTGCAGGCACTGGTCCCTGGCTGCGACAAGgtcaga--ttagttagttact-tggattaactgcctgcctgcatgcacgtgatatctagtaactttgagcgaaggaacaaattaatgt--gcttcttcttggacgacgacag-----------------------------------------------------
upper sequence: LOC_Os08g42470.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM5G882527_T03 (Zea mays), 5'ss of exon 3
GTGAGGAGGGAGAGGATCAGTGAGAGGATGAGGATGCTGCAAGCACTGGTCCCTGGTTGTGACAAGgtaaaaaataagttggtt--actatttaactattacatgctctagttcaattctttcctctcatttttatttttgagagtaattattgttgagttgtacagttgtagtgacatcttgctaatgcatggctctaactttgataagaaacaactgtgcttttcttcag
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GTGAGGAGAGAGAGGATCAGTGAGAGGATGAGGATGCTGCAAGCACTGGTCCCTGGTTGTGACAAGgtcaga--ttagttacttggattaactatatttgatatactgatatctgcttataagttatagtaggccgtttaagtagtaaactttgagaag--gaacaaatgtgcttttttttggacag---------------------------------------------
upper sequence: LOC_Os08g42470.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv17s0000g00430.t01 (Vitis vinifera), 5'ss of exon 3
GTGAGGAGGGAGAGGATCAGTGAGAGGATGAGGATGCTGCAAGCACTGGTCCCTGGTTGTGACAAGgtaaaaaataagttggttactatttaactattacatgct----ctagttcaattctttcctctcatttttatttttgagagtaattattgttgagttgtacagttgtagtgacatcttgctaatgcatggctctaactttgataagaaacaactgtgcttttcttcag
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GTAAGAAGAGAGAAAATCAGTGAGAGGATGAAGCTCTTGCAAGCACTTGTTCCTGGTTGTGACAAGgtgaag--ttgattctcttctaaatgataatgacttgtttttcctagacaagtatttttctgacactgtcat--------gtggtttggcttgaaatatag-------------------------------------------------------------------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|163926679|gb|EG713695.1|EG713695EST: TCAGTGAGAGGATGAGGATGCTGCAAGCACTGGTCCCTGGTTGTGACAAG GTTACTGGAAAGGCTCTCATTTTGGATGAGATCATCAACTATGTACAGTCG
genomic: TCAGTGAGAGGATGAGGATGCTGCAAGCACTGGTCCCTGGTTGTGACAAGgtaaaaaata ... ttttcttcagGTTACTGGAAAGGCTCTCATTTTGGATGAGATCATCAACTATGTACAGTCG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTGAGGAGGGAGAGGATCAGTGAGAGGATGAGGATGCTGCAAGCACTGGTCCCTGGTTGTGACAAGgtaaaaaataagttggttactatttaactattacatgctctagttcaattctttcctctcatttttatttttgagagtaattattgttgagttgtacagttgtagtgacatcttgctaatgcatggctctaactttgataagaaacaactgtgcttttcttcag
- - - - - - - - - - GAGAGG
- - - - - - - - - - - AGAGGA
- - - - - - - - - - - GAGGAT
- - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - TGCTGC