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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCAGCTGCTGATGTGGGAGTAGCTATGCGAACAAACTCAAAAGAGAGTGCTGCCTCTGACGCGGCTTCAGTTGTTCTATTAGGAAACAGACTTTCTCAGgtaggattctgttctctatgatattgtaactgcatagttcaagtggcattcgtgctaataaacaagaaccaccctacggcttag

Basic information

species Oryza sativa
transcript LOC_Os03g08070.3
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g08070.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM5G855347_T03 (Zea mays), 5'ss of exon 5
AGCAGCTGCTGATGTGGGAGTAGCTATGCGAACAAACTCAAAAGAGAGTGCTGCCTCTGACGCGGCTTCAGTTGTTCTATTAGGAAACAGACTTTCTCAGgtaggattctgttctcta-tgatattgtaactgcatagttcaagtggcattcgtgctaataaacaagaaccaccctacggcttag
|||||| || ||||| ||| |||| ||||||||  | ||||||||||  ||||||||||| || ||||||||||||||| |||| |||||||||||||||||| | |||| | || || || |  | |  |||  ||  |||| |    | |    |||     |  || ||  || | |   ||
AGCAGCCGCAGATGTTGGAATAGCCATGCGAACTCATTCAAAAGAGAACGCTGCCTCTGATGCAGCTTCAGTTGTTCTACTAGGCAACAGACTTTCTCAGgtaaggttctttcctgtaatgtttctttctctgagtaactcaactcaagtgc-cattaacggggatcaaacaatctcctgtgcag
















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|87014157|gb|CI273347.1|CI273347
EST:     TGTTCTATTAGGAAACAGACTTTCTCAG                         GTAATGGATGCTTTATCACTTTCGAAAGCAACTATGGCCAAAGTTCACCAA
genomic: TGTTCTATTAGGAAACAGACTTTCTCAGgtaggattct ... tacggcttagGTAATGGATGCTTTATCACTTTCGAAAGCAACTATGGCCAAAGTTCACCAA
EST: gi|87030976|gb|CI270124.1|CI270124
EST:     CTGCCTCTGACGCGGCTTCAGTTGTTCTATTAGGAAACAGACTTTCTCAG                         GTAATGGATGCTTTATCACTTTCGAAAGCAACTATGGCCAAAGTTCACCAA
genomic: CTGCCTCTGACGCGGCTTCAGTTGTTCTATTAGGAAACAGACTTTCTCAGgtaggattct ... tacggcttagGTAATGGATGCTTTATCACTTTCGAAAGCAACTATGGCCAAAGTTCACCAA
EST: gi|86477373|gb|CI120006.1|CI120006
EST:     GCTTCAGTTGTTCTATTAGGAAACAGACTTTCTCAG                         GTAATGGATGCTTTATCACTTTCGAAAGCAACTATGGCCAAAGTTCACCAA
genomic: GCTTCAGTTGTTCTATTAGGAAACAGACTTTCTCAGgtaggattct ... tacggcttagGTAATGGATGCTTTATCACTTTCGAAAGCAACTATGGCCAAAGTTCACCAA
EST: gi|58611302|gb|CK039014.1|CK039014
EST:     GACTTTCTCAG                         GTAATGGATGCTTTATCACTTTCGAAAGCAACTATGGCCAAAGTTCACCAA
genomic: GACTTTCTCAGgtaggattct ... tacggcttagGTAATGGATGCTTTATCACTTTCGAAAGCAACTATGGCCAAAGTTCACCAA
EST: gi|116875530|gb|EC366038.1|EC366038
EST:     CTGCCTCTGACGCGGCTTCAGTTGTTCTATTAGGAAACAGACTTTCTCAG                         GTAATGGATGCTTTATCACTTTCGAAAGCAACTATGGCCAAAGTTCACCAA
genomic: CTGCCTCTGACGCGGCTTCAGTTGTTCTATTAGGAAACAGACTTTCTCAGgtaggattct ... tacggcttagGTAATGGATGCTTTATCACTTTCGAAAGCAACTATGGCCAAAGTTCACCAA
EST: gi|116875017|gb|EC365525.1|EC365525
EST:     CTGCCTCTGACGCGGCTTCAGTTGTTCTATTAGGAAACAGACTTTCTCAG                         GTAATGGATGCTTTATCACTTTCGAAAGCAACTATGGCCAAAGTTCACCAA
genomic: CTGCCTCTGACGCGGCTTCAGTTGTTCTATTAGGAAACAGACTTTCTCAGgtaggattct ... tacggcttagGTAATGGATGCTTTATCACTTTCGAAAGCAACTATGGCCAAAGTTCACCAA
EST: gi|29681030|gb|CB677305.1|CB677305
EST:     CTGCCTCTGACGCGGCTTCAGTTGTTCTATTAGGAAACAGACTTTTTCAG                         GTAATGGATGCTTTATCACTTTCGAAAGCAACTATGGCCAAAGTTCACCAA
genomic: CTGCCTCTGACGCGGCTTCAGTTGTTCTATTAGGAAACAGACTTTCTCAGgtaggattct ... tacggcttagGTAATGGATGCTTTATCACTTTCGAAAGCAACTATGGCCAAAGTTCACCAA
EST: gi|29622947|gb|CB627958.1|CB627958
EST:     CTGCCTCTGACGCGGCTTCAGTTGTTCTATTAGGAAACAGACTTTCTCAG                         GTAATGGATGCTTTATCACTTTCGAAAGCAACTATGGCCAAAGTTCACCAA
genomic: CTGCCTCTGACGCGGCTTCAGTTGTTCTATTAGGAAACAGACTTTCTCAGgtaggattct ... tacggcttagGTAATGGATGCTTTATCACTTTCGAAAGCAACTATGGCCAAAGTTCACCAA
EST: gi|29662866|gb|CB659141.1|CB659141
EST:     CTGCCTCTGACGCGGCTTCAGTTGTTCTATTAGGAAACAGACTTTCTCAG                         GTAATGGATGCTTTATCACTTTCGAAAGCAACTATGGCCAAAGTTCACCAA
genomic: CTGCCTCTGACGCGGCTTCAGTTGTTCTATTAGGAAACAGACTTTCTCAGgtaggattct ... tacggcttagGTAATGGATGCTTTATCACTTTCGAAAGCAACTATGGCCAAAGTTCACCAA
EST: gi|116875544|gb|EC366052.1|EC366052
EST:     CTGCCTCTGACGCGGCTTCAGTTGTTCTATTAGGAAACAGACTTTCTCAG                         GTAATGGATGCTTTATCACTTTCGAAAGCAACTATGGCCAAAGTTCACCAA
genomic: CTGCCTCTGACGCGGCTTCAGTTGTTCTATTAGGAAACAGACTTTCTCAGgtaggattct ... tacggcttagGTAATGGATGCTTTATCACTTTCGAAAGCAACTATGGCCAAAGTTCACCAA
EST: gi|116875028|gb|EC365536.1|EC365536
EST:     CTGCCTCTGACGCGGCTTCAGTTGTTCTATTAGGAAACAGACTTTCTCAG                         GTAATGGATGCTTTATCACTTTCGAAAGCAACTATGGCCAAAGTTCACCAA
genomic: CTGCCTCTGACGCGGCTTCAGTTGTTCTATTAGGAAACAGACTTTCTCAGgtaggattct ... tacggcttagGTAATGGATGCTTTATCACTTTCGAAAGCAACTATGGCCAAAGTTCACCAA
EST: gi|87027726|gb|CI274290.1|CI274290
EST:     CTGCCTCTGACGCGGCTTCAGTTGTTCTATTAGGAAACAGACTTTCTCAG                         GTAATGGATGCTTTATCACTTTCGAAAGCAACTATGGCCAAAGTTCACCAA
genomic: CTGCCTCTGACGCGGCTTCAGTTGTTCTATTAGGAAACAGACTTTCTCAGgtaggattct ... tacggcttagGTAATGGATGCTTTATCACTTTCGAAAGCAACTATGGCCAAAGTTCACCAA

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: 75 (upstream exon), 72 (downstream exon)
Score: 15

AGCAGCTGCTGATGTGGGAGTAGCTATGCGAACAAACTCAAAAGAGAGTGCTGCCTCTGACGCGGCTTCAGTTGTTCTATTAGGAAACAGACTTTCTCAGgtaggattct ... tacggcttagGTAATGGATGCTTTATCACTTTCGAAAGCAACTATGGCCAAAGTTCACCAAAATTTAGCCTGGGCTGTCGCATATAACATAGTAGCTATCCCTATTGCCG




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