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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgaaccctcccctcccctccccatctcgctctccgtttgatcgcttgcactaggtctagtgttgtttgggtttgggggtacggtggtgatccccttttgtgggggttgtgtggttcgtgtgctgattggatgacttagatcgatttattgtgaaagCGCAGCTGGTGCCGGAGGAGGAGGACGACCTGTGGCATGCCTACAACCTTATTGTTCCGGGGGATACCCTCCAGTCCGTCACTGTGAG

Basic information

species Oryza sativa
transcript LOC_Os04g56480.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g56480.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G044011_T01 (Zea mays), 3'ss of exon 1
gtgtgaaccctcccctc-ccctccccatctcgctctccgtttgatcgct-----tgc--actaggtctagtgttgtttgggtttgggggtacggtggtgatccccttttgtgggggttgtgtggttcg-tgtgctgattggatgacttagatcgatttattgtgaaagCGCAGCTGGTGCCGGAGGAGGAGGACGACCTGTGGCATGCCTACAACCTTATTGTTCCGGGGGATACCCTCCAGTCCGTCACTGTGAG
  ||   |   || ||| |||  ||| |   |||||| ||  || | ||     |||    | ||| |    |  | |||||    ||||   | | |||  |||    |  ||| ||  |||| | | | |  || ||   ||| |  | |       | |||    ||||| ||||||||||||||||||||||| ||||||| || |||||||| ||||     || || | ||||||| ||||||| ||  |
--gtcctcttacctctcgcccctccccttgtgctctctgtgcgagcactccggttgcttgttgggtttgccttgttctgggtggctgggtctagggctga--cccaaccgctgggattcagtgggttgctttattgctt--ctgattaggctta--cggtcgtgctc-cgcagTTGGTGCCGGAGGAGGAGGACGACTTGTGGCACGCGTACAACCTCATTGCCATTGGTGACAGCCTCCAGGCCGTCACCGTACG
















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|29659831|gb|CB656106.1|CB656106
EST:     TGAAGCTCGTCTACCGCAACCTCGCCCGCAACGGCCCCGGCTCCGTC-A-                         ---AGCTGGTGCCGGAGGAGGAGGACGACCTGTGGCATGCCTACAACCTTA
genomic: TGAAGCTCGTCTACCGCAACCTCGCCCGCAACGGCCCCGGCTCCGTCAAGgtgtgaaccc ... attgtgaaagCGCAGCTGGTGCCGGAGGAGGAGGACGACCTGTGGCATGCCTACAACCTTA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggggttgtgtggttcgtgtgctgattggatgacttagatcgatttattgtgaaagCGCAGCTGGTGCCGGAGGAGGAGGACGACCTGTGGCATGCCTACAACCTTATTGTTCCGGGGGATACCCTCCAGTCCGTCACTGTGAG
                  tgctgat  putative branch site (score: 3)
                                         atttattgt  TA-rich tract