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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCAAAACGGGACGGAAGTGTTACAATTGTAGGGGCTGTCTCTCCACCTGGTGGTGATTTTTCAGATCCTGTTACCTCTGCAACCCTTAGTATTGTTCAGgtaaggaagcagctaagtctgtcatgattaataatgtttatcgtttcagtgttgttaaaccacatgttcttgtttgtag

Basic information

species Oryza sativa
transcript LOC_Os02g07870.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 13
TCCAAAACGGGACGGAAGTGTTACAATTGTAGGGGCTGTCTCTCCACCTGGTGGTGATTTTTCAGATCCTGTTACCTCTGCAACCCTTAGTATTGTTCAGgtaaggaagcagctaa----------------------------------gtctgtcatgattaataatgtttatcgtttcagtgttgttaaaccacatg------ttcttgtttgtag
|||| |  || | || ||||| |||||||| || ||||||||||| |||||||||||||||||||| ||||||||||| |||||||| ||||||||||||||||| | || || ||                                  |||   | ||||| | |  |||| | |||||| | |  ||||| || |||      || || |||| ||
TCCAGACAGGAATGGCAGTGTCACAATTGTTGGAGCTGTCTCTCCTCCTGGTGGTGATTTTTCAGACCCTGTTACCTCCGCAACCCTCAGTATTGTTCAGgtaagaaggctgccaaattacttcaatatacttcagtcctctgatcattagtccagcctgatttacagcgtttgttgtttcaatat-attaaatcatatgctgctctttttttttgcag

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G128877_T02 (Zea mays), 5'ss of exon 13
TCCAAAACGGGACGGAAGTGTTACAATTGTAGGGGCTGTCTCTCCACCTGGTGGTGATTTTTCAGATCCTGTTACCTCTGCAACCCTTAGTATTGTTCAGgtaaggaagcagctaa-------------------------------gtctgtcatgattaataatgtttatcgtttcagtgt--tgttaaaccacatgtt-cttgtttgtag
|||| |  ||   || ||||| |||||||| || || |||||||| || ||||||||||||||||| |||||||||||||||||||| |||||||||||||||||   || || ||                               |||  || ||||| | | ||||| | |||||| | |  ||||||| ||  || | ||| |||| ||
TCCAGACAGGACTGGCAGTGTCACAATTGTTGGAGCCGTCTCTCCTCCAGGTGGTGATTTTTCAGACCCTGTTACCTCTGCAACCCTCAGTATTGTTCAGgtaagacggctgccaattacttcaatacttcagtcccccaatcattggtccatcctgatttacagtgtttgttgtttcaatatattgttaaatcatgtgctgcttttttgcag

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 14
TCCAAAACGGGACGGAAGTGTTACAATTGTAGGGGCTGTCTCTCCACCTGGTGGTGATTTTTCAGATCCTGTTACCTCTGCAACCCTTAGTATTGTTCAGgtaaggaagcagctaagtctgtcatgattaataatgtttatcgttt-cagtgttgttaaaccacatgttcttgtttgtag-----------------------
 ||  ||||    || ||||| |||||||| || ||||| || |||||||| || ||||| ||||| ||||| || ||||||||||| || || ||||||||||   | |   |   ||    ||| |||| |  | | |  |  | ||  ||   | | ||  | ||| |  |   ||                        
CCCTGAACGTACAGGTAGTGTAACAATTGTTGGTGCTGTTTCGCCACCTGGAGGAGATTTCTCAGACCCTGTGACATCTGCAACCCTCAGCATAGTTCAGgtaa---aactattctttcaaatatggttaaaatgggtaactgcctgcaaagtaagtcagcctaaggttgtcttgactaattcccgcaaattgttaaaaccct

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 14
TCCAAAACGGGACGGAAGTGTTACAATTGTAGGGGCTGTCTCTCCACCTGGTGGTGATTTTTCAGATCCTGTTACCTCTGCAACCCTTAGTATTGTTCAGgtaaggaagcagctaagtctgtcatgattaataatgtttatcgttt-cagtgttgttaaaccacatgttcttgtttgtag-----------------------
 ||  ||||    || || || || ||||| || ||||| || |||||||| || ||||| ||||||||||| || ||||||||||| || || ||||||||||      |  | |       ||| |||| |  |   |  |  | ||  ||   | | ||  | ||| |  |    |                        
CCCTGAACGTACAGGTAGCGTAACTATTGTTGGTGCTGTTTCGCCACCTGGAGGAGATTTCTCAGATCCTGTGACATCTGCAACCCTGAGCATAGTTCAGgtaaaactatactttaa---aatatggttaaaatgggaaactgcctgcaaagtaagtcagccttaggttgtcatgaccaatgcccacaaattgttaaaagcct

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 13
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 14
TCCAAAACGGGACGGAAGTGTTACAATTGTAGGGGCTGTCTCTCCACCTGGTGGTGATTTTTCAGATCCTGTTACCTCTGCAACCCTTAGTATTGTTCAGgtaaggaagcagctaa-------------gtctgtcatgattaataatgt--ttat-cgtttcagtgttgttaaaccacatgtt-cttgtttgtag-------------------------------------------------------------------------------------------
 ||| ||||  ||||||||||||||||||| || || || || || ||||| || || |||||||||||||| || || ||||||||||||||||| ||||| |  |    | | |              |||  |||  |  || |  |  |  |   | |  ||   | | ||||| ||| |  ||  || |||                                                                                           
ACCAGAACGTAACGGAAGTGTTACAATTGTTGGTGCAGTTTCGCCTCCTGGAGGAGACTTTTCAGATCCTGTGACTTCAGCAACCCTTAGTATTGTGCAGgtgattatttggttcatgtctgcttccctatcttccattgtagattacatagtcgtatatgttggttgagatgaaccagatggtgtttagttttagatctgccgcagactcgtatatttaagcattttttttctccactttgaaatgcttactcttccattctggttgtttctcttttcttctgcag

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 13
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 14
TCCAAAACGGGACGGAAGTGTTACAATTGTAGGGGCTGTCTCTCCACCTGGTGGTGATTTTTCAGATCCTGTTACCTCTGCAACCCTTAGTATTGTTCAGgtaaggaagcagctaagtctgtcatgattaataatgtttatcgtttcagtgttgttaaaccacatgttcttgtttgtag--------------------------
 ||| ||||    || ||||| || ||||| || || || |||||||| ||||| |||||||||||||| || || || || || ||||||||||| |||||||        | || | |  ||  |||   | | ||   | |||||    |  | |   |||   | | |||    |                          
GCCAGAACGCACAGGTAGTGTCACCATTGTGGGTGCAGTTTCTCCACCAGGTGGAGATTTTTCAGATCCAGTGACATCAGCTACACTTAGTATTGTCCAGgtaa-----tctccaaattttccagcattttcatttttgcccatttcacgtctcatgagtaacaacatttagttaaaggagacacaggaaaagtttcctagcact

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 13
lower sequence: PP1S10_201V6.1 (Physcomitrella patens), 5'ss of exon 14
TCCAAAACGGGACGGAAGTGTTACAATTGTAGGGGCTGTCTCTCCACCTGGTGGTGATTTTTCAGATCCTGTTACCTCTGCAACCCTTAGTATTGTTCAGgtaaggaa--gcagctaagtctgtcatgattaataatgtttatcgtttcagtgtt--gttaaaccacatgttc--ttgtttgtag---------------------------------------------------------
 || || ||    ||||||||||| ||||| || || || || || |||||||| ||||||||||| ||||| ||  | || |||||| |||||||||||||  | |   | | ||       ||  |   |  |   | || |   |      |  |  ||| | ||||     |||  | |                                                           
CCCGAATCGTACTGGAAGTGTTACCATTGTTGGAGCAGTGTCCCCTCCTGGTGGAGATTTTTCAGACCCTGTCACAGCAGCTACCCTTGGTATTGTTCAGgttggtatttgtacctcctctcatccagtgcaccacattctaccagatattctctaagccaaagcccatgagaagttggctatgatgttgcatgtcttccaagcgaaggaactaaagcatattgtaaatgcatgttgattag

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|66925761|gb|CX112609.1|CX112609
EST:     GTGGTGATTTTTCAGATCCTGTTACCTCTGCAACCCTTAGTATTGTTCAG                         GTCTTCTGGGGATTAGATAAAAAGCTTGCCCAGAGGAAGCATTTCCCATCA
genomic: GTGGTGATTTTTCAGATCCTGTTACCTCTGCAACCCTTAGTATTGTTCAGgtaaggaagc ... ttgtttgtagGTCTTCTGGGGATTAGATAAAAAGCTTGCCCAGAGGAAGCATTTCCCATCA




















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: 75 (upstream exon), 60 (downstream exon)
Score: 9

TCCAAAACGGGACGGAAGTGTTACAATTGTAGGGGCTGTCTCTCCACCTGGTGGTGATTTTTCAGATCCTGTTACCTCTGCAACCCTTAGTATTGTTCAGgtaaggaagc ... ttgtttgtagGTCTTCTGGGGATTAGATAAAAAGCTTGCCCAGAGGAAGCATTTCCCATCAGTGAATTGGCTCATATCTTATTCGAAATATTCTAAG




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