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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTCAGTTCAGATTCTGGCCAAATAACAACAGCAGAATGTATGTCTTGGAGGGGGTTACACCATGCATACAATCATTACAATTACAGGCTGGTGATACAGgttaaatctccttggacatgatatcacctgttctttttttacaattttattactgatgcctgattacatataagcaatgattttcctattgcataccttc...

Basic information

species Oryza sativa
transcript LOC_Os07g48200.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g48200.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G158162_T03 (Zea mays), 5'ss of exon 6
TTTCAGTTCAGATTCTGGCCAAATAACAACAGCAGAATGTATGTCTTGGAGGGGGTTACACCATGCATACAATCATTACAATTACAGGCTGGTGATACAGgttaaatctccttggacatgatatcacctgttctttttttacaattttatt-actgatgcctgattaca-ta-taagca-atgattttcctattgcataccttc
|||||||| || || ||||||||||| |||||||||||||||||||||||||| ||||||||||||||||||||||| |||||||| ||||| ||||||||| |       ||   |||  |||   |     |   || ||   ||| || | ||| |  || ||  | || || | | ||| | |  ||| |   ||     
TTTCAGTTTAGGTTTTGGCCAAATAATAACAGCAGAATGTATGTCTTGGAGGGTGTTACACCATGCATACAATCATTGCAATTACAAGCTGGCGATACAGgtaattagcaatttagcatc-tatttgcaagcatgcattcacttctttcttgattgaagtttgtttttaatactacgtatatggtatagctacttattatt---

upper sequence: LOC_Os07g48200.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G172621_T01 (Zea mays), 5'ss of exon 6
TTTCAGTTCAGATTCTGGCCAAATAACAACAGCAGAATGTATGTCTTGGAGGGGGTTACACCATGCATACAATCATTACAATTACAGGCTGGTGATACAGgttaaa-------tctccttggacatgatatcacctgttctttttttacaattttattactgatgcctgattacatataagcaatgattttcctattgcataccttc
|||||||| || || ||||||||||| |||||||||||||||||||||||||| ||||||||||||||||| || || |||||||| ||||| ||||||||| |||       | ||||||||||||||   |    |    | ||| |||         | |   ||   |  ||  |||   || ||||  || | | ||     
TTTCAGTTTAGGTTTTGGCCAAATAATAACAGCAGAATGTATGTCTTGGAGGGTGTTACACCATGCATACAGTCTTTGCAATTACAAGCTGGCGATACAGgtaaaacatcttatttccttggacatgatcataagcat---ctatttgcaagcacgcgcttcacttcttccttgattgaagtt-tgtttttaatactacctata---

upper sequence: LOC_Os07g48200.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA11G31270.1 (Glycine max), 5'ss of exon 2
TTTCAGTTCAGATTCTGGCCAAATAACAACAGCAGAATGTATGTCTTGGAGGGGGTTACACCATGCATACAATCATTACAATTACAGGCTGGTGATACAGgt-taaatctccttggacatgatatcacctgttctttttttacaattttattactgatgcctgattacatataagcaatgattttcctattgcataccttc-
|||||||||||||| ||||| |||||||||||||| |||||||| |||||||| || || || ||||||||  |  | ||||||   ||||||||||| ||| | ||||   || |  |  | | |           | || || ||  | |  |||  | ||| |   |||    |   | |||  |||   ||   |   
TTTCAGTTCAGATTTTGGCCTAATAACAACAGCAGGATGTATGTATTGGAGGGTGTGACCCCTTGCATACAGGCCATGCAATTATGTGCTGGTGATACTGgtatgaatcaagttagggaaaaaaccttgcacatacctattgca-ttgcaattttga-acttgaatttttatttatatcaaattttatatgaaatgtgtgtt

upper sequence: LOC_Os07g48200.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA02G40280.1 (Glycine max), 5'ss of exon 5
TTTCAGTTCAGATTCTGGCCAAATAACAACAGCAGAATGTATGTCTTGGAGGGGGTTACACCATGCATACAATCATTACAATTACAGGCTGGTGATACAGgt-taaatct-ccttggacatgatatcacctgttctttttttacaattttattactgatgcctgattacatataagcaatgattttcctattgcataccttc
|||||||||||||| ||||| |||||||| || ||||||||||| |||||||| || || || ||||| ||  |  | |||||| | ||||||||||| ||| || |||   |||||  ||||  | |         || || || | | |||  | |    | |||   |||     ||  || |   | ||  || ||  
TTTCAGTTCAGATTTTGGCCTAATAACAATAGTAGAATGTATGTATTGGAGGGAGTAACCCCTTGCATGCAGGCCATGCAATTAAATGCTGGTGATACTGgtatacatccatcttggcaatgaattgatgcacatacttatttcattatcatttgttaaaatttatttagtattc-tgatttttgtgaaaatgt-tatctaa

upper sequence: LOC_Os07g48200.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA18G05840.1 (Glycine max), 5'ss of exon 8
TTTCAGTTCAGATTCTGGCCAAATAACAACAGCAGAATGTATGTCTTGGAGGGGGTTACACCATGCATACAATCATTACAATTACAGGCTGGTGATACAGgt-taaatctccttggacatgatatcacctgttctttttttacaattttattactgatgcctgattacatataagcaatgattttcctattgcataccttc-
|||||||||||||| ||||| |||||||||||||| |||||||| |||||||| || || || ||||||||  |  | ||||||   ||||||||||| ||| | ||||    | |  |  | | |           | || || ||  | |  |||  | | | |    ||        | |||   ||   |||| |   
TTTCAGTTCAGATTTTGGCCTAATAACAACAGCAGGATGTATGTATTGGAGGGTGTGACTCCTTGCATACAGGCCATGCAATTATGTGCTGGTGATACTGgtatgaatcaagctagggaacaaaccttgcacatacctattgca-ttacaattttga-acttaaattttgatttatgtcaaattttacatgaaatacgtgtg

upper sequence: LOC_Os07g48200.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA14G38490.1 (Glycine max), 5'ss of exon 3
---------TTTCAGTTCAGATTCTGGCCAAATAACAACAGCAGAATGTATGTCTTGGAGGGGGTTACACCATGCATACAATCATTACAATTACAGGCTGGTGATACAGgt-taaatctccttggacatgatatcacctgttctttttttacaattttattactgatgcctgattacatataagca-atgattttcctattgcataccttc
         |||||||||||||| ||||| |||||||| || || |||||||| |||||||| || || || ||||||||  |  | |||||| | ||||||||||  ||| || |||    | || |  || | | ||    |  ||    | ||||||     |  | |  | | | ||| ||| ||  || |   |||  | |  |  
GACTGGACATTTCAGTTCAGATTTTGGCCTAATAACAATAGTAGGATGTATGTATTGGAGGGAGTAACCCCTTGCATACAGGCCATGCAATTAAATGCTGgtgatattggtatacatccatcttgaaa--atgttatctaaattacttg---agttttat-----actcatagtcatacataggcagatcgttatagaattttagaattg-

upper sequence: LOC_Os07g48200.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA03G04330.1 (Glycine max), 5'ss of exon 8
TTTCAGTTCAGATTCTGGCCAAATAACAACAGCAGAATGTATGTCTTGGAGGGGGTTACACCATGCATACAATCATTACAATTACAGGCTGGTGATACAGgttaaatctccttggacatgatatcacctgttctttttttacaattttattactgatgcctgattacatataagcaatgattttcctattgcataccttc-----
|||||||| ||||| ||||||||||| |||||||| |||||||| || || || || || || ||||| || ||  | ||||| || ||||| ||||| ||| |  | |   ||   ||    | |  | ||    |  | || | |||  |  |||     |  |||| ||  |  | ||||||  |  | ||| |  |     
TTTCAGTTTAGATTTTGGCCAAATAATAACAGCAGGATGTATGTTTTAGAAGGTGTAACCCCCTGCATTCAGTCTATGCAATTGCAAGCTGGAGATACTGgt-atgttttactgaggatcccttaatttattaaactact-cattcttagaatagata---aaccacatgtacactttcattttctaagagtatatcaactacta

upper sequence: LOC_Os07g48200.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv06s0004g08100.t01 (Vitis vinifera), 5'ss of exon 6
TTTCAGTTCAGATTCTGGCCAAATAACAACAGCAGAATGTATGTCTTGGAGGGGGTTACACCATGCATACAATCATTACAATTACAGGCTGGTGATACAGgt-taaatctccttggacatgat--atcacctgttctttttttacaattttattactgatgcctgattacatataagcaatgattttcctattgcataccttc
||||| |||||||| ||||| ||||| |||||| | |||||||| || || ||||| || || |||||||| ||  | |||||||  ||||||||||| ||| ||  ||  ||    | |  |   |     ||     ||   ||  |||  ||   |||  |       |||     |||||| | ||  ||  || |   
TTTCAATTCAGATTTTGGCCCAATAATAACAGCCGGATGTATGTTTTAGAAGGGGTAACCCCTTGCATACAGTCCATGCAATTACGAGCTGGTGATACTGgtatatttcatctcattctttctcagtgggtggtatacattacccatctttgatatacatgtttttcatagtattttgtatgattatgct--tgtgtaacaa-

upper sequence: LOC_Os07g48200.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv08s0058g01300.t01 (Vitis vinifera), 5'ss of exon 7
TTTCAGTTCAGATTCTGGCCAAATAACAACAGCAGAATGTATGTCTTGGAGGGGGTTACACCATGCATACAATCATTACAATTACAGGCTGGTGATACAGgttaaatctcct-tggacatgatatcacctgttctttttttacaattttattactgatgcctgattacatataagcaatgattttcctattgcataccttc
|| || ||||| || ||||| ||||| |||||||| |||||||| || ||||| || || ||||||||||| ||| | || ||||| ||||| ||||| ||| |  |||  |     | |  |||    |||     |   ||||   | |||   ||   | || |   | ||  | | ||  |  |   |     | ||
TTCCAATTCAGGTTTTGGCCCAATAATAACAGCAGGATGTATGTTTTAGAGGGTGTGACCCCATGCATACAGTCAATGCAGTTACAAGCTGGAGATACTGgtaacttctattgcctgcttcgtattttatgtaggcatgccacaacaattttagc-atatttaataatcaacaaaaactaatggttgtgaagtcattcgtc

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|58671720|gb|CK060406.1|CK060406
EST:     GGGGGTTACACCATGCATACAATCATTACAATTACAGGCTGGTGATACAG                         TGACTTTTAGTCGGATAGAACCTGGAGGGAAACTTGTTATGGGCTTC
genomic: GGGGGTTACACCATGCATACAATCATTACAATTACAGGCTGGTGATACAGgttaaatctc ... ttcttttcagTGACTTTTAGTCGGATAGAACCTGGAGGGAAACTTGTTATGGGCTTC
EST: gi|58682644|gb|CK071331.1|CK071331
EST:     GGGGGTTACACCATGCATACAATCATTACAATTACAGGCTGGTGATACAG                         TGACTTTTAGTCGGATAGAACCTGGAGGGAAACTTGTTATGGGCTTCCGGA
genomic: GGGGGTTACACCATGCATACAATCATTACAATTACAGGCTGGTGATACAGgttaaatctc ... ttcttttcagTGACTTTTAGTCGGATAGAACCTGGAGGGAAACTTGTTATGGGCTTCCGGA
EST: gi|58672846|gb|CK061532.1|CK061532
EST:     AATCATTACAATTACAGGCTGGTGATACAG                         TGACTTTTAGTCGGATAGAACCTGGAGGGAAACTTGTTATGGGCTTCCGGA
genomic: AATCATTACAATTACAGGCTGGTGATACAGgttaaatctc ... ttcttttcagTGACTTTTAGTCGGATAGAACCTGGAGGGAAACTTGTTATGGGCTTCCGGA