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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAACAGCGAGTGGGTTGAATGGCAGACAACTGCCCTGGTCAAACGCAATGAGGTTGAGAACGTTTATCATTGGGCCTGTGGgtaggttatcaccatgttttgtgatgcttttgtgattgcgtacacttgtcttcgctgacttttggctatcaatgctttgtgctgcag

Basic information

species Oryza sativa
transcript LOC_Os05g51490.2
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g51490.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM5G812498_T01 (Zea mays), 5'ss of exon 5
GAGAACAGCGAGTGGGTTGAATGGCAGACAACTGCCCTGGTCAAACGCAATGAGGTTGAGAACGTTTATCATTGGGCCTGTGGgtaggttatcaccat----gttttgtgatgcttttgtg-attgcgta---------cacttgtcttcgctgactttt------------ggctatc----aatgctttgtgctgcag
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GAGAACAGTGAGTGGGCTGTATGGCAAATAGATGTCCTGATCAAACGCAATGAGGTGGAGAATGTTTACCATTGGGCATGTGGgtatgttcttccattctgggttctctgattattgtctacactgctgaaacacttgtcatttgtctgtggtaaattttatatttcttcctgactgttggctaatgttttatgctgcag
















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|58612771|gb|CK040483.1|CK040483
EST:     GCCCTGGTCAAACGCAATGAGGTTGAGAACGTTTATCATTGGGCCTGTGG                         TCGTCCGACTTCTCTACATGATCGTGGTAGGGATAGCGATGATGATGACTT
genomic: GCCCTGGTCAAACGCAATGAGGTTGAGAACGTTTATCATTGGGCCTGTGGgtaggttatc ... tgtgctgcagTCGTCCGACTTCTCTACATGATCGTGGTAGGGATAGCGATGATGATGACTT
EST: gi|58653975|gb|CK042655.1|CK042655
EST:     GCCCTGGTCAAACGCAATGAGGTTGAGAACGTTTATCATTGGGCCTGTGG                         TCGTCCGACTTCTCTACATGATCGTGGTAGGGATAGCGATGATGATGACTT
genomic: GCCCTGGTCAAACGCAATGAGGTTGAGAACGTTTATCATTGGGCCTGTGGgtaggttatc ... tgtgctgcagTCGTCCGACTTCTCTACATGATCGTGGTAGGGATAGCGATGATGATGACTT
EST: gi|58689163|gb|CK077850.1|CK077850
EST:     GCCCTGGTCAAACGCAATGAGGTTGAGAACGTTTATCATTGGGCCTGTGG                         TCGTCCGACTTCTCTACATGATCGTG
genomic: GCCCTGGTCAAACGCAATGAGGTTGAGAACGTTTATCATTGGGCCTGTGGgtaggttatc ... tgtgctgcagTCGTCCGACTTCTCTACATGATCGTG
EST: gi|58608385|gb|CK036418.1|CK036418
EST:     CCCTGGTCAAACGCAATGAGGTTGAGAACGTTTATCATGTGGGCCTGTGG                         TCGTCCGACTTCTCTACATGATCGTGGTAGGGATAGCGATGATGATGACTT
genomic: CCCTGGTCAAACGCAATGAGGTTGAGAACGTTTATCAT-TGGGCCTGTGGgtaggttatc ... tgtgctgcagTCGTCCGACTTCTCTACATGATCGTGGTAGGGATAGCGATGATGATGACTT
EST: gi|58660503|gb|CK049183.1|CK049183
EST:     AGAACGTTTATCATTGGGCCTGTGG                         TCGTCCGACTTCTCTACATGATCGTGGTAGGGATAGCGATGATGATGACTT
genomic: AGAACGTTTATCATTGGGCCTGTGGgtaggttatc ... tgtgctgcagTCGTCCGACTTCTCTACATGATCGTGGTAGGGATAGCGATGATGATGACTT

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: 61 (upstream exon), 63 (downstream exon)
Score: 6

GAGAACAGCGAGTGGGTTGAATGGCAGACAACTGCCCTGGTCAAACGCAATGAGGTTGAGAACGTTTATCATTGGGCCTGTGGgtaggttatc ... tgtgctgcagTCGTCCGACTTCTCTACATGATCGTGGTAGGGATAGCGATGATGATGACTTCCGAGACAGGGACTATGATGTGGCGGCACTTGCTAATAACCTGAGCCAG




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