Sequence
atgc intronic sequence ATGC exonic sequenceGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAGgtatatgctcagtttgttgcactggatcttgtttgccgcatcctgctaaaaaggactcattgcgctattcaacatatgctgcagatcatttttaaatcgatttttagtttgtgtgaactgaccatagtcaacatgtaatgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os11g33240.3 |
intron # | 13 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G063909_T03 (Zea mays), 5'ss of exon 13
GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAGgtatatgctcagtttgttgcactggatcttgtttgccgcatcctgctaaaaaggactcattgcgctattcaacatatgctgcagatcatttttaaatcgatttttagtttgtgtgaactgaccatagtcaacatgtaatgcag
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GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCATCATCTGTGAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAGgtat--gctcagtttaacgtactagatctgatctggtacataat-ctctgcattgtgcttccttttacttgagatttgaaaaaagtt-ctcatcaataaatttc---------------------------------------
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G063851_T04 (Zea mays), 5'ss of exon 14
GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAGgtatatgctcagtttgttgcactggatcttgtttgccgcatcctgctaaaaaggactcattgcgctattcaacatatgctgcagatcatttttaaatcgatttttagtttgtgtgaactgaccatagtcaacatgtaatgcag
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GTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAATGGGCTAGCTGGGCCACTGCATGGCCTTGCAAATCAGgtgtgt--tcagtttgatatactatttctgatctggtattaaatttctgccttgcttccttttact----tgcagattttgaaaag-aggcttatataaattctcac------------------------------------
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G064023_T01 (Zea mays), 5'ss of exon 15
GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAGgtatatgctcagtttgttgcactggatcttgtttgccgcatcctgctaaaaaggactcattgcgctattcaacatatgctgcagatcatttttaaatcgatttttagtttgtgtgaactgaccatagtcaacatgtaatgcag
||||||||||||||||||||||||||||||||||| ||||| || || ||||| |||||||| ||| | || ||||| || |||||||||| |||||||||| | ||| |||||| | || || || | | || || || | | || | | | | ||| ||| ||
GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAGgtat--gctcagtttggcgtactagatcttatctggtacaatctctgctttatgcttccttttact--tgtagattttgaaaaaaaaaggtttccatcaataac---------------------------------------
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA15G42300.2 (Glycine max), 5'ss of exon 14
GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAGgtatatgctcagtttgttgcactggatcttgtttgccgcatcctgctaaaaaggactcattgcgctattcaacatatgctgcagatcatttttaaatcgatttttagtttgtgtgaactgaccatagtcaacatgtaatgcag
|||| ||| | || ||||||||||||||| | ||||||||||| ||||||| |||||||| || |||| || |||| |||||||| |||||| | | || | | ||| | ||| | || | |||| ||| | |||| || || | ||| | ||| | | ||| || | ||| |
GTTGCTAGTCCGCTATCAGATCCTTATCTTGCATTTGCAGCTGCTTTGAATGGGTTAGCTGGGCCCCTGCATGGTTTGGCCAATCAGgtt--------atttgttattttattttttatat-ccgttttctg-----------tttttctggtatt-aactt-tgctatagttcgtcttt----tggtttagaaatcatgt---ttggctataatg--------------
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA08G16770.1 (Glycine max), 5'ss of exon 14
GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAGgtatatgctcagtttgttgcactggatcttgtttgccgcatcctgctaaaaaggactcattgcgctattcaacatatgctgcagatcatttttaaatcgatttttagtttgtgtgaactgaccatagtcaacatgtaatgcag
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GTTGCTAGCCCGCTATCAGATCCTTATCTTGCATTTGCGGCTGCTTTGAATGGGTTAGCTGGGCCCCTGCATGGTCTGGCCAATCAGgt-------tattttgtt-------atttggtttttccttttttttttcagttttctgtttctcttgtattaaatttgctatagttcatctttcggttgagaaatcatgtttgg-----------------------------
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 14
lower sequence: AT3G60100.1 (Arabidopsis thaliana), 5'ss of exon 13
GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAGgtatatgctcagtttgttgcactggatcttgtttgccgcatcctgctaaaaaggactcattgcgctattcaacatatgctgcagatcatttttaaatc--gatttttagtttgtgtgaactgaccatagtcaacatgtaatgcag
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GTTGGGAGTGCACTTTCAGATCCATATCTTTCATTTGCTGCTGCATTGAATGGTTTAGCTGGGCCACTCCATGGTTTGGCTAATCAGgtattta-tatccttaatgagtcttatattgttcg----aatctacaagtgtatataacttgaactctaagattgactcttaattataagcttaaacttggaatcttactctgttt---tttttcgttgtcttgttgtag-----
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 14
lower sequence: AT2G44350.2 (Arabidopsis thaliana), 5'ss of exon 14
GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAGgtatatgc-----tcagtttgttgcac------tggatctt--gtttgccgcatcctgctaaaaaggactcattgcgctat-tcaacatatgctgcagatcatttttaaatcgatttttagtttgtgtgaactgac-catagtcaacatgtaatgcag---------
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GTTGGTAGTGCACTTTCAGACCCATATCTGTCATTTGCAGCTGCATTAAATGGTTTAGCTGGGCCACTCCATGGTTTGGCTAATCAGgtatcctcccttgtctatatcttgaataagtcttaaatcttcaatctacaatagagcttcgtaagtggctttttgtattttatctaggtaggttgtgatagtttgatgatacaaccataaattggagaaaacaaattcttagtctttttttattattgtttcaacag
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 14
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 5'ss of exon 14
GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAGgtatatgctcagtttgttgcactggatcttgtttgccgcatcctgctaaaaaggactcattgcgctattcaacatatgctgcagatcatttttaaatcgatttttagtttgtgtgaactgaccatagtcaacatgtaatgcag
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GTTGCTAGTGCATTGGCAGATCCTTACCTTTCATTTGCAGCTGCATTAAATGGTCTAGCTGGCCCACTCCATGGTTTGGCTAACCAGgtat-tgcatcttctgttga--tatacatagacatacacattcctaattttttgtttcattg-gctgttcag-atcctcagc------ttttttcattcacgtttatccttcattatttgactacag----------------Mapped 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|3758954|gb|C96653.1|C96653EST: CAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAG GAAGTGCTGTTGTGGATCAAATCTGTAATAGGTGAGACAGGTAGTGATGTT
genomic: CAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAGgtatatgctc ... tgtaatgcagGAAGTGCTGTTGTGGATCAAATCTGTAATAGGTGAGACAGGTAGTGATGTT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAGgtatatgctcagtttgttgcactggatcttgtttgccgcatcctgctaaaaaggactcattgcgctattcaacatatgctgcagatcatttttaaatcgatttttagtttgtgtgaactgaccatagtcaacatgtaatgcag
- - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA