Sequence
atgc intronic sequence ATGC exonic sequenceATGTGCATATATCGATGGATATAATTGGTCACTGGTTAGATCTAATAAATGCGGATGGATGGATTCCTCGGGAGCAAATATTAGGAGCTGAAGCTTTAAGgtggttcccctggcgagcaatgaaccattgtcatatctagctatgagtttagagtgtcagttcttatataatctgtttttacatttctgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g69210.1 |
intron # | 11 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g69210.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G126468_T01 (Zea mays), 5'ss of exon 11
ATGTGCATATATCGATGGATATAATTGGTCACTGGTTAGATCTAATAAATGCGGATGGATGGATTCCTCGGGAGCAAATATTAGGAGCTGAAGCTTTAAGgtggttcccctggcgagcaatgaaccattgtcatatctagctatgagtttagagtgtcagttcttatataatctg-tttttacatttctgcag
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ATGTGCATATATCTATGGATATCATTGGACATTGGTTAGATCTGCTTAATTCAGATGGATGGATTCCTAGGGAGCAAATCTTAGGAGCTGAAGCTTTAAGgttgtttct------accgac-aacca--gtgataactg---ataagtttagtgcgaca---cttatataatccaacttttgcaatcatgcag
upper sequence: LOC_Os01g69210.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA05G27890.1 (Glycine max), 5'ss of exon 11
ATGTGCATATATCGATGGATATAATTGGTCACTGGTTAGATCTAATAAATGCGGATGGATGGATTCCTCGGGAGCAAATATTAGGAGCTGAAGCTTTAAGgtggttcccctggcgagcaatgaaccattgtcatatctagctatgagtttagagtgtc-agttcttatataatct---gtttttacatttctgcag
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ATATCCATATTTCATTGGATATCATTGGACACTGGTTAGATTTGATGAATGCTGATGGATGGATACCACGTGAACAAATTCTCGGGGCTGAAGCACTCAGgtg-------tagtaaa-aacatttagttcaaataatt-gcagtaaatgtaaagtttttagctgtcctactgacttagattcttctgcacttgcag
upper sequence: LOC_Os01g69210.2 (Oryza sativa), 5'ss of exon 12
lower sequence: AT1G67490.1 (Arabidopsis thaliana), 5'ss of exon 11
ATGTGCATATATCGATGGATATAATTGGTCACTGGTTAGATCTAATAAATGCGGATGGATGGATTCCTCGGGAGCAAATATTAGGAGCTGAAGCTTTAAGgtggttcccctggcgagcaatgaaccattgtcatatctagctatgagtttagagtgtcagttcttatataatctgtttttacatttctgcag
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ATATTCGTATAACCTTGGATATCGTTGGACACTGGTTAGACCTATTGAACATAGATGGATGGATTCCACGTGAGCAAATTTTGGGTGCTGAAGCTTTGAGgtatttactctctc---tcactaaccgtggt-------agtcatgg--ttattgttgtaattgttttatagtgtttctctac----ctgcag
upper sequence: LOC_Os01g69210.2 (Oryza sativa), 5'ss of exon 12
lower sequence: AT1G24320.1 (Arabidopsis thaliana), 5'ss of exon 10
ATGTGCATATATCGATGGATATAATTGGTCACTGGTTAGATCTAATAAATGCGGATGGATGGATTCCTCGGGAGCAAATATTAGGAGCTGAAGCTTTAAGgtggttcccctggcgagcaatgaaccattgtcatatc-tagctatgagtttagagtgtcagttcttatataatctgtttttacatttctgcag
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ATGTCCATATAACCTTGGAAATAGTTGGAAACTGGTTAGATTTAATGAATATAGATGGATGGATTCCACGTGAGCAAGTTTTGGGAGCTGAAGCTCTCAGgttgttatatatatcatacactcttactagccacaaaatattcatcattactgcttgtt-gctattatggattctaacattcttctgctgcag
upper sequence: LOC_Os01g69210.2 (Oryza sativa), 5'ss of exon 12
lower sequence: Vv01s0010g03300.t01 (Vitis vinifera), 5'ss of exon 11
ATGTGCATATATCGATGGATATAATTGGTCACTGGTTAGATCTAATAAATGCGGATGGATGGATTCCTCGGGAGCAAATATTAGGAGCTGAAGCTTTAAGgtggttcccctggcgagcaatgaaccattgtcatatctagctatgagtttagagtgtcagttcttatat---aatctgtttttacatttctgcag
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ACATCCGCATTTGTTTGGATATAATTGGACATTGGTTAGATTTAATGAACATTGATGGATGGATACCAAGGGAGCAAATTTTGGGTGCCGAAGCTCTAAGgtggtacc------aagcatc---ttgttatagtattta-tgataaatacagaggtttgcattctgtgagtaaatatcttattgtgtgtttgcagMapped 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|58672225|gb|CK060911.1|CK060911EST: GCGGATGGATGGATTCCTCGGGAGCAAATATTAGGAGCTGAAGCTTTAAG TAAAGTTCCTGAGGAATTTGTTCTGCAGTACCCTTCCAATGGAAATCCCCC
genomic: GCGGATGGATGGATTCCTCGGGAGCAAATATTAGGAGCTGAAGCTTTAAGgtggttcccc ... atttctgcagTAAAGTTCCTGAGGAATTTGTTCTGCAGTACCCTTCCAATGGAAATCCCCC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATGTGCATATATCGATGGATATAATTGGTCACTGGTTAGATCTAATAAATGCGGATGGATGGATTCCTCGGGAGCAAATATTAGGAGCTGAAGCTTTAAGgtggttcccctggcgagcaatgaaccattgtcatatctagctatgagtttagagtgtcagttcttatataatctgtttttacatttctgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC