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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTGGCAACAGGAGTCCTGAACCTTGCAATCGTTGTTCCGCAGgttagcatgttcataagaaacaaaatgtatttctatatgtgctgtcactgaagatgtcttgaccatttaatactccattattctgtgcag

Basic information

species Oryza sativa
transcript LOC_Os02g58080.1
intron # 13
splice site 5'
intron type U2

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|88994172|gb|CI116136.1|CI116136
EST:     ATCGTTGTTCCGCAG                         ATAGTAGTGTCACTAGGAGCAGGTCCATGGGATGCTCTCTTTGGGGGAGGG
genomic: ATCGTTGTTCCGCAGgttagcatgt ... ttctgtgcagATAGTAGTGTCACTAGGAGCAGGTCCATGGGATGCTCTCTTTGGGGGAGGG
EST: gi|89193755|gb|CI116388.1|CI116388
EST:     GTCTGGCAACAGGAGTCCTGAACCTTGCAATCGTTGTTCCGCAG                         ATAGTAGTGTCACTAGGAGCAGGTCCATGGGATGCTCTCTTTGGGGGAGGG
genomic: GTCTGGCAACAGGAGTCCTGAACCTTGCAATCGTTGTTCCGCAGgttagcatgt ... ttctgtgcagATAGTAGTGTCACTAGGAGCAGGTCCATGGGATGCTCTCTTTGGGGGAGGG
EST: gi|86485320|gb|CI127953.1|CI127953
EST:     TTCTGGCAACAGGAGTCCTGAACCTTGCAATCGTTGTTCCGCAG                         ATAGTAGTGTCACTAGGAGCAGGTCCATGGGATGCTCTCTTTGGGGGAGGG
genomic: GTCTGGCAACAGGAGTCCTGAACCTTGCAATCGTTGTTCCGCAGgttagcatgt ... ttctgtgcagATAGTAGTGTCACTAGGAGCAGGTCCATGGGATGCTCTCTTTGGGGGAGGG
EST: gi|25798277|gb|CA754238.1|CA754238
EST:     GTCTGGGCA-CAGGAGTCCTGAACCTTGNCA-TCGTTGTTCCGCAG                         ATAGTAGTGTCACTAGGAGCAGGTCCATG
genomic: GTCTGG-CAACAGGAGTCCTGAACCTTG-CAATCGTTGTTCCGCAGgttagcatgt ... ttctgtgcagATAGTAGTGTCACTAGGAGCAGGTCCATG

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: 44 (upstream exon), 67 (downstream exon)
Score: 10

GTCTGGCAACAGGAGTCCTGAACCTTGCAATCGTTGTTCCGCAGgttagcatgt ... ttctgtgcagATAGTAGTGTCACTAGGAGCAGGTCCATGGGATGCTCTCTTTGGGGGAGGGAACGTCCCTGCTTTCGCCTTGGCTTCCGTTTTCTCACTAGGAGCTGGTG




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