Sequence
atgc intronic sequence ATGC exonic sequenceCAATTGGAGCCATCTTTTCTGCGACAGATTCTGTCTGCACATTGCAGgttagttgaacaaattttgccatacctcgagagagacctggattcaacgtgctaatgtaatgatcttaaccccaaaacag
Basic information
species | Oryza sativa |
transcript | LOC_Os07g47100.3 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g47100.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G027851_T03 (Zea mays), 5'ss of exon 3
CAATTGGAGCCATCTTTTCTGCGACAGATTCTGTCTGCACATTGCAGgttagttgaacaaatt-ttgcc---atacctcgagagagacctggatt----caacgtg------ctaatgtaatgatcttaaccccaaaacag----------------------------------------
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CTATTGGAGCTATCTTTTCTGCAACGGATTCTGTGTGCACGCTGCAGgttggttggttggttggttgctggaacaatctcatggacatttcatttgaaacagtatatcttgcctcttgaggggaacctggtccctgcttagtaaattatttgacctgtaatcaccattttactggaaacag
upper sequence: LOC_Os07g47100.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA19G42900.1 (Glycine max), 5'ss of exon 5
CAATTGGAGCCATCTTTTCTGCGACAGATTCTGTCTGCACATTGCAGgttagttgaacaaattttgccatacctcgagagagacctggattcaacgtgctaatgtaatgatcttaaccccaaaacag--------
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CAATTGGTGCAATATTTGCTGCTACAGATTCTGTCTGCACATTGCAGgtttg--gaacgatatgtgcc-tttttcgcaatgtagcagcaacgaaggtgtcaatgctaagtactgaatttataaatgatgttgcag
upper sequence: LOC_Os07g47100.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA07G38160.1 (Glycine max), 5'ss of exon 5
CAATTGGAGCCATCTTTTCTGCGACAGATTCTGTCTGCACATTGCAGgt-ta---gttgaacaaattttgccatacctcgagagagacctggattcaacgtgct-aatgtaatgatcttaaccccaaaacag---
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CAATTGGAGCAATATTTTCAGCAACAGATTCTGTTTGCACGTTGCAGgtataaatgtcaaaagaaacactgcaaacctttgttttaattttcccttattgtactgaaaatgatgatgagtatgtggatgcttcag
upper sequence: LOC_Os07g47100.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA03G40290.1 (Glycine max), 5'ss of exon 5
CAATTGGAGCCATCTTTTCTGCGACAGATTCTGTCTGCACATTGCAGgttagttgaacaaattttgccatacctcgagagagacctggattcaacgtgctaatgtaatgatcttaaccccaaaacag--------
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CAATTGGTGCAATATTTGCTGCAACAGATTCTGTCTGCACATTGCAGgtttg--gaacaatatgtgcctttttccgcaacgttgcagcaaccaaggtgtcaatgcttagtactgaacttataaatgatgttgcag
upper sequence: LOC_Os07g47100.2 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv05s0020g01960.t01 (Vitis vinifera), 5'ss of exon 6
CAATTGGAGCCATCTTTTCTGCGACAGATTCTGTCTGCACATTGCAGgt-tagttgaacaaattttgccat-acctcgagagagacctggattcaacgtgctaatgtaatgatcttaaccccaaaacag--------
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CACTTGGAGCAATATTTTCTGCAACAGATTCCGTTTGCACATTGCAGgtacagatggccttactaagctgtgatcctgttactagttctaagggacaacacttccacaacttattta--tccaatccaattgtgcag
upper sequence: LOC_Os07g47100.2 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv07s0104g01280.t01 (Vitis vinifera), 5'ss of exon 5
CAATTGGAGCCATCTTTTCTGCGACAGATTCTGTCTGCACATTGCAGgt-----tagttgaacaaa--ttttgccatacctcgagagagacctggattcaacgtgctaatgtaatgatcttaaccc-caaaacag
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CAATTGGAGCAATTTTTTCAGCTACAGATTCTGTTTGCACCTTGCAGgtatagatatcttctcaaggctgtgattctgcttccataatggggacaatagaacatttctgactaaagtttgcatctgatatggcag
upper sequence: LOC_Os07g47100.2 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S169_48V6.1 (Physcomitrella patens), 5'ss of exon 5
CAATTGGAGCCATCTTTTCTGCGACAGATTCTGTCTGCACATTGCAGgttagttgaaca-aattttgcc--atacctcgagagagacctggattcaacgtgctaatgta-atgatcttaaccccaaaacag----------------
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CTATTGGAGTCATCTTTTCTGCTACCGATTCCGTCTGCACGTTGCAGgtacgttggatgtaagcacactcgatagattggcttagaacatcactttgttcgaaggtttttggggtcttaacacaagttcagtcttacgtagtgttttMapped 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|27549114|gb|CA767092.2|CA767092EST: TGTCTGCACATTGCAG GTCCTCAATCAGGATGAGACACCCTTTTTGTACAGTCTGGTATTCGGTGAA
genomic: TGTCTGCACATTGCAGgttagttgaa ... cccaaaacagGTCCTCAATCAGGATGAGACACCCTTTTTGTACAGTCTGGTATTCGGTGAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CAATTGGAGCCATCTTTTCTGCGACAGATTCTGTCTGCACATTGCAGgttagttgaacaaattttgccatacctcgagagagacctggattcaacgtgctaatgtaatgatcttaaccccaaaacag
- TTGGAG