Sequence
atgc intronic sequence ATGC exonic sequence...cttgctgtgtctacctacccatgttaactctcgattaagtgttcccttttctctcgcttgtttgacaatgtgcttactagtgagttctgatgcatgatagCCGTGAGATATTCAACAAATGGCAAGCGCAAAGATGGTGGGCCGAAAATTATGAGAAAGTCATGGAGCTTTACAATGTTCAGAGGTTCAACCAGCAAACT
Basic information
species | Oryza sativa |
transcript | LOC_Os08g36020.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g36020.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G037941_T01 (Zea mays), 3'ss of exon 2
-cttgctgtgtctacctacccatgttaactctcgattaagtgttcccttttctctcgcttgtttg-acaatgtgcttactagtgagttctgatgcatgatagCCGTGAGATATTCAACAAATGGCAAGCGCAAAGATGGTGGGCCGAAAATTATGAGAAAGTCATGGAGCTTTACAATGTTCAGAGGTTCAACCAGCAAACT
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gtttcaggtgacgaaa-gtacaaactaagtgttttctgtatga-caatgacaacttaccagtttctgttgtgttccttcatgcatggactaatgcataatagCCGTGAAATGTTCAACAAATGGCAAGCACAAAGATGGTGGACTGAAAATTACGAGAAGGTCATGGAGCTTTACAACGTTCAGAAGTCTAACAGTCAAGTT
upper sequence: LOC_Os08g36020.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA09G07930.1 (Glycine max), 3'ss of exon 1
cttgctgtgtctacctacccatgttaactctcgat--taagtgttcccttttctctcgcttgtttgacaatgtgcttactagtgagttctgatgcatg-atagCCGTGAGATATTCAACAAATGGCAAGCGCAAAGATGGTGGGCCGAAAATTATGAGAAAGTCATGGAGCTTTACAATGTTCAGAGGTTCAACCAGCAAACT
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--attaattattagctagg-atggttagttacgatagttcatatgatatgatgacttaacaactgagtggtgaactaaattaaggtttatattttatgtatagCCGTGAGATATTTAACAAATGGCAAGCTCAAAGATGGTGGGCAGAGAACTATGACAAGGTGATGGAACTTTACAATGTGCAAAGGCTTAATCGTCAAGCT
upper sequence: LOC_Os08g36020.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA17G05900.1 (Glycine max), 3'ss of exon 2
cttgctgtgtctacctacccatgttaactctcgattaagtgttcccttttctctcgcttgtttgacaatgtgcttactagtgagttctgatgcatg-atagCCGTGAGATATTCAACAAATGGCAAGCGCAAAGATGGTGGGCCGAAAATTATGAGAAAGTCATGGAGCTTTACAATGTTCAGAGGTTCAACCAGCAAACT
||| | | | | | | | | | || | | | | ||| || | | || || | ||| |||| || ||||| ||||| ||||||||||| ||||| |||||||| || || || || || || ||||| |||||||||||||| ||||| |||| ||| |
aatgccaatggtgctttgttctaatgcacatagttcatatgatgacatcaggactagagagaagtgaat-tgaattttggtttattttctattatgtatagTCGAGAGATGTTCAATAAATGGCAAGCTCAAAGGTGGTGGGCAGAGAACTACGACAAGGTTATGGAACTTTACAATGTTCAAAGGTTTAACCGCCAAGCA
upper sequence: LOC_Os08g36020.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA13G16800.1 (Glycine max), 3'ss of exon 3
cttgctgtgtctacctacccatgttaactctcgattaagtgttcccttttctctcgcttgtttga--caatgtgcttactagtgagttctgatgcatg-atagCCGTGAGATATTCAACAAATGGCAAGCGCAAAGATGGTGGGCCGAAAATTATGAGAAAGTCATGGAGCTTTACAATGTTCAGAGGTTCAACCAGCAAACT
|| | | | | | | | | | | || | | | || | || | || | | || || | ||| | || || ||||| ||||| ||||||||||| ||||| |||||||| || || || || ||||| ||||| |||||||||||||| ||||| |||| ||| |
---gccaatggtgctttgttctaatgcatatagttcatatgatgacatcaggacgactagagagaagtgaattgaattttggtttattttctattatgtacagTCGAGAGATGTTCAATAAATGGCAAGCTCAAAGGTGGTGGGCAGAGAACTACGACAAAGTTATGGAACTTTACAATGTTCAAAGGTTTAACCGCCAAGCA
upper sequence: LOC_Os08g36020.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA15G18980.1 (Glycine max), 3'ss of exon 1
cttgct-gtgtctacctacccatgttaactctcgat-taagtgtt-cccttttctctcgcttgtttgacaatgtgcttactagtgagttctgatgcatgatagCCGTGAGATATTCAACAAATGGCAAGCGCAAAGATGGTGGGCCGAAAATTATGAGAAAGTCATGGAGCTTTACAATGTTCAGAGGTTCAACCAGCAAACT
||| | | || | | || | || || | | | | | | | | | || |||| ||| | || || | | | |||| || |||||||| |||||||||||||| |||||||||||||| || || ||||| || || ||||| |||||||||||||| ||| | | | ||| ||
-ttgttcatttccaaaattctgatgtacgtgtcaatgttattatagttcatatgatatgatgacttaacaactgaatta-tggtttatttttttatgt-atagTCGCGAGATATTTAACAAATGGCAAGCTCAAAGATGGTGGGCAGAGAACTATGACAAGGTGATGGAACTTTACAATGTTCAAAGGCTTGATCGCCAAGCT
upper sequence: LOC_Os08g36020.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G20540.1 (Arabidopsis thaliana), 3'ss of exon 2
-----cttgctgtgtctacctacccatgttaactctcgattaagtgttcccttttctctcgcttgtttgacaatgtgcttactagtgagttctgatgcatgat-agCCGTGAGATATTCAACAAATGGCAAGCGCAAAGATGGTGGGCCGAAAATTATGAGAAAGTCATGGAGCTTTACAATGTTCAGAGGTTCAACCAGCAAACT
| || | | | | | || | | || | | |||| | |||| ||| || ||| | || | | |||| ||||| || || |||||||| | ||||| ||| |||||||||| || || ||||| ||||| ||||| |||||||||||||| | | | || ||| ||
gtaacttaatcatgaccttttcctagtagcagct-tgaagaaaattaacatgtttccaaaatgtatttg----tgt-ctcactttttgttttgggtttttgattagCCGAGACATGTTCAACAAGTTACAAGCTCAACGATGGTGGGCAGATAACTATGACAAAGTAATGGAACTTTACAATGTTCAAAAACTAAGCCGCCAAGCT
upper sequence: LOC_Os08g36020.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv11s0016g01460.t01 (Vitis vinifera), 3'ss of exon 3
------cttgctgtgtctacctacccatgttaactctcgattaagtgttcccttttctctcgcttgtttgacaatgtgcttactagtgagttctgatgcatgatagCCGTGAGATATTCAACAAATGGCAAGCGCAAAGATGGTGGGCCGAAAATTATGAGAAAGTCATGGAGCTTTACAATGTTCAGAGGTTCAACCAGCAAACT
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tgtaagatgcctttgtttaatggcaaaggtgcaatgtgctcta---gttctcactgctcatacaagtgaagggttttgattggttgttgtttcctttg---attagTCGAGAAATGTTTAACAAATGGCAAGCTCAAAGGTGGTGGGCAGAGAATTATGATAGGGTCATGGAACTCTACAATGTTCAAAGGTTTAACCGCCAAGCCMapped 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|58677645|gb|CK066332.1|CK066332EST: TTCCTCTCGCTGCCGGAGGGCGGCAACGACCTCAAACGGATCCGATTCAG CCGTGAGATATTCAACAAATGGCAAGCGCAAAGATGGTGGGCCGAAAATTA
genomic: TTCCTCTCGCTGCCGGAGGGCGGCAACGACCTCAAACGGATCCGATTCAGgtgagttttt ... tgcatgatagCCGTGAGATATTCAACAAATGGCAAGCGCAAAGATGGTGGGCCGAAAATTA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttgctgtgtctacctacccatgttaactctcgattaagtgttcccttttctctcgcttgtttgacaatgtgcttactagtgagttctgatgcatgatagCCGTGAGATATTCAACAAATGGCAAGCGCAAAGATGGTGGGCCGAAAATTATGAGAAAGTCATGGAGCTTTACAATGTTCAGAGGTTCAACCAGCAAACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
-ttgctgt
- - - - - - - - - -catgtta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgtgc