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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtacaggccttgtctttcttgagaatatttttgtttgcttgttgattttttttttttagttctgatcggtatttttggatgctttgaatgtagAACACTAGATAAGACAATAGCAAGCTTAGAGACAGAACTCTCAGCTGCAAGATCTCTACAAGAGTCCTTGCTCAATGGTTCCCCAGTTGCAGAAGAGTTC

Basic information

species Oryza sativa
transcript LOC_Os02g06840.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G132866_T02 (Zea mays), 3'ss of exon 3
gtacgtacaggccttgtctttcttga------gaatatttttgtttgc--ttgttgattttttttttttag-ttctgatcggtatttttgga--tgc-----tttgaatgtagAACACTAGATAAGACAATAGCAAGCTTAGAGACAGAACTCTCAGCTGCAAGATCTCTACAAGAGTCCTTGCTCAATGGTTCCCCAGTTGCAGAAGAGTTC
||| |||  ||||||  ||||||| |      |  |     ||||||    | | |||  ||||| |||   ||||||| ||| |||    |  | |      ||| |||||||||||| |||||||| ||||||||| |||||||||| ||||||||||||||||| || || || ||| |||| || || ||||| || || |||||||  
gtatgtattggcctt-cctttcttaacctactgtctgcccctgtttgagactatcgatcctttttatttgacttctgattggtgtttacaaaattacaaacacttggatgtagAACACTGGATAAGACGATAGCAAGCCTAGAGACAGAGCTCTCAGCTGCAAGATCGCTGCAGGAATCCCTGCTGAACGGCTCCCCTGTCGCGGAAGAGTAT
















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|33796729|gb|CF324232.1|CF324232
EST:     CCGATTACAAAGATANTATTGCGGGTTCAAGATACTCATCATGGTGTACA                         AACACTAGATAAGACAATAGCAAGCTTAGAGACAGAACTCTCAGCTGCAAG
genomic: CCGATTACAAAGATA-TATTGCGGGTTCAAGATACTCATCATGGTGTACAgtacgtacag ... ttgaatgtagAACACTAGATAAGACAATAGCAAGCTTAGAGACAGAACTCTCAGCTGCAAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttgattttttttttttagttctgatcggtatttttggatgctttgaatgtagAACACTAGATAAGACAATAGCAAGCTTAGAGACAGAACTCTCAGCTGCAAGATCTCTACAAGAGTCCTTGCTCAATGGTTCCCCAGTTGCAGAAGAGTTC
                     ttctgat  putative branch site (score: 3)
      attttttttttttagt  TA-rich tract