Sequence
atgc intronic sequence ATGC exonic sequenceAGCGGATAAATGTGTTTTGGCCTCATCTGGATTTCAAGGTGATGTTAAAGCTTTGCAGAGGAACCTTACTGCCAAGGAATTGgtaagtctgaacaattctctaaaaccatctgtaactgcaagaaattttcatgattaaccacattttcgacaactttatcgcaataatctgatctactatc...
Basic information
species | Oryza sativa |
transcript | LOC_Os08g41730.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g41730.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G124417_T01 (Zea mays), 5'ss of exon 2
AGCGGATAAATGTGTTTTGGCCTCATCTGGATTTCAAGGTGATGTTAAAGCTTTGCAGAGGAACCTTACTGCCAAGGAATTGgtaagtctgaacaattctctaaaacc--atctgt--aactgcaagaaattttcatgattaaccacattttcgacaactttatcgcaataatctgatctactatc
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GTCAGACAAATGTGTTTTGGCTTCATCTGGGTTTCAAGGTGATATCAAAGCTTTGCAGAAGGCTCTGGCTGCTAAGGAATTAgtaagtcgctaaggctattgattccttgagctgttgaactagttgaaacctacattaagattattgtatttttgcagttgacgacatcaa--cgatcaacct--
upper sequence: LOC_Os08g41730.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA08G39420.3 (Glycine max), 5'ss of exon 1
------------------AGCGGATAAATGTGTTTTGGCCTCATCTGGATTTCAAGGTGATGTTAAAGCTTTGCAGAGGAACCTTACTGCCAAGGAATTGgtaagtctgaacaattctctaaaaccatctgtaactgcaagaaa---ttttcatgattaaccacattttcgacaactttatcgcaataatctgatctactatc
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TATTGTTTCGCCTGACAGGGCTGAGAAGTGTGTGATGGCTTCATCTGGCTTTCAAGCTGATGTCAAAGCTTTGCAGAAGGTTTTGTCTGCTAGGCATTTGgtgagtc--gaaaacttaaaacaacaacttagtagtgcttgtgaattcttttggggttgcttagaatgttacaaactacaatattctattttaatctcttgg-
upper sequence: LOC_Os08g41730.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA08G39420.1 (Glycine max), 5'ss of exon 3
AGCGGATAAATGTGTTTTGGCCTCATCTGGATTTCAAGGTGATGTTAAAGCTTTGCAGAGGAACCTTACTGCCAAGGAATTGgtaagtctgaacaattctctaaaaccatctgtaactgcaagaaa---ttttcatgattaaccacattttcgacaactttatcgcaataatctgatctactatc
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GGCTGAGAAGTGTGTGATGGCTTCATCTGGCTTTCAAGCTGATGTCAAAGCTTTGCAGAAGGTTTTGTCTGCTAGGCATTTGgtgagtc--gaaaacttaaaacaacaacttagtagtgcttgtgaattcttttggggttgcttagaatgttacaaactacaatattctattttaatctcttgg-
upper sequence: LOC_Os08g41730.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv15s0048g00900.t01 (Vitis vinifera), 5'ss of exon 3
AGCGGATAAATGTGTTTTGGCCTCATCTGGATTTCAAGGTGATGTTAAAGCTTTGCAGAGGAACCTTACTGCCAAGGAATTGgtaagtctgaacaattctctaaaaccatctgtaactgcaagaaatt--ttcatgattaaccacattttcgacaactttatcgcaataatctgatctactatc-
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AGCAGACAAATGTGTAATGGCCTCATCTGGATTTCAAGCTGATGTAAGAGCTTTACAGAAGCACTTGGCAGCTAGGCACTTGgtgaggtttcataaacatt---aaccatatagcacttttatattatgatccattttttcctaaagaatatgaactttttggagcatgataagttcaaataaacMapped 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|27576638|gb|CA999332.1|CA999332EST: TTCAAGGTGATGTTAAAGCTTTGCAGAGGAACCTTACTGCCAAGGAATTG CTTTATGAACACAACCATAACAAGAAAATGAGCTGCCCTGCGATGGCGCAA
genomic: TTCAAGGTGATGTTAAAGCTTTGCAGAGGAACCTTACTGCCAAGGAATTGgtaagtctga ... gcttttatagCTTTATGAACACAACCATAACAAGAAAATGAGCTGCCCTGCGATGGCGCAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGCGGATAAATGTGTTTTGGCCTCATCTGGATTTCAAGGTGATGTTAAAGCTTTGCAGAGGAACCTTACTGCCAAGGAATTGgtaagtctgaacaattctctaaaaccatctgtaactgcaagaaattttcatgattaaccacattttcgacaactttatcgcaataatctgatctactatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA