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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTACGTAAACATTAAAGATGATCAAGCTCATGCAGTGAATACTGCCTGGGCAATGTTAGCTTTAATTTGTGCAGGACAGgtgtgttttgtttattttcaattcaattctgataggaatgacctttttatcgaatgatctctataaccatttggatgtcag

Basic information

species Oryza sativa
transcript LOC_Os11g35710.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g35710.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G006937_T01 (Zea mays), 5'ss of exon 16
GTTTACGTAAACATTAAAGATGATCAAGCTCATGCAGTGAATACTGCCTGGGCAATGTTAGCTTTAATTTGTGCAGGACAGgtgtgttttgtttattttcaattcaattctga-taggaatgacctttttatcgaa-tgatctct-ataaccatttggatgtcag
|| || |||||  | |||| ||| |  ||||| || |||||||| |||||||||||| | |||||||||| ||| ||||||||     |  ||   | | | ||||  | |||  | |||    |  |||| | |  || || || |   |   |   ||   ||
GTGTATGTAAATCTCAAAGGTGACCGTGCTCACGCTGTGAATACCGCCTGGGCAATGCTCGCTTTAATTTATGCTGGACAGgtacaggtcattc--tgtaatttcacatatgaacaagaacctacaatttaccaatctgttcactcacctcttctctaatactag
















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|86844024|gb|CI336718.1|CI336718
EST:     GTGAATACTGCCTGGGCAATGTTAGCTTTAATTTGTGCAGGACAG                         ATGGAGCGGGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATCAAT
genomic: GTGAATACTGCCTGGGCAATGTTAGCTTTAATTTGTGCAGGACAGgtgtgttttg ... tggatgtcagATGGAGCGGGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATCAAT
EST: gi|86885403|gb|CI318554.1|CI318554
EST:     ATGCAGTGAATACTGCCTGGGCAATTTTAGCTTTAA-TTGTGCAGGACAG                         ATGGAGC-GGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATCAAT
genomic: ATGCAGTGAATACTGCCTGGGCAATGTTAGCTTTAATTTGTGCAGGACAGgtgtgttttg ... tggatgtcagATGGAGCGGGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATCAAT
EST: gi|86874705|gb|CI318264.1|CI318264
EST:     ATGCAGTGAATACTGCCTGGGCAATGTTAGC-TTAATTT-TGCAGGACAG                         ATGGAGC-GGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATCAAT
genomic: ATGCAGTGAATACTGCCTGGGCAATGTTAGCTTTAATTTGTGCAGGACAGgtgtgttttg ... tggatgtcagATGGAGCGGGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATCAAT
EST: gi|29639294|gb|CB644303.1|CB644303
EST:     ATGCAGTGAATACTGCCTGGGCAATGTTAGCTTTAATTTGTGCAGGACAG                         ATGGAGCGGGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATCAAT
genomic: ATGCAGTGAATACTGCCTGGGCAATGTTAGCTTTAATTTGTGCAGGACAGgtgtgttttg ... tggatgtcagATGGAGCGGGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATCAAT
EST: gi|88837630|gb|CI078990.1|CI078990
EST:     ATGCAGTGAATACTGCCTGGGCAATGTTAGCTTTAATTTGTGCAGGACAG                         ATGGAGCGGGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATCAAT
genomic: ATGCAGTGAATACTGCCTGGGCAATGTTAGCTTTAATTTGTGCAGGACAGgtgtgttttg ... tggatgtcagATGGAGCGGGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATCAAT
EST: gi|29631086|gb|CB636095.1|CB636095
EST:     ATGCAGTGAATACTGCCTGGGCAATGTTAGCTTTAATTTGTGCAGGACAG                         ATGGAGCGGGATCCAGCACCAATGCATCGTGCTGCAAAAGAATTAATCAAT
genomic: ATGCAGTGAATACTGCCTGGGCAATGTTAGCTTTAATTTGTGCAGGACAGgtgtgttttg ... tggatgtcagATGGAGCGGGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATCAAT
EST: gi|88244547|gb|CI243669.1|CI243669
EST:     ATGCAGTGAATACTGCCTGGGCAATGTTAGCTTTAATTTGTGCAGGACAG                         ATGGAGCGGGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATCAAT
genomic: ATGCAGTGAATACTGCCTGGGCAATGTTAGCTTTAATTTGTGCAGGACAGgtgtgttttg ... tggatgtcagATGGAGCGGGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATCAAT
EST: gi|86838894|gb|CI330320.1|CI330320
EST:     ATGCAGTGAATACTGCCTGGGCAATGTTAGCTTTAATTTGTGCAGGACAG                         ATGGAGCGGGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATCAAT
genomic: ATGCAGTGAATACTGCCTGGGCAATGTTAGCTTTAATTTGTGCAGGACAGgtgtgttttg ... tggatgtcagATGGAGCGGGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATCAAT
EST: gi|87009292|gb|CI313765.1|CI313765
EST:     ATGCAGTGAATACTGCCTGGGCAATGTTAGCTTTAATTTGTGCAGGACAG                         ATGGAGCGGGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATCAAT
genomic: ATGCAGTGAATACTGCCTGGGCAATGTTAGCTTTAATTTGTGCAGGACAGgtgtgttttg ... tggatgtcagATGGAGCGGGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATCAAT
EST: gi|58691093|gb|CK079780.1|CK079780
EST:     ATGCAGTGAATACTGCCTGGGCAATGTTAGCTTTAATTTGTGCAGGACAG                         ATGGAGCGGGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATCAAT
genomic: ATGCAGTGAATACTGCCTGGGCAATGTTAGCTTTAATTTGTGCAGGACAGgtgtgttttg ... tggatgtcagATGGAGCGGGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATCAAT
EST: gi|29636672|gb|CB641681.1|CB641681
EST:     ATGCAGTGAATACTGCCTGGGCAATGTTAGCTTTAATTTGTGCAGGACAG                         ATGGAGCGGGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATCAAT
genomic: ATGCAGTGAATACTGCCTGGGCAATGTTAGCTTTAATTTGTGCAGGACAGgtgtgttttg ... tggatgtcagATGGAGCGGGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATCAAT

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), 63 (downstream exon)
Score: 17

GTTTACGTAAACATTAAAGATGATCAAGCTCATGCAGTGAATACTGCCTGGGCAATGTTAGCTTTAATTTGTGCAGGACAGgtgtgttttg ... tggatgtcagATGGAGCGGGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAA




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