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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_Os07g48200.2
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

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: 70 (upstream exon), 55 (downstream exon)
Score: 14

TTTCAGTTCAGATTCTGGCCAAATAACAACAGCAGAATGTATGTCTTGGAGGGGGTTACACCATGCATACAATCATTACAATTACAGGCTGGTGATACAGgttaaatctc ... ttcttttcagTGACTTTTAGTCGGATAGAACCTGGAGGGAAACTTGTTATGGGCTTCCGGAAGGCCACAAACACTGTCAGTTTGCCA




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