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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGATTTCGAAAAGTTGGTTTCCAACTTCCGTCGCATGAGATTTGAATCTACTgtatgcatacgccactagtaattccttcgtttcactattgaatgttattatatttgtttttcatggaaattctttcctttatttgatctgggattgtatg...

Basic information

species Oryza sativa
transcript LOC_Os12g03190.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g03190.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G151977_T01 (Zea mays), 5'ss of exon 5
GAGGATTTCGAAAAGTTGGTTTCCAACTTCCGTCGCATGAGATTTGAATCTACTgtatgcatacgcc-actagtaattccttcgtttcactat-tgaatgttattatatttgtttttcatggaaattctttcc--tttatttgatctgggattgtatg
||||||||  | |||||||| |||||||||||||| || ||||||||||||||||||||  |  |     |  |  ||| | | |||   |   || |  || ||| |  |   |   ||| |  || ||||    |  |   |||   ||       
GAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACTgtatgtttgtgtttggttttttttcttccattttgatgcctgtacatttttacaaattgctgctatgcattttttttctaactactactatccatgacca----
















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|700649|gb|D46940.1|D46940
EST:     ATTTCGAAAAGTTGGTTTCCAACTTCCGTCGCATGANATTTGAATCTACT                         GNTGGAGCCGGTTTGCCTGTAATAGCTTCTGTGACCCGTATTATTGCCTCT
genomic: ATTTCGAAAAGTTGGTTTCCAACTTCCGTCGCATGAGATTTGAATCTACTgtatgcatac ... ctactcttagGTTGGAGCCGGTTTGCCTGTAATAGCTTCTGTGACCCGTATTATTGCCTCT
EST: gi|702505|gb|D48796.1|D48796
EST:     ATTTCGAAAAGTTGGTTTCCAACTTCCGTCGCATGAGATTTGAATCTACT                         GTTGGAGCCGGTTTGCCTGTAATAGCTTCTGTGACCCGTATTATTGCCTCT
genomic: ATTTCGAAAAGTTGGTTTCCAACTTCCGTCGCATGAGATTTGAATCTACTgtatgcatac ... ctactcttagGTTGGAGCCGGTTTGCCTGTAATAGCTTCTGTGACCCGTATTATTGCCTCT
EST: gi|6481237|gb|AU065815.2|AU065815
EST:     ATTTCGAAAAGTTGGTTTCCAACTTCCGTCGCATGAGATTTGAATCTACT                         GTTGGAGCCGGTTTGCCTGTAATAGCTTCTGTGACCCGTATTATTGCCTCT
genomic: ATTTCGAAAAGTTGGTTTCCAACTTCCGTCGCATGAGATTTGAATCTACTgtatgcatac ... ctactcttagGTTGGAGCCGGTTTGCCTGTAATAGCTTCTGTGACCCGTATTATTGCCTCT

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: 41 (upstream exon), 51 (downstream exon)
Score: 30

GAGGATTTCGAAAAGTTGGTTTCCAACTTCCGTCGCATGAGATTTGAATCTACTgtatgcatac ... ctactcttagGTTGGAGCCGGTTTGCCTGTAATAGCTTCTGTGACCCGTATTATTGCCTCTGGAGATCCAGTTTCTCGTATTGTTGGCAGTCTGAGTG




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