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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCATGCCAACCCAGGAGTGCTTGGACCAATGATGGGTGGTCCTGCGCCAATTATAACCATGCCTCCATCTTTTCGTCAAGATCCTCGCCGTTTGCGAAGgttagtaattattcattcataccattgaattccatgatgtctattctcctattttgcttggattggcttgattatgccacattctgaccaacaatttggc...

Basic information

species Oryza sativa
transcript LOC_Os06g48530.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g48530.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM5G817439_T01 (Zea mays), 5'ss of exon 11
CTCATGCCAACCCAGGAGTGCTTGGACCAATGATGGGTGGTCCTGCGCCAATTATAACCATGCCTCCATCTTTTCGTCAAGATCCTCGCCGTTTGCGAAGgtt-------------agtaattattcattcataccattgaattccatgatgtctattctcctattttgcttggattggcttgattatgccacattc--tgacc----aacaatttggc---------------------------------------------------------------
| |||| |||  | ||| ||||||| |||||||||||||| || || || |||||| | |||||||||  ||| || || |||||||||||  || |||||||             || |  |  |  | |  |   |||  | |  ||||||  || |   | | |||||  ||   |  | ||||| |    ||   ||| |    || ||| | ||                                                               
CACATGGCAATGCTGGAATGCTTGGGCCAATGATGGGTGGCCCAGCACCGATTATAGCTATGCCTCCAAATTTCCGCCATGATCCTCGCCGCCTGAGAAGgtttacccccagtttcagaatcttgttttcctcatgtttgggtgctctgatgttcatgcaattttgttgctgcga--aggctaattattcttttttggatgaactttaaaaaatgtcgctgtagtttttagtgggattttttttggcaacaaaatgcaactcatacctggctttggttgcag
















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|33685942|gb|CF314181.1|CF314181
EST:     ATTATAACCATGCCTCCATCTTTTCGTCAAGATCCTCGCCGTTTGCGAAG                         TTACAATGACCTTGATGCTCCGGACGAGGAAGTTACCGTTCTTGACTACAG
genomic: ATTATAACCATGCCTCCATCTTTTCGTCAAGATCCTCGCCGTTTGCGAAGgttagtaatt ... tcttctgcagTTACAATGACCTTGATGCTCCGGACGAGGAAGTTACCGTTCTTGACTACAG
EST: gi|86535979|gb|CI176185.1|CI176185
EST:     ATTATAACCATGCCTCCATCTTTTCGTCAAGATCCTCGCCGTTTGCGAAG                         TTACAATGACCTTGATGCTCCGGACGAGGAAGTTACCGTTCTTGACTACAG
genomic: ATTATAACCATGCCTCCATCTTTTCGTCAAGATCCTCGCCGTTTGCGAAGgttagtaatt ... tcttctgcagTTACAATGACCTTGATGCTCCGGACGAGGAAGTTACCGTTCTTGACTACAG
EST: gi|88491611|gb|CI428883.1|CI428883
EST:     ATTATAACCATGCCTCCATCTTTTCGTCAAGATCCTCNCCGTTTGCGAAG                         TTACAATGACCTTGATGCTCCGGACGAGGAAGTTACCGTTCTTGACTACAG
genomic: ATTATAACCATGCCTCCATCTTTTCGTCAAGATCCTCGCCGTTTGCGAAGgttagtaatt ... tcttctgcagTTACAATGACCTTGATGCTCCGGACGAGGAAGTTACCGTTCTTGACTACAG
EST: gi|29680660|gb|CB676935.1|CB676935
EST:     ATTATAACCATGCCTCCATCTTTTCGTCAAGATCCTCGCCGTTTGCGAAG                         TTACAATGACCTTGATGCTCCGGACGAGGAAGTTACCGTTCTTGACTACAG
genomic: ATTATAACCATGCCTCCATCTTTTCGTCAAGATCCTCGCCGTTTGCGAAGgttagtaatt ... tcttctgcagTTACAATGACCTTGATGCTCCGGACGAGGAAGTTACCGTTCTTGACTACAG
EST: gi|33685941|gb|CF314180.1|CF314180
EST:     TTATAACCATGCCTCCATCTTTTCGTCAAGATCCTCGCCGTTTGGCGAAG                         TTACAATGACCTTGATGCTC
genomic: TTATAACCATGCCTCCATCTTTTCGTCAAGATCCTCGCCGTTTG-CGAAGgttagtaatt ... tcttctgcagTTACAATGACCTTGATGCTC
EST: gi|88483634|gb|CI420905.1|CI420905
EST:     ATTATAACCATGCCTCCATCTTTTCGTCAAGATCCTCGCCGTTTGCGAAG                         TTACAATGACCTTGATGCTCCGGACGAGGAAGTTACCGTTCTTGACTACAG
genomic: ATTATAACCATGCCTCCATCTTTTCGTCAAGATCCTCGCCGTTTGCGAAGgttagtaatt ... tcttctgcagTTACAATGACCTTGATGCTCCGGACGAGGAAGTTACCGTTCTTGACTACAG
EST: gi|88842070|gb|CI081326.1|CI081326
EST:     ATTATAACCATGCCTCCATCTGTTCGTCAAGATCCTCGCCGTTTGCGAAG                         TTACAATGACCTTGATGCTCCGGACGAGGAAGTTACCGTTCTTGACTACAG
genomic: ATTATAACCATGCCTCCATCTTTTCGTCAAGATCCTCGCCGTTTGCGAAGgttagtaatt ... tcttctgcagTTACAATGACCTTGATGCTCCGGACGAGGAAGTTACCGTTCTTGACTACAG
EST: gi|88560667|gb|CI491352.1|CI491352
EST:     ATTATAACCATGCCTCCATCTTTTCGTCAAGATCCTCGCCGTTTGCGAAG                         TTACAATGACCTTGATGCTCC-GACGGAGGAAGTTACCGTTCTTGACTACA
genomic: ATTATAACCATGCCTCCATCTTTTCGTCAAGATCCTCGCCGTTTGCGAAGgttagtaatt ... tcttctgcagTTACAATGACCTTGATGCTCCGGAC-GAGGAAGTTACCGTTCTTGACTACA
EST: gi|88282991|gb|CI404239.1|CI404239
EST:     TTATAACCATGCCTCCATCTTGTTCGTCAAGATCCTCGCCGTTTGCGAAG                         TTACAATGACCTTGATGGTCCGGACGAGGGAGTTACCGTTTTTGACTACAG
genomic: TTATAACCATGCCTCCATCTT-TTCGTCAAGATCCTCGCCGTTTGCGAAGgttagtaatt ... tcttctgcagTTACAATGACCTTGATGCTCCGGACGAGGAAGTTACCGTTCTTGACTACAG
EST: gi|86837528|gb|CI345733.1|CI345733
EST:     ATTATAACCATGCCTCCATCTTTTCGTCAAGATCCTCGCCGTTTGCGAAG                         TTACAATGACCTTGATGCTCCGGAGCGAGGAAGTTACCGTTCTTGACTACA
genomic: ATTATAACCATGCCTCCATCTTTTCGTCAAGATCCTCGCCGTTTGCGAAGgttagtaatt ... tcttctgcagTTACAATGACCTTGATGCTCCGGA-CGAGGAAGTTACCGTTCTTGACTACA

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: 54 (upstream exon), 42 (downstream exon)
Score: 2

CTCATGCCAACCCAGGAGTGCTTGGACCAATGATGGGTGGTCCTGCGCCAATTATAACCATGCCTCCATCTTTTCGTCAAGATCCTCGCCGTTTGCGAAGgttagtaatt ... tcttctgcagTTACAATGACCTTGATGCTCCGGACGAGGAAGTTACCGTTCTTGACTACAGAAGTTTGTAGAGCTTGCCCTGGTGTAATTGTAATTTGCCAATCACAACT




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