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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATAGCCTGAAGGAAGTTTTGGATAGCCCAAGTGTGATGACACTAATAAAAGATACAAAGGCGGCGCAGGAGgtaagccatattcagaacaagatatatcactaaatgccctaatgtacacctatggtgctttctcaaacagttcccccatgttgatataatacgcactaaggcactaagcacattcaaaacaatttctaagtacagacagcttctcatatttgttttctgacgctcttatatttcctttctaatttgcag

Basic information

species Oryza sativa
transcript LOC_Os04g56480.3
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g56480.3 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G044011_T02 (Zea mays), 5'ss of exon 11
GCATAGCCTGAAGGAAGTTTTGGATAGCCCAAGTGTGATGACACTAATAAAAGATACAAAGGCGGCGCAGGAGgtaagccatattcagaacaagatatatcactaaatgccctaatgtacacctatggtgctttctcaaacagttcccccatgttgatataatacgcactaaggcactaagcacattcaaaacaatttctaagtacagacagcttctcatatttgttttctgacgctcttatatttcctttctaatttgcag
||||||  | |||||||||||||| |  ||| |||||||| |||| |||||||||||||| || || ||||||||||| |  | |   ||  | | |  |||||| ||   ||||| ||    |   |   | | | ||| |    |  ||   |  | |||| |  | ||||                                                                                         
GCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAGgtaagactgactataaatcacacacgtcactagatatactaatttatgtatg-agctttctttaaaataacaacaacaaagtcttttaatcccaagtaagt----------------------------------------------------------------------------------------
















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|89182762|gb|CI114131.1|CI114131
EST:     ATAGCCCAAGTGTGATGACACTAATAAAAGATACAAAGGCGGCGCAGGAG                         GTCCAAGCTTTGAAGGACTTCTTCAACATGCTTACAAAT
genomic: ATAGCCCAAGTGTGATGACACTAATAAAAGATACAAAGGCGGCGCAGGAGgtaagccata ... taatttgcagGTCCAAGCTTTGAAGGACTTCTTCAACATGCTTACAAAT
EST: gi|88224189|gb|CI224038.1|CI224038
EST:     ATAGCCCAAGTGTGATGACACTAATAAAAGATACAAAGGCGGCGCAGGAG                         GTCCAAGCTTTGAAGGACTTCTTCAACATGCTTACAAAT
genomic: ATAGCCCAAGTGTGATGACACTAATAAAAGATACAAAGGCGGCGCAGGAGgtaagccata ... taatttgcagGTCCAAGCTTTGAAGGACTTCTTCAACATGCTTACAAAT
EST: gi|86505661|gb|CI148294.1|CI148294
EST:     ATAGCCCAAGTGTGATGACACTAATAAAAGATACAAAGGCGGCGCAGGAG                         GTCCAAGCTTTGAAGGACTTCTTCAACATGCTTACAAAT
genomic: ATAGCCCAAGTGTGATGACACTAATAAAAGATACAAAGGCGGCGCAGGAGgtaagccata ... taatttgcagGTCCAAGCTTTGAAGGACTTCTTCAACATGCTTACAAAT
EST: gi|87006648|gb|CI295031.1|CI295031
EST:     ATAGCCCAAGTGTGATGACACTAATAAAAGATACAAAGGCGGCGCAGGAG                         GTCCAAGCTTTGAAGGACTTCTTCAACATGCTTACAAATGA
genomic: ATAGCCCAAGTGTGATGACACTAATAAAAGATACAAAGGCGGCGCAGGAGgtaagccata ... taatttgcagGTCCAAGCTTTGAAGGACTTCTTCAACATGCTTACAAATGA
EST: gi|88227542|gb|CI227022.1|CI227022
EST:     AGCCCAAGTGTGATGACACTAATAAAAGATACAAAGGCGGCGCAGGAG                         GTCCAAGCTTTGAAGGACTTCTTCAACATGCTTACAAAT
genomic: AGCCCAAGTGTGATGACACTAATAAAAGATACAAAGGCGGCGCAGGAGgtaagccata ... taatttgcagGTCCAAGCTTTGAAGGACTTCTTCAACATGCTTACAAAT
EST: gi|86854586|gb|CI258879.1|CI258879
EST:     ATAGCCCAAGTGTGATGACCCTAATAAAAGATACAAAGGCGGCGCAGGAG                         GTCCAAGCTTTGAAGGACTTCTTCAACATGCTTACAAAT
genomic: ATAGCCCAAGTGTGATGACACTAATAAAAGATACAAAGGCGGCGCAGGAGgtaagccata ... taatttgcagGTCCAAGCTTTGAAGGACTTCTTCAACATGCTTACAAAT

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: 64 (upstream exon), 39 (downstream exon)
Score: 16

GCATAGCCTGAAGGAAGTTTTGGATAGCCCAAGTGTGATGACACTAATAAAAGATACAAAGGCGGCGCAGGAGgtaagccata ... taatttgcagGTCCAAGCTTTGAAGGACTTCTTCAACATGCTTACAAAT




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