Sequence
atgc intronic sequence ATGC exonic sequence...atgggaatgcttagactattgatgttaacagaaagtattgttatgctatataccctttgtataaatttctaatttggttccagcatttgctgcatcgcagGTTGTTGCAGTTAAACAGCTTGATCTAAATGGGCTTCAGGGAAACAGAGAATTCCTTGTGGAGGTTCTCATGCTCAGTCTCTTGCATCATCCTAATTTAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g15470.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g15470.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G074381_T01 (Zea mays), 3'ss of exon 2
atgggaatgcttagactattg-atgttaacagaaagtattgttatgctatataccctttgtataaatttctaatttggttccagcatttgctgcatcgcagGTTGTTGCAGTTAAACAGCTTGATCTAAATGGGCTTCAGGGAAACAGAGAATTCCTTGTGGAGGTTCTCATGCTCAGTCTCTTGCATCATCCTAATTTAG
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-tcgttgtgctgattgcaatgtgagctgtttcaaactattgtaacttaatttttgttttctatatatgtctaatgctgctttagcttttgctacatggcagGTTGTTGCAGTCAAACAACTTGATCTAAATGGGCTTCAAGGGAACAGAGAATTCCTCGTGGAGGTTCTCATGCTCAACCTCCTGCATCACCCTAATCTTG
upper sequence: LOC_Os01g15470.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA13G28730.1 (Glycine max), 3'ss of exon 2
atgggaatgcttagactattgatgttaacagaaagtattgttatgctatataccctttgtataaatttctaattt--ggttccagcatttgctgcatcgcagGTTGTTGCAGTTAAACAGCTTGATCTAAATGGGCTTCAGGGAAACAGAGAATTCCTTGTGGAGGTTCTCATGCTCAGTCTCTTGCATCATCCTAATTTAG
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-aagttatctgtctgctctcaattttcctgttgattattgctctgttactataactctgcctct-ttcataatttttaatgatgaaatcattctcgttgcagGTAGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG
upper sequence: LOC_Os01g15470.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA15G10360.1 (Glycine max), 3'ss of exon 2
atgggaatgcttagactattgatgttaacagaaagtattgttatgctatataccctttgtataaatttctaatttggttccagcatttgctg-catcgcagGTTGTTGCAGTTAAACAGCTTGATCTAAATGGGCTTCAGGGAAACAGAGAATTCCTTGTGGAGGTTCTCATGCTCAGTCTCTTGCATCATCCTAATTTAG
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-aagttatttgtctgctggaaattttcccattgattattgctctgttactataactatgcctctttcgtaatcttcattaatgaaatcattctcttcgcagGTGGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG
upper sequence: LOC_Os01g15470.3 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G18610.1 (Arabidopsis thaliana), 3'ss of exon 3
atgggaatgcttagactattgatgttaacagaaagtattgttatgctatataccctttgtataaatttctaatttggttccagcatttgctgcatcgcagGTTGTTGCAGTTAAACAGCTTGATCTAAATGGGCTTCAGGGAAACAGAGAATTCCTTGTGGAGGTTCTCATGCTCAGTCTCTTGCATCATCCTAATTTAG
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------------------gtgaagttcgtaaattgaatt-taatgtttcataatca------agattcgtcttctaatt---ggatttaatattttgcagATAGTAGCTGTTAAACAGCTTGATCGAAACGGTCTACAAGGAAACAGAGAGTTTCTTGTAGAGGTTCTTATGCTGAGCCTTCTGCATCATCCCAATCTTG
upper sequence: LOC_Os01g15470.3 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 2
atgggaatgcttagactattga-tgttaacaga-aagtattgttatgctatataccctttgtataaatttctaattt--ggttccagcatttgctgcatc-gcagGTTGTTGCAGTTAAACAGCTTGATCTAAATGGGCTTCAGGGAAACAGAGAATTCCTTGTGGAGGTTCTCATGCTCAGTCTCTTGCATCATCCTAATTTAG
||| || ||| || | | | | | || ||||| | | | | | | | || | |||| ||||| | | || || || |||||| ||||| || ||||| ||||| | |||||| ||||| ||||| ||||||||| | ||||||||||||||||| || ||||| ||||| || || | |
-----aatcttttatatatggaatatggattgctgaataatgttaatcactgtgtctcatctggtatttattgatttttggttcaatgaattattgtatttgcagGTAGTTGCTGTGAAACAACTTGACCGAAATGGCCTTCAAGGAAATAGAGAATTCTTGGTGGAGGTTCTCATGCTTAGCCTCTTACATCACCCAAACCTTG
upper sequence: LOC_Os01g15470.3 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ25419 (Selaginella moellendorffii), 3'ss of exon 2
atgggaatgcttagactattgatgttaacagaaagtattgttatgctatataccctttgtataaatttctaatttggttccagcatttgctgcatcgcagGTTGTTGCAGTTAAACAGCTTGATCTAAATGGGCTTCAGGGAAACAGAGAATTCCTTGTGGAGGTTCTCATGCTCAGTCTCTTGCATCATCCTAATTTAG
| | | | || || | | | | | | | | | |||| | |||||| | || | | || | || ||||||||| ||||| || ||||| ||| ||| || ||||| ||||||||||||||| | ||||| ||||| |||||||| | | || ||||| ||| | |
--------gttcgg--tgttcttgctctcttgcaaaaccagttttttctttcttgtttg-gttttgttctaacaagttttcctc-cttccaacactgcagGTTGTGGCAGTGAAGCAGCTGGATAGAAACGGACTTCAAGGAAACAGAGAATTCTTGGTGGAAGTTCTGATGCTCAGCTTGCTTCACCATCCAAATCTCG
upper sequence: LOC_Os01g15470.3 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ23436 (Selaginella moellendorffii), 3'ss of exon 2
atgggaatgcttagactattgatgttaacagaaagtattgttatgctatataccctttgtataaatttctaatttggttccagcatttgctgcatcgcagGTTGTTGCAGTTAAACAGCTTGATCTAAATGGGCTTCAGGGAAACAGAGAATTCCTTGTGGAGGTTCTCATGCTCAGTCTCTTGCATCATCCTAATTTAG
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--------gttcggtgttcttgctctcttgcaagttttttctttcttgtttggt-tttgtctaa----caaattttcctcc-----ttccaacactgcagGTTGTGGCAGTGAAGCAGCTGGATAGAAACGGACTTCAAGGAAACAGAGAATTCTTGGTGGAAGTTCTGATGCTCAGCTTGCTTCACCATCCAAATCTCGMapped 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|2317565|gb|C22619.1|C22619EST: GCCGAGGAGGATTCGGCAGTGTGTATAAAGCATTTCTCAATGATAGACAG GTTGTTGCAGTTAAACAGCTTGATCTAAATGGGCTTCAGGGAAACAGAGAA
genomic: GCCGAGGAGGATTCGGCAGTGTGTATAAAGCATTTCTCAATGATAGACAGgtttgtattt ... tgcatcgcagGTTGTTGCAGTTAAACAGCTTGATCTAAATGGGCTTCAGGGAAACAGAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctatataccctttgtataaatttctaatttggttccagcatttgctgcatcgcagGTTGTTGCAGTTAAACAGCTTGATCTAAATGGGCTTCAGGGAAACAGAGAATTCCTTGTGGAGGTTCTCATGCTCAGTCTCTTGCATCATCCTAATTTAG
ttctaat putative branch site (score: 2)
tttgtataaatttcta 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 |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgggaatgcttagactattgatgttaacagaaagtattgttatgctatataccctttgtataaatttctaatttggttccagcatttgctgcatcgcagGTTGTTGCAGTTAAACAGCTTGATCTAAATGGGCTTCAGGGAAACAGAGAATTCCTTGTGGAGGTTCTCATGCTCAGTCTCTTGCATCATCCTAATTTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG