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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGCTGCTTCGTTAGGAGCAGTTGAAAGTATTTCCATGAAAGATACCCGTATTCTTGTTGATGCCCGAAAGTCAAAGATCTACACTGCGGAGgtattttgctaattgcactttgcttgctttaataaatatatttttctcaataaataagtcacaacataagtgtgcagtactcatgtatctaagaacatta...

Basic information

species Oryza sativa
transcript LOC_Os10g10170.1
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g10170.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G335703_T01 (Zea mays), 5'ss of exon 2
GAAGCTGCTTCGTTAGGAGCAGTTGAAAGTATTTCCATGAAAGATACCCGTATTCTTGTTGATGCCCGAAAGTCAAAGATCTACACTGCGGAGgtatt-ttgctaattgcactttgcttgctttaataaatatatttttctcaataaataagtcacaacataagtgtgcagtactcatgtatctaagaacatta-
|| |||||||| ||||||||||||| ||| |||||||| ||||| ||||| ||| || |||||||  |||||| |||||||| ||| || |||||| | ||||| |||| |   |||   | | |   ||| | | |        || | |   ||| ||| |   ||   |  |  | | | |  | |  ||| 
GAGGCTGCTTCATTAGGAGCAGTTGCAAGCATTTCCATAAAAGAAACCCGGATTGTTATTGATGCTAGAAAGTTAAAGATCTTCACAGCCGAGgtactattgctgattggaacatgcc-acataagcgaatctgtatccaaatgcaattcaaggaca-catcaacatgtcctgtttct-tgtttctgtattttag

upper sequence: LOC_Os10g10170.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G018929_T02 (Zea mays), 5'ss of exon 9
GAAGCTGCTTCGTTAGGAGCAGTTGAAAGTATTTCCATGAAAGATACCCGTATTCTTGTTGATGCCCGAAAGTCAAAGATCTACACTGCGGAGgtatt-ttgctaattgcactttgcttgctttaataaatatatttttctcaataaataagtcacaacataagtgtgcagtactcatgtatctaagaacatta--
|| |||||||| ||||||||||||| ||| |||||||| ||||| ||||| ||| || |||||||  |||||| |||||||| ||| || |||||| | ||||| |||| |   |||   | | |   ||| | | |        || | |   ||| ||| |   ||   |  |  | | | |  | |  |||  
GAGGCTGCTTCATTAGGAGCAGTTGCAAGCATTTCCATAAAAGAAACCCGGATTGTTATTGATGCTAGAAAGTTAAAGATCTTCACAGCCGAGgtactattgctgattggaacatgcc-acataagcgaatctgtatccaaatgcaattcaaggaca-catcaacatgtcctgtttct-tgtttctgtattttagg
















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|25803304|gb|CA759265.1|CA759265
EST:     ATACCCGTATTCTTGTTGATGCCCGAAAGACAAAGATCTACACTGGGGAG                         GTTTCAGTTCTTACAACATTGAGGTCTTTAAAGCATTGACTAGCTGCAG
genomic: ATACCCGTATTCTTGTTGATGCCCGAAAGTCAAAGATCTACACTGCGGAGgtattttgct ... tttttgacagGTTTCAGTTCTTACAACATTGAGGTCTTTAAAGCATCGACTAGCTGCAG
EST: gi|58693842|gb|CK082529.1|CK082529
EST:     ATGCCCGAAAGTCAAAGATCTACACTGCAGAG                         GTTTCAGTTCTTACAACATTGAGGTCTTTAAAGCATCGACTAGCTGCAG
genomic: ATGCCCGAAAGTCAAAGATCTACACTGCGGAGgtattttgct ... tttttgacagGTTTCAGTTCTTACAACATTGAGGTCTTTAAAGCATCGACTAGCTGCAG
EST: gi|29678934|gb|CB675209.1|CB675209
EST:     ATACCCGTATTCTTGTTGATGCCCGAAAGTCAAAGATCTACACTGCGGAG                         GTTTCAGTTCTTACAACATTGAGGTCTTTAAAGCATCGACTAGCTGCAG
genomic: ATACCCGTATTCTTGTTGATGCCCGAAAGTCAAAGATCTACACTGCGGAGgtattttgct ... tttttgacagGTTTCAGTTCTTACAACATTGAGGTCTTTAAAGCATCGACTAGCTGCAG
EST: gi|29614516|gb|CB619529.1|CB619529
EST:     ATACCCGTATTCTTGTTGATGCCCGAAAGTCAAAGATCTACACTGCAGAG                         GTTTCAGTTCTTACAACATTGAGGTCTTTAAAGCATCGACTAGCTGCAG
genomic: ATACCCGTATTCTTGTTGATGCCCGAAAGTCAAAGATCTACACTGCGGAGgtattttgct ... tttttgacagGTTTCAGTTCTTACAACATTGAGGTCTTTAAAGCATCGACTAGCTGCAG
EST: gi|58692218|gb|CK080905.1|CK080905
EST:     ATACCCGTATTCTTGTTGATGCCCGAAAGTCAAAGATCTACACTGCAGAG                         GTTTCAGTTCTTACAACATTGAGGTCTTTAAAGCATCGACTAGCTGCAG
genomic: ATACCCGTATTCTTGTTGATGCCCGAAAGTCAAAGATCTACACTGCGGAGgtattttgct ... tttttgacagGTTTCAGTTCTTACAACATTGAGGTCTTTAAAGCATCGACTAGCTGCAG

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: 71 (upstream exon), 64 (downstream exon)
Score: 19

GAAGCTGCTTCGTTAGGAGCAGTTGAAAGTATTTCCATGAAAGATACCCGTATTCTTGTTGATGCCCGAAAGTCAAAGATCTACACTGCGGAGgtattttgct ... tttttgacagGTTTCAGTTCTTACAACATTGAGGTCTTTAAAGCATCGACTAGCTGCAG




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