Sequence
atgc intronic sequence ATGC exonic sequenceATTCATCATATGCTTTACCCTATAACCATTGAAGTGCTTCATCAAGTGTTTTCTCCCTATGGATTTGTGGAGAAGATAGTCACATTTCAAAAGTCAGCCGgtcagattctttctacctctcattctcactctattcttgcatttaatgcagtgttttccttgccagatagcatgcagattatgaggcgtatttcatagtt...
Basic information
species | Oryza sativa |
transcript | LOC_Os01g64770.5 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g64770.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA10G36770.1 (Glycine max), 5'ss of exon 5
ATTCATCATATGCTTTACCCTATAACCATTGAAGTGCTTCATCAAGTGTTTTCTCCCTATGGATTTGTGGAGAAGATAGTCACATTTCAAAAGTCAGCCGgtcagattctttc---tacctctcattctcactctattcttgcatttaatgcagtgttttccttgccagatagcatgcagattatgaggcgtatttcatagtt
||||||| ||| | || ||||| || | || ||||| ||||||| ||||||||| |||||| |||||| ||||| || |||||||| |||||||| ||||||||||| || | ||| | ||||| | | ||| | ||| || || | | | | | |||| ||||| ||| | | ||
GTTCATCACATGTTGTATCCTATGACTGTGGATGTGCTGTATCAAGTATTTTCTCCCCATGGATCTGTGGAAAAGATTGTAACATTTCAGAAGTCAGCTGgtcagattctgtcagatttctccctttctcttctttccatcctattaacatttttgtgtttctggactttaactaggtagat--tgaggt-tatatttttgtc
upper sequence: LOC_Os01g64770.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA20G30820.1 (Glycine max), 5'ss of exon 6
ATTCATCATATGCTTTACCCTATAACCATTGAAGTGCTTCATCAAGTGTTTTCTCCCTATGGATTTGTGGAGAAGATAGTCACATTTCAAAAGTCAGCCGgtcagattctttct-acctctcattctcactctattcttgcatttaatgcagtgttttccttgccagatagcatgcagatta--tgaggcgtatttcatagtt
||||||| ||||| || ||||| || | || ||||| ||||||| ||||||||| |||||| |||||| ||||| || |||||||| |||||||| ||||||||||| || | |||| | || || ||| | || | | ||| || | ||| | || | ||||| ||| | | ||
GTTCATCACATGCTGTATCCTATGACAGTGGATGTGCTGTATCAAGTATTTTCTCCCCATGGATCTGTGGAAAAGATTGTAACATTTCAGAAGTCAGCTGgtcagattctctcagatttctccctttctcttctttccatc-cctattaacatttttgtgttcctagactttaactaggtagcttgaggt-tatatttttgt-
upper sequence: LOC_Os01g64770.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA02G08870.1 (Glycine max), 5'ss of exon 6
ATTCATCATATGCTTTACCCTATAACCATTGAAGTGCTTCATCAAGTGTTTTCTCCCTATGGATTTGTGGAGAAGATAGTCACATTTCAAAAGTCAGCCGgtcagattctttct-acctctcattctcactctattcttgcattta-atgcagtgttttccttgccagatagcatgcagattatgaggcgtatttcatagtt
||||||| ||||| || |||||||| || ||||| |||||||||||||||||| ||||||||||||| ||||| || ||||| || |||||||| ||||||||||| || | ||| |||| || | || | ||| | || | ||| ||| | || | | || | ||| | | ||
GTTCATCACATGCTGTATCCTATAACAGCGGATGTGCTACATCAAGTGTTTTCTCCCCATGGATTTGTGGAAAAGATTGTAACATTCCAGAAGTCAGCTGgtcagattctctcagatttcttcctctctctttcttttcctattaagattttttttttgtcttaggggccttcacggggtgaattgaggatatatt-tggt-
upper sequence: LOC_Os01g64770.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA16G27970.1 (Glycine max), 5'ss of exon 4
ATTCATCATATGCTTTACCCTATAACCATTGAAGTGCTTCATCAAGTGTTTTCTCCCTATGGATTTGTGGAGAAGATAGTCACATTTCAAAAGTCAGCCGgtcagattctttct-acctctcattctcactctattcttgcatttaatgcagtgttttccttgccag---atagcatgcagattatgaggcgtatttcatagtt
||||||| ||||| || |||||||| || ||||| |||||||||||||||||| ||||||||||||| ||||| || |||||||| |||||||| ||||||||||| || | ||| |||| || | || | ||| | | ||| || | ||| | || | | ||||| |
GTTCATCACATGCTGTATCCTATAACAGCGGATGTGCTACATCAAGTGTTTTCTCCCCATGGATTTGTGGAAAAGATTGTAACATTTCAGAAGTCAGCTGgtcagattctctcagatttcttcctctctctttcttttcctattaagatttttttttgttttagggggccataatggggtgaattgaggatatatttggt----
upper sequence: LOC_Os01g64770.2 (Oryza sativa), 5'ss of exon 6
lower sequence: AT1G43190.1 (Arabidopsis thaliana), 5'ss of exon 6
ATTCATCATATGCTTTACCCTATAACCATTGAAGTGCTTCATCAAGTGTTTTCTCCCTATGGATTTGTGGAGAAGATAGTCACATTTCAAAAGTCAGCCGgtcagattctttctacctctcattctcactctattcttgcatttaatgcagtgttttccttgccagatagcatgcagattatgaggcgtatttcatagtt-------------------------------------------------------------------------------------------
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ATCCATCACATGCTGTATCCAATTACTGTTGACGTCCTGCATCAAGTTTTTTCTCCCTATGGATTTGTCGAGAAGCTCGTCACTTTCCAGAAGTCTGCTGgtcagcttctccgcatttctt-ttctctctctctctctctcttctattc-gttttagcttagagaattatttgaaagtttgtctgtttcatgttattggtctctttaaaataatattgctgttaaaactttgtatttgccatctaacagtttgatgattgttaactataagcttgtttgttgactatttag
upper sequence: LOC_Os01g64770.2 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv18s0072g00310.t01 (Vitis vinifera), 5'ss of exon 5
ATTCATCATATGCTTTACCCTATAACCATTGAAGTGCTTCATCAAGTGTTTTCTCCCTATGGATTTGTGGAGAAGATAGTCACATTTCAAAAGTCAGCCGgtcagattctttctacctctcattctcactctattcttgcatttaatgcagtgttttccttgccagatagcatgcagattatgaggcgtatttc-atagtt
|||||||| |||| ||||||||||| | || ||||| ||||||||||||||||| |||| |||||||||||||| ||||| ||||| |||||||| |||||| ||||| | | | | | ||| | | | || | | | | || | ||||| || | || ||
ATTCATCACCTGCTATACCCTATAACAGTGGAGGTGCTGCATCAAGTGTTTTCTCCTCATGGTTTTGTGGAGAAGATTGTCACGTTTCAGAAGTCAGCTGgtcagcttcttcaagttttctctctttatctctcttgtgctgtctctctatctcttaattcttaattctcctttcaactcttgaggactagctggatggt-
upper sequence: LOC_Os01g64770.2 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv07s0031g02030.t01 (Vitis vinifera), 5'ss of exon 6
ATTCATCATATGCTTTACCCTATAACCATTGAAGTGCTTCATCAAGTGTTTTCTCCCTATGGATTTGTGGAGAAGATAGTCACATTTCAAAAGTCAGCCGgtcagattctttctacctctcattctcactctattcttgcatttaatgcagtgttttccttgccagatagcatgcagattatgaggcgta---tttcatagtt-
|||||||| | || || || ||||| | |||||||| ||||||||||||||||| |||| ||||| |||||||| ||||||||||||||||| || |||||||||||| | | | ||| | | ||| | | ||||| || | | || |||| || | || | | | |
ATTCATCACCTACTATATCCCATAACAGTGGAAGTGCTCCATCAAGTGTTTTCTCCTCATGGGTTTGTTGAGAAGATTGTCACATTTCAAAAGTCGGCGGgtcagattcttcaagttttctctctctatcttatgcattgtcttagttct-tgtttattttatta---atgattttgattttggagtttaagatactagaatgt
upper sequence: LOC_Os01g64770.2 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S36_37V6.1 (Physcomitrella patens), 5'ss of exon 4
ATTCATCATATGCTTTACCCTATAACCATTGAAGTGCTTCATCAAGTGTTTTCTCCCTATGGATTTGTGGAGAAGATAGTCACATTTCAAAAGTCAGCCGgtcagattctttctacctctcattctcactctattct-tgcatttaatgcagtgttttccttgccagatagcatgcagattatgaggcgtatttcatagtt--
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ATACACAACCCGCTCTATCCTATCACCGTGGATGTGCTGCACCAAGTGTTTTCCCCCCATGGCTTTGTCGAGAAGATCGTCACCTTCACAAAGTCAGCTGgtcagcttctcttctgtcttggctatctctctgccttctgcctttttcgggcccttttctttcac---catttttctctttctggcgggtagtcaaaggtgggMapped 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|29656748|gb|CB653023.1|CB653023EST: TTCTCCCTATGGATTTGTGGAGAAGATAGTCACATTTCAAAAGTCAGCCG GCTTTCAAACCCTCATACAATATCAGTCACGTCAAAGTGCAATACAAGCTT
genomic: TTCTCCCTATGGATTTGTGGAGAAGATAGTCACATTTCAAAAGTCAGCCGgtcagattct ... ggtggtgcagGCTTTCAAACCCTCATACAATATCAGTCACGTCAAAGTGCAATACAAGCTT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATTCATCATATGCTTTACCCTATAACCATTGAAGTGCTTCATCAAGTGTTTTCTCCCTATGGATTTGTGGAGAAGATAGTCACATTTCAAAAGTCAGCCGgtcagattctttctacctctcattctcactctattcttgcatttaatgcagtgttttccttgccagatagcatgcagattatgaggcgtatttcatagtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA