Sequence
atgc intronic sequence ATGC exonic sequenceCGAGAACTTGGAAAATCCAGAGCTCTACCACTATGCACTTTTCTCAGACAATGTCTTGGCAGCATCTGTTGTTGTGAACTCAACCATAATGAATGCTAAGgtagtttctgtcttcctctttaatcaaatgcaaactgtgataagtgataagtgttctgacaactatgtatggcataaccttttcag
Basic information
species | Oryza sativa |
transcript | LOC_Os09g36190.1 |
intron # | 7 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g36190.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G379577_T01 (Zea mays), 5'ss of exon 7
CGAGAACTTGGAAAATCCAGAGCTCTACCACTATGCACTTTTCTCAGACAATGTCTTGGCAGCATCTGTTGTTGTGAACTCAACCATAATGAATGCTAAGgtagtttctgtcttcctctttaatcaaatgca-aactgtgataagtgataagtgttctgacaactatgtatggcataaccttttcag
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TGAAAATTTAGAAAATCCAAATCTCTATCACTATGCACTTTTCTCAGATAATGTCTTGGCAGCTTCTGTTGTTGTGAACTCAACCATCATGAATGCTAAGgtattttccatgcact--tttagtcaattattcaattgcattcctcaaagtagttcctaacattgatgtttggaatgtccttttcag
upper sequence: LOC_Os09g36190.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G386971_T01 (Zea mays), 5'ss of exon 7
CGAGAACTTGGAAAATCCAGAGCTCTACCACTATGCACTTTTCTCAGACAATGTCTTGGCAGCATCTGTTGTTGTGAACTCAACCATAATGAATGCTAAGgtagtttctgtcttcctctttaatcaaatgca-aactgtgataagtgataagtgttctgacaactatgtatggcataaccttttcag
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TGAAAATTTAGAAAACCCAAATCTCTATCACTATGCACTTTTCTCTGATAATGTTTTGGCAGCCTCTGTTGTTGTGAACTCAACCATAATGAATGCTAAGgtattttgcgtgtact--tttagtcaattattcaattgcactccactaagtagtttctaatggtgatgtttggcatgtctttttcag
upper sequence: LOC_Os09g36190.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA07G08910.1 (Glycine max), 5'ss of exon 5
CGAGAACTTGGAAAATCCAGAGCTCTACCACTATGCACTTTTCTCAGACAATGTCTTGGCAGCATCTGTTGTTGTGAACTCAACCATAATGAATGCTAAGgtagtttctgtcttcctctttaatcaaatgcaaac-tgtg-ataagtgataagtgttctgaca---actatgtatggcataaccttttcag----------
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TGAGAATTTGGAGAATCCCAGTCTTTATCACTACGCACTGTTCTCAGACAATGTCTTGGCTGCATCTGTTGTTGTCAACTCAACTATTATGAATGCAAAGgtgacttg-gactgtctttttaaccataccagtatgtgtgtgcaagtgcattgtttccttttatagattgcaaataatggtgccttgaaggagcaccaaaa
upper sequence: LOC_Os09g36190.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA09G40260.1 (Glycine max), 5'ss of exon 8
CGAGAACTTGGAAAATCCAGAGCTCTACCACTATGCACTTTTCTCAGACAATGTCTTGGCAGCATCTGTTGTTGTGAACTCAACCATAATGAATGCTAAGgtagtttctgtcttcctctttaat-caaatgcaaactgtgataagtg-ataagtgttctgacaactatgtatggcataaccttttcag--------------------------------------------------------------------------------------------------------------
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TGAGAATTTGGAGAATCCTAGTCTCTATCATTATGCCCTGTTCTCGGACAATGTCTTGGCTGCATCTGTTGTTGTCAACTCAACTATTGTGAATGCAAAGgtgacttaaacagtcttttaccataccagtgtgtatgtgcatgtctatatagatattcttttatatagatgatgaataatttgtgcttgcactgtacaacccggacatattttgtttgtgcagtgcatccctgactcagtaaataatataattaaactttgccttcattatcttatgtttgtgtcttcaacattgcag
upper sequence: LOC_Os09g36190.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA03G02250.1 (Glycine max), 5'ss of exon 13
CGAGAACTTGGAAAATCCAGAGCTCTACCACTATGCACTTTTCTCAGACAATGTCTTGGCAGCATCTGTTGTTGTGAACTCAACCATAATGAATGCTAAGgtagtttctgtcttcctctttaatcaaatgcaaactgtgataagtgataagtgttc-----------tgacaactatgtatggcataaccttt-tcag--------------------------------------------------------------------------------------------
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TGAGAATTTGGAGAATCCCAGTCTTTATCACTACGCACTGTTCTCAGATAATGTCTTGGCTGCATCTGTTGTTGTCAACTCAACTATTATGAATGCTAAGgtgacttggg-ctgtctttttaaccataccagtatttgtgtgcaagttcattgtttccttttatagattgcaaataagggtgccttgaccatggtcaacatatcgtgcatgtgaaagtgtatctatgatttagtaaattatattattaaaaccaggcctcataacttagtttctgtcttcaatgttgcag
upper sequence: LOC_Os09g36190.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA18G45750.1 (Glycine max), 5'ss of exon 7
CGAGAACTTGGAAAATCCAGAGCTCTACCACTATGCACTTTTCTCAGACAATGTCTTGGCAGCATCTGTTGTTGTGAACTCAACCATAATGAATGCTAAGgtagttt---ctgtcttcctcttta--atcaaatgcaaac---tgtgataagtgataagtgttctgacaactatgtatggcataacctttt-cag--------------------------------------------------------------------------------------------------------
||||| ||||| ||||| ||||| || ||||| || ||||| |||||||||||||| |||||||||||||| ||||||||||| ||||||| ||||| || ||||||| || || | || || | || ||||| | || | | ||| || | ||| | |
TGAGAATTTGGAGAATCCTAGTCTCTATCATTATGCCCTGTTCTCGGACAATGTCTTGGCTGCATCTGTTGTTGTCAACTCAACCATTGTGAATGCAAAGgtgacttggactgtctttttccataccagtgtgtgtgtacatgtctgtatagtgaatttttttttatagatgatgaataatttgtgcttgcactgtacaacccggacatagtttgtttgcttgtgcatccctgacaaaataaataatataattaaactttgccttcattatcttatgttcgtgtcttccaacgttgtag
upper sequence: LOC_Os09g36190.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv15s0048g01300.t01 (Vitis vinifera), 5'ss of exon 8
CGAGAACTTGGAAAATCCAGAGCTCTACCACTATGCACTTTTCTCAGACAATGTCTTGGCAGCATCTGTTGTTGTGAACTCAACCATAATGAATGCTAAGgtagtttctgtcttcctctttaatcaaatgcaaactgtgataagtgata----------agtgttctgacaactat----gtatggcataaccttttcag--
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TGAGAATTTGGAAAATCCAAATCTTTACCATTATGCTCTCTTCTCTGATAATGTATTGGCTGCTTCAGTTGTTGTCAACTCAACCATCTTGAATGCCAAGgtgaagtg-gtggatttatttacttta-tactagcatctttaagtgatcttcttatcctagacttaaaacaccagtattagtatcccctaatttatctacatMapped 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|88728709|gb|CI752219.1|CI752219EST: ATGTCTTGGCAGCATCTGTTGTTGTGAACTCAACCATAATGAATGCTAAG GAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTG
genomic: ATGTCTTGGCAGCATCTGTTGTTGTGAACTCAACCATAATGAATGCTAAGgtagtttctg ... accttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTG
EST:
gi|33793273|gb|CF322517.1|CF322517EST: ATGTCTTGGCAGCATCTGTTGTTGTGAACTCAACCATAATGAATGCTAAG GAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGA
genomic: ATGTCTTGGCAGCATCTGTTGTTGTGAACTCAACCATAATGAATGCTAAGgtagtttctg ... accttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGA
EST:
gi|66913045|gb|CX099893.1|CX099893EST: ATGTCTTGGCAGCATCTGTTGTTGTGAACTCAACCATAATGAATGCTAAG GAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGA
genomic: ATGTCTTGGCAGCATCTGTTGTTGTGAACTCAACCATAATGAATGCTAAGgtagtttctg ... accttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGA
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
60 (upstream exon),
32 (downstream exon)
Score:
30CGAGAACTTGGAAAATCCAGAGCTCTACCACTATGCACTTTTCTCAGACAATGTCTTGGCAGCATCTGTTGTTGTGAACTCAACCATAATGAATGCTAAGgtagtttctg ... accttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGAGCCATGAACATGTGGTTTTTGCTGAACCCACCTGGGAAGGCCACCATCC
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