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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttttccatctttctttttgtcaatttagttgttaggatttctcatgtgctcagctgacagaagtgtgcttgtttttttttttgggggtttcagGGTGTCATTATTCTGATCGCCTACTTCAATAGCGGCTCAG

Basic information

species Oryza sativa
transcript LOC_Os01g05070.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g05070.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G037134_T02 (Zea mays), 3'ss of exon 2
gtagttttccatctttctttttgtcaattta--gttgttaggatttctcatgtgctcagctgacagaagtgtg-cttgtttttttttttgggggtttcagGGTGTCATTATTCTGATCGCCTACTTCAATAGCGGCTCAG
||| || |  | || ||| ||||| |    |  | |  |    || ||   |   |   ||||  |   || | | | |  |  | ||||       |||||||||||| ||||  ||||||||||||| ||||||||||
gtaattct--agctctctgtttgttacccgactgctactgctgttactt-cgaattttcctgatggtgatggggcatatgctcatgtttg-------cagGGTGTCATTCTTCTCGTCGCCTACTTCAACAGCGGCTCAG

upper sequence: LOC_Os01g05070.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G037134_T04 (Zea mays), 3'ss of exon 2
gtagttttccatctttctttttgtcaattta--gttgttaggatttctcatgtgctcagctgacagaagtgtg-cttgtttttttttttgggggtttcagGGTGTCATTATTCTGATCGCCTACTTCAATAGCGGCTCAG------------------
||| || |  | || ||| ||||| |    |  | |  |    || ||   |   |   ||||  |   || | | | |  |  | ||||       |||||||||||| ||||  ||||||||||||| ||||||||||                  
gtaattct--agctctctgtttgttacccgactgctactgctgttactt-cgaattttcctgatggtgatggggcatatgctcatgtttg-------cagGGTGTCATTCTTCTCGTCGCCTACTTCAACAGCGGCTCAGGTCGGTTAAAGATTCTCG
















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|58674474|gb|CK063161.1|CK063161
EST:     ACCCCAAGTCACGCTCGCCGCCCGTGCTCACCATCGCCCTCGTGGTCCTG                         GGTGTCATTATTCTGATCGCCTACTTCAATAGCGGCTCAG
genomic: ACCCCAAGTCACGCTCGCCGCCCGTGCTCACCATCGCCCTCGTGGTCCTGgtagttttcc ... ggggtttcagGGTGTCATTATTCTGATCGCCTACTTCAATAGCGGCTCAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctcatgtgctcagctgacagaagtgtgcttgtttttttttttgggggtttcagGGTGTCATTATTCTGATCGCCTACTTCAATAGCGGCTCAG
             agctgac  putative branch site (score: 3)
                              ttgttttttttttt  TA-rich tract