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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTAGTTGAGCACTTTTTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAGgtacatattgctttgcttcagatcaaatttccatccagtgttggatcattattacaagagtgctgtttggcactgaataaattgcatccctagttgaacataagagtcaatctttgcttttcctccagttaagcgagctaagaagtacgtatatcatacctgagcctgccttttctttgctcttatgaag

Basic information

species Oryza sativa
transcript LOC_Os04g52710.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52710.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G094255_T01 (Zea mays), 5'ss of exon 6
CTAGTTGAGCACTTTTTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAGgtacatattgctttgc-ttcagatcaaatttccatccagt--gttggatcattattacaagagtgctgtttggcactgaata-aattgcatcc-ctagttgaacataagagtca-atctttgcttttcctccagtta----agcgagctaagaag--tacgtatatcatacctgagcctgccttttctttgctcttatgaag
|| ||||||||||| ||||||||| | ||||| |||||||||||||| ||||||||||||||||||||||||||| | |  ||| ||||||||  | || |    | ||||||| |  |||||   |  |    |||| |   || |||   ||   || | ||| ||||||    | ||  |||  ||| ||| | ||     |||||  |   | |    |||   |   |||||| |  ||    |  |   |||| |||||
CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattgctgtccgctcaaatcaaattctcctcaaaacagctggatcagtgatacaattttagtcacgggcattttgtagaatcatattgactggctgagcataaggccaagatggttgagttttctctattttttatagcgaatttgcatgaccccgtccctatcacctgatctcgctccatactg--tcttttgaag

upper sequence: LOC_Os04g52710.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G094255_T02 (Zea mays), 5'ss of exon 5
-------------------------------------CTAGTTGAGCACTTTTTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAGgtacatattgctttgc-ttcagatcaaatttccatccagt--gttggatcattattacaagagtgctgtttggcactgaata-aattgcatcc-ctagttgaacataagagtca-atctttgcttttcctccagtta----agcgagctaagaag--tacgtatatcatacctgagcctgccttttctttgctcttatgaag
                                     || ||||||||||| ||||||||| | ||||| |||||||||||||| ||||||||||||||||||||||||||| | |  ||| ||||||||  | || |    | ||||||| |  |||||   |  |    |||| |   || |||   ||   || | ||| ||||||    | ||  |||  ||| ||| | ||     |||||  |   | |    |||   |   |||||| |  ||    |  |   |||| |||||
CTTACAGAAAAGTTTCATTTATTCGTTTTGGTCCCAGCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattgctgtccgctcaaatcaaattctcctcaaaacagctggatcagtgatacaattttagtcacgggcattttgtagaatcatattgactggctgagcataaggccaagatggttgagttttctctattttttatagcgaatttgcatgaccccgtccctatcacctgatctcgctccatactg--tcttttgaag

upper sequence: LOC_Os04g52710.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT3G22425.1 (Arabidopsis thaliana), 5'ss of exon 5
-------------------------------------CTAGTTGAGCACTTTTTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAGgtacatattgctttgcttcagatcaaatttccatccagtgttggatcattattacaagagtgctgtttggcactgaataaattgcatccctagttgaacataagagtcaatctttgctt-ttcctccagttaagcgagctaagaagtacgtatatcatacctgagcctgccttttctttgctcttatgaag
                                      | || |||||||||||||| ||  | |||||||| ||||| ||||| ||||||||||| ||||||| |  || ||    ||    ||||     |   | |  || |      || || ||||  | ||     ||   |    ||    ||   ||  | |  ||  | ||| |||| || || |  |||                                                              
AGTGTTGCCAAAAATTGTTTAACCTTTCGATTTGTAGTTGGTGGAGCACTTTTTCCAGTCGTTGGTGAATACTTCTGGTATGACTCTTCACATCCGGCAGgtactttgtgattcaaatctt-ccaaaagctaacaaaatcatgca-----gtttcatgagt-ttcttctatcctctgt---ctgtggacc--atttcataacagttttaatatttgtttgttacaacag--------------------------------------------------------------

upper sequence: LOC_Os04g52710.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT3G22425.2 (Arabidopsis thaliana), 5'ss of exon 6
CTAGTTGAGCACTTTTTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAGgtacatattgctttgcttcagatcaaatttccatccagtgttggatcattattacaagagtgctgtttggcactgaataaattgcatccctagttgaacataagagtcaatctttgctt-ttcctccagttaagcgagctaagaagtacgtatatcatacctgagcctgccttttctttgctcttatgaag
 | || |||||||||||||| ||  | |||||||| ||||| ||||| ||||||||||| ||||||| |  || ||    ||    ||||     |   | |  || |      || || ||||  | ||     ||   |    ||    ||   ||  | |  ||  | ||| |||| || || |  |||                                                              
TTGGTGGAGCACTTTTTCCAGTCGTTGGTGAATACTTCTGGTATGACTCTTCACATCCGGCAGgtactttgtgattcaaatctt-ccaaaagctaacaaaatcatgca-----gtttcatgagt-ttcttctatcctctgt---ctgtggacc--atttcataacagttttaatatttgtttgttacaacag--------------------------------------------------------------

upper sequence: LOC_Os04g52710.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv05s0020g03430.t01 (Vitis vinifera), 5'ss of exon 6
CTAGTTGAGCACTTTTTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAGgtacatattgctttgcttcagatcaaatttccatccagtgttggatcattattacaagagtgctgtttggcactgaataaattgcatccctagttgaacataagagtcaatctttgcttttcctccagttaagcgagctaagaagtacgtatatcatacctgagcctgccttttctttgctcttatgaag
 | || |||||||||||||| ||| | |||||||| || || |||||||||||||| || |||||| |    |  || | | | ||  |  ||  | | | |  |   || |      || | |  ||||        || |||   |||| | | |  |   |                                                                                         
TTGGTGGAGCACTTTTTCCAGTCTTTGGTGAATACTTCAGGCATGACACTTCACATTCGACAGgtataatgagagtttcctaacattta--ttgtagcaaatagtaactcctcca---aatattcttgttaatttagaaagaaaacacatctccattcaatggtcttc-------------------------------------------------------------------------------------

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|88846550|gb|CI373318.1|CI373318
EST:     ATCTGGGATGACACTTCACATCCGTCAG                         CTTGCTGGAAAAAACTCACACCATATTATTGAGGCAACTTTCAAAGCATTT
genomic: ATCTGGGATGACACTTCACATCCGTCAGgtacatattg ... tcttatgaagCTTGCTGGAAAAAACTCACACCATATTATTGAGGCAACTTTCAAAGCATTT
EST: gi|89186200|gb|CI048069.1|CI048069
EST:     TGGGATGACACTTCACATCCGTCAG                         CTTGCTGGAAAAAACTCACACCATATTATTGAGGCAACTTTCAAAGCATTT
genomic: TGGGATGACACTTCACATCCGTCAGgtacatattg ... tcttatgaagCTTGCTGGAAAAAACTCACACCATATTATTGAGGCAACTTTCAAAGCATTT
EST: gi|29658247|gb|CB654522.1|CB654522
EST:     TTTTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAG                         CTTGCTGGAAAAAACTCACACCATATTATTGAGGCAACTTTCAAAGCATTT
genomic: TTTTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAGgtacatattg ... tcttatgaagCTTGCTGGAAAAAACTCACACCATATTATTGAGGCAACTTTCAAAGCATTT
EST: gi|58666132|gb|CK054818.1|CK054818
EST:     TTGTGAATACATCTGGGATGACACTTCACATCCGTCAG                         CTTGCTGGAAAAAACTCACACCATATTATTGAGGCAACTTTCAAAGCATTT
genomic: TTGTGAATACATCTGGGATGACACTTCACATCCGTCAGgtacatattg ... tcttatgaagCTTGCTGGAAAAAACTCACACCATATTATTGAGGCAACTTTCAAAGCATTT
EST: gi|86504503|gb|CI147136.1|CI147136
EST:     TTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAG                         CTTGCTGGAAAAAACTCACACCATATTATTGAGGCAACTTTCAAAGCATTT
genomic: TTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAGgtacatattg ... tcttatgaagCTTGCTGGAAAAAACTCACACCATATTATTGAGGCAACTTTCAAAGCATTT
EST: gi|89182904|gb|CI045662.1|CI045662
EST:     GACACTTCACATCCGTCAG                         CTTGCTGGAAAAAACTCACACCATATTATTGAGGCAACTTTCAAAGCATTT
genomic: GACACTTCACATCCGTCAGgtacatattg ... tcttatgaagCTTGCTGGAAAAAACTCACACCATATTATTGAGGCAACTTTCAAAGCATTT

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: 63 (upstream exon), 62 (downstream exon)
Score: 21

CTAGTTGAGCACTTTTTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAGgtacatattg ... tcttatgaagCTTGCTGGAAAAAACTCACACCATATTATTGAGGCAACTTTCAAAGCATTTGCTAGAGCCCTTCGACAAGCAACAGAATATGACTTGCGCCGACGCGGCA




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