Sequence
atgc intronic sequence ATGC exonic sequenceACCAAGGATAGGTGACCCATCTGAGTTCAGCCTGTCACAGATCTGGGTTATCTCTGGCTCCTTCGGCAATGATCTGAACACCATTGAAGCTGGATGGCAGgtacatgaacggaggaattagattctgccatcttaaacaaaaagtgatgaataattatatgtactattttgaacgagcacttgtaatttatttttcttttgctccttctgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os06g28000.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g28000.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G129947_T01 (Zea mays), 5'ss of exon 5
ACCAAGGATAGGTGACCCATCTGAGTTCAGCCTGTCACAGATCTGGGTTATCTCTGGCTCCTTCGGCAATGATCTGAACACCATTGAAGCTGGATGGCAGgtacat--gaacggaggaattagattctgccatcttaaacaaaaagtgatgaataattatatgtactattttgaacgagcacttgtaatttatttttctt-ttgctc-cttctgcag---------------------
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GCCAAGGATAGGTGACCCATCGGAGTCCAGCCTGTCTCAGATCTGGGTCCTCTCTGGCTCCTCGGGCAATGATCTCAACACCATCGAAGCTGGATGGCAGgtacatttgaaccaaatgagtaggcatggtcctgctatatgcatgcagacacaaacacccctgcatcactatgtaatactctctccattcttttttatttgtcgcccactagtccaatgatatgtcatgcttttatag
upper sequence: LOC_Os06g28000.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA02G04240.1 (Glycine max), 5'ss of exon 7
ACCAAGGATAGGTGACCCATCTGAGTTCAGCCTGTCACAGATCTGGGTTATCTCTGGCTCCTTCGGCAATGATCTGAACACCATTGAAGCTGGATGGCAGgtacatgaacggaggaattagattctgccatc-ttaaacaaaaagtgatgaataattatatgtactattttgaacgagcacttgtaatttatttttcttttgctccttc-tgcag
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----CGAGTGGAAAATCAAGATGAATTCAGCTTGTCCCAAATGTGGGTCATCTCTGGCTCATTTGGGGATGATCTCAACACCATTGAGGCTGGTTGGCAGGCAAgt-----------ttcaattcagccattgctgcatcttaatttatttataagaataaaatgaagtttacattaactcacggactctattcaagaactacacatccatggac
upper sequence: LOC_Os06g28000.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA18G20700.1 (Glycine max), 5'ss of exon 4
ACCAAGGATAGGTGACCCATCTGAGTTCAGCCTGTCACAGATCTGGGTTATCTCTGGCTCCTTCGGCAATGATCTGAACACCATTGAAGCTGGATGGCAGgtacatgaacggaggaattagattctgccatcttaaacaaaaagtgatgaataattatatgtactattttgaacgagcacttgta---atttatttttcttttgctccttctgcag
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----CTTGTGGAAAACCCATATGAATTCAGCTTGTCTCAAATGTGGGTCATTTCTGGTTCATTTGGGGATGATCTCAACACCATTGAAGCTGGTTGGCAGGCATgtttctatcattattttatcttaa----ttaatttctcatttactttgtactatttattttctttagagaaaaaaattatacatgtgtaaaaataatttatactttcag---
upper sequence: LOC_Os06g28000.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA05G02460.1 (Glycine max), 5'ss of exon 4
ACCAAGGATAGGTGACCCATCTGAGTTCAGCCTGTCACAGATCTGGGTTATCTCTGGCTCCTTCGGCAATGATCTGAACACCATTGAAGCTGGATGGCAGgtacatgaacggaggaattagattctgccatcttaaacaaaaagtgatgaataattatatgtactattttgaacgagcacttgtaatttatttttcttttgctccttctgcag
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----AGCGTAACTGATCCATACGAATTCAGTTTGTCACAGATATGGGTTATTGCTGGATCGTTTGGTAATGATCTAAATACCATAGAAGCTGGATGGCAGGCATgtccaatgtccatatata---------cttgtccaaaaattcacattcatctattttttttag----------------------------------------------
upper sequence: LOC_Os06g28000.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA17G09450.1 (Glycine max), 5'ss of exon 4
ACCAAGGATAGGTGACCCATCTGAGTTCAGCCTGTCACAGATCTGGGTTATCTCTGGCTCCTTCGGCAATGATCTGAACACCATTGAAGCTGGATGGCAGgtacatgaacgga-----------ggaattagattctgccatctt-----aaacaaaaagtgatgaata-attatatgtactatt----ttgaacgagcacttgtaatttattttt-cttttgctccttctgcag-------------------------------
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GCCTAGCGTAACCGATCCATACGAATTCAGTTTGTCACAGATATGGGTTATTGCTGGATCGTTTGGTAATGATCTGAATACCATAGAAGCTGGATGGCAGgcatgttcatatacacttggccacaaaatcacattcatccattttttttagtactaaatgttgtgaaggtgttgaagaaagtactaggattaaatttctctttgtgatttgctttagtttttagtccatcaatttctagctaaataacaagcatactttccttcag
upper sequence: LOC_Os06g28000.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT1G10750.1 (Arabidopsis thaliana), 5'ss of exon 4
ACCAAGGATAGGTGACCCATCTGAGTTCAGCCTGTCACAGATCTGGGTTATCTCTGGCTCCTTCGGCAATGATCTGAACACCATTGAAGCTGGATGGCAGgta-ca--tgaacggaggaattagattctgccatcttaaacaaaaagtgatgaataattatatgtactattttgaacgagcacttgtaatttatttttcttttgctccttctgcag
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TCCACAAGTTCAGAACCAATACGAATTTAGTTTATCTCAGATTTGGATTATCTCTGGTTCCTTTGGCAATGATCTCAACACCATTGAAGCTGGTTGGCAGgtaacaattttcttcatatatttatttcaaagattatatcacatcaatagcttaaaactatagatgcttagct--tctaactgttgataattatttgccattag------------
upper sequence: LOC_Os06g28000.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT5G50150.1 (Arabidopsis thaliana), 5'ss of exon 4
ACCAAGGATAGGTGACCCATCTGAGTTCAGCCTGTCACAGATCTGGGTTATCTCTGGCTCCTTCGGCAATGATCTGAACACCATTGAAGCTGGATGGCAGgtacatgaacggaggaattagattctgccatctta---aacaaaaagtgatgaataattatatgtactattttgaacgagcacttgtaatttatttttcttttgctccttctgcag
||| | | ||| | | |||||| || | || ||||| ||| | |||||||| ||||| || |||| || ||||||||||||||||| |||||||||| | ||| | | | | | ||| || | | ||||| | | | ||||||| | | |||||| | | || ||
GCCACGTGTCACTGATGCTTATGAGTTTAGTTTATCTCAGATTTGGCTCATCTCTGGATCCTTTGGTCATGACCTAAACACCATTGAAGCTGGTTGGCAGgtac-----cattcactttacactttacaaaattatttgccactagttttcgaatagaaaaagagaatattttg--tcaatatatgtaatattacctactaaacatc---------
upper sequence: LOC_Os06g28000.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv01s0127g00010.t01 (Vitis vinifera), 5'ss of exon 4
ACCAAGGATAGGTGACCCATCTGAGTTCAGCCTGTCACAGATCTGGGTTATCTCTGGCTCCTTCGGCAATGATCTGAACACCATTGAAGCTGGATGGCAGgtacatgaacggaggaattagattctgccatcttaaacaaaaagtgatgaataattatatgtactattttgaacgagcacttgtaatttatttttcttttgctccttctgcag
||| || | | | | | || ||| |||||| | ||||| || ||||| ||||| || || ||||| ||||||| ||||||||||||||||| ||||||| |||| | | ||| || | | | |||| ||| ||| | ||||| | | ||||| | | | | | | | |
ACCCCGGGTGGCTAATCAATATGAATTCAGCTTATCACAAATGTGGGTCATCTCCGGTTCATTCGGTGATGATCTCAACACCATTGAAGCTGGCTGGCAGg--catgttcttgctcttctgatattgatttttctcctagaaag----gaaagcttactcgagttatttcaattttgaacttgaactggagaatacatgagaaacc-------
upper sequence: LOC_Os06g28000.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv17s0000g08870.t01 (Vitis vinifera), 5'ss of exon 4
ACCAAGGATAGGTGACCCATCTGAGTTCAGCCTGTCACAGATCTGGGTTATCTCTGGCTCCTTCGGCAATGATCTGAACACCATTGAAGCTGGATGGCAGgtacatgaacggaggaatta-gattctgccatcttaaacaaaaagtgatgaataattatatgtactattttgaacgagcacttg-taatttatttttcttttgctccttctg-cag
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-----------------------AATTCAGCTTGTCACAAATATGGATCATCTCTGGTTCATTTGGCAATGATCTTAATACCATAGAAGCTGGTTGGCAGGCATGTATTTACACTCTTTTCGGgtccccaattttacataaaccattgttcatccttagaagcagttcctgtagtttttaattactaagaaattgttttcatattcttcaggtcagMapped 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|58654016|gb|CK042696.1|CK042696EST: TCTCTGGCTCCTTCGGCAATGATCTGAACACCATTGAAGCTGGATGGCAG GTCAGCCCCGAGCTGTATGGAGACAGTAACCCAAGGTTCTTCACATTTTGG
genomic: TCTCTGGCTCCTTCGGCAATGATCTGAACACCATTGAAGCTGGATGGCAGgtacatgaac ... ccttctgcagGTCAGCCCTGAGCTGTATGGAGACAGTAACCCAAGGTTCTTCACATATTGG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ACCAAGGATAGGTGACCCATCTGAGTTCAGCCTGTCACAGATCTGGGTTATCTCTGGCTCCTTCGGCAATGATCTGAACACCATTGAAGCTGGATGGCAGgtacatgaacggaggaattagattctgccatcttaaacaaaaagtgatgaataattatatgtactattttgaacgagcacttgtaatttatttttcttttgctccttctgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA