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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATATGGAGATCCAGAAGCAGCTGACATAGTTTTTACCTCAGGAGCAGATGTTGACGTGGTTGGCATTAACATAACAACTCAAGTCTGTTTTACAGgtttgttccttgatagtgtcatttgcatggttcgagtccagctgtggggtcaattatattcatcaagtaaaatctgtttctttcag

Basic information

species Oryza sativa
transcript LOC_Os08g44370.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g44370.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G085960_T01 (Zea mays), 5'ss of exon 6
ATATATGGAGATCCAGAAGCAGCTGACATAGTTTTTACCTCAGGAGCAGATGTTGACGTGGTTGGCATTAACATAACAACTCAAGTCTGTTTTACAGgtttgttccttgatagtgtcatttgcatggttcgagtccagctgtggggtcaattatattcatcaagtaaaatctgtttctttcag
||   |||||| |||||||||||||||||||||||||| ||||||||||||||    ||||||||||||||||||||||| ||||||||||| ||||||| | || |||||| |    | || |  |||| ||| |      || ||  | |||||| | |  || | || |  || ||| ||
ATTCTTGGAGACCCAGAAGCAGCTGACATAGTTTTTACTTCAGGAGCAGATGTCATTGTGGTTGGCATTAACATAACAACACAAGTCTGTTTGACAGgttggctcattgataatcaattgtgtacagttcaagttc-----cggagttgactatattaaccttgtgagat-tccttgttttag

upper sequence: LOC_Os08g44370.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G015344_T02 (Zea mays), 5'ss of exon 6
ATATATGGAGATCCAGAAGCAGCTGACATAGTTTTTACCTCAGGAGCAGATGTTGACGTGGTTGGCATTAACATAACAACTCAAGTCTGTTTTACAGgtttgttccttgatagtgtcatttgcatggttcgagtccagctgtggggtcaattatattcatcaagtaaaatctgtttctttcag
||  ||||||| |||||||||||||||||||||||||| |||||||||||| | |  ||||||||||||||||||||||| ||||||||  | ||||||| |||| ||| |||| |  | || || |||| ||| |     |||||| || |||||||| || || | ||   ||  |||   
ATCCATGGAGACCCAGAAGCAGCTGACATAGTTTTTACTTCAGGAGCAGATATCGTTGTGGTTGGCATTAACATAACAACACAAGTCTGCCTGACAGgttggttcattggtagtctattgtgtatagttcaagttc-----tggggtaaactatattcaccatgtgagattcattgttttag-
















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|38471404|gb|CF955535.1|CF955535
EST:     AGATATTGACGTGGTTGGCATTAACATAACAACTCAAGTCTGTTTTACAG                         ATAAGGATCTCCTGGAGCTAAGAAACTCAAAAGGGAAGCATGCACATTTCT
genomic: AGATGTTGACGTGGTTGGCATTAACATAACAACTCAAGTCTGTTTTACAGgtttgttcct ... tttctttcagATGAGGATCTCCTGGAGCTAAGAAACTCAAAAGGGAAGCATGCACAGTTCT
EST: gi|29658032|gb|CB654307.1|CB654307
EST:     AGATGTTGACGTGGTTGGCATTAACATAACAACTCAAGTCTG-TTTACAG                         ATGAGGATCTCCTGGAGCTAAGAAACTCAAAAGGGAAGCATGCACAGTTCT
genomic: AGATGTTGACGTGGTTGGCATTAACATAACAACTCAAGTCTGTTTTACAGgtttgttcct ... tttctttcagATGAGGATCTCCTGGAGCTAAGAAACTCAAAAGGGAAGCATGCACAGTTCT
EST: gi|29670960|gb|CB667235.1|CB667235
EST:     AGATGTTGACGTGGTTGGCATTAACATAACAACTCAAGTCTGTTTTACAG                         ATGAGGATCTCCTGGAGCTAAGAAACTCAAAAGGGAAGCATGCACAGTTCT
genomic: AGATGTTGACGTGGTTGGCATTAACATAACAACTCAAGTCTGTTTTACAGgtttgttcct ... tttctttcagATGAGGATCTCCTGGAGCTAAGAAACTCAAAAGGGAAGCATGCACAGTTCT
EST: gi|29623183|gb|CB628194.1|CB628194
EST:     AGATGTTGACGTGGTGGGCATTAACATAACAACTCAAGTCTGTTTTACAG                         ATGAGGATCTCCTGGAGCTAAGAAACTCAAAAGGGAAGCATGCACAGTTCT
genomic: AGATGTTGACGTGGTTGGCATTAACATAACAACTCAAGTCTGTTTTACAGgtttgttcct ... tttctttcagATGAGGATCTCCTGGAGCTAAGAAACTCAAAAGGGAAGCATGCACAGTTCT
EST: gi|29614023|gb|CB619036.1|CB619036
EST:     AGATGTTGACGTGGTGGGCATTAACATAACAACTCAAGTCTGTTTTACAG                         ATGAGGATCTCCTGGAGCTAAGAAACTCAAAAGGGAAGCATGCACAGTTCT
genomic: AGATGTTGACGTGGTTGGCATTAACATAACAACTCAAGTCTGTTTTACAGgtttgttcct ... tttctttcagATGAGGATCTCCTGGAGCTAAGAAACTCAAAAGGGAAGCATGCACAGTTCT
EST: gi|163920050|gb|EG712004.1|EG712004
EST:     AGATGTTGACGTGGTTGGCATTAACATAACAACTCAAGTCTGTTTTACAG                         ATGAGGATCTCCTGGAGCTAAGAAACTCAAAAGGGAAGCATGCACAGTTCT
genomic: AGATGTTGACGTGGTTGGCATTAACATAACAACTCAAGTCTGTTTTACAGgtttgttcct ... tttctttcagATGAGGATCTCCTGGAGCTAAGAAACTCAAAAGGGAAGCATGCACAGTTCT
EST: gi|58678875|gb|CK067562.1|CK067562
EST:     AGATGTTGACGTGGTTGGCATTAACATAACAACTCAAGTCTGTTTTACAG                         ATGAGGATCTCCTGGAGCTAAGAAACTCAAAAGGGAAGCATGCACAGTTCT
genomic: AGATGTTGACGTGGTTGGCATTAACATAACAACTCAAGTCTGTTTTACAGgtttgttcct ... tttctttcagATGAGGATCTCCTGGAGCTAAGAAACTCAAAAGGGAAGCATGCACAGTTCT
EST: gi|29614025|gb|CB619038.1|CB619038
EST:     CATAACAACTCAAGTCTGTTTTTACAG                         ATGAGGATCTCCTGGGAGGTAAGAAACTCAAAAGGGAAGCATGCACAGTT
genomic: CATAACAACTCAAGTCTG-TTTTACAGgtttgttcct ... tttctttcagATGAGGATCTCCT-GGAGCTAAGAAACTCAAAAGGGAAGCATGCACAGTT

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: 65 (upstream exon), 60 (downstream exon)
Score: 19

ATATATGGAGATCCAGAAGCAGCTGACATAGTTTTTACCTCAGGAGCAGATGTTGACGTGGTTGGCATTAACATAACAACTCAAGTCTGTTTTACAGgtttgttcct ... tttctttcagATGAGGATCTCCTGGAGCTAAGAAACTCAAAAGGGAAGCATGCACAGTTCTTATGTGACATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGG




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