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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccggttcctacatcctactactagcagtctctaatctgcttggtgatctgtttcgcatgcgtgatttctgttcttggatctcactgtgatgaatggattatttttcgcagATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACACTACTCCACTCCGGTTGACATCTGGTCTGTGGGCTGCATTTTTG

Basic information

species Oryza sativa
transcript LOC_Os08g40170.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g40170.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G068193_T02 (Zea mays), 3'ss of exon 2
gtccggttcctacatcctactactagcagtctctaatctgcttggtgatctgtttcgcatgcgtgatttctgttcttggatctcactgtgatgaatggattatttttcgcagATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACACTACTCCACTCCGGTTGACATCTGGTCTGTGGGCTGCATTTTTG
                                    || | ||    ||| |   |||| |  ||||   ||||||||||||  | |    | |   ||    ||   |||||| || || |||||||||||||| |||||| |||| ||||| ||  | ||||||||||| ||||||||||| ||||| || ||||||||||| |
-----------------------------------gtcggttt--ccatcag--ccgcacggatgatccttgttcttggatccgatta-attaacctgaaacgttgctgcagATACTTACCCTGTGGTACAGGGCCCCCGAGATTCTGCTTGGAGCCACGCACTACTCCACCCCGGTTGACATATGGTCCGTTGGCTGCATTTTCG
















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|29663133|gb|CB659408.1|CB659408
EST:     TCGGGCTCAGCCGCTCGTTCACTGTCCCTCTCAAGAAGTACACCCACGAG                         ATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
genomic: TCGGGCTCAGCCGCTCGTTCACTGTCCCTCTCAAGAAGTACACCCACGAGgtccggttcc ... tttttcgcagATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
EST: gi|29663132|gb|CB659407.1|CB659407
EST:     TCGGGCTCAGCCGCTCGTTCACTGTCCCTCTCAAGAAGTACACCCACGAG                         ATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
genomic: TCGGGCTCAGCCGCTCGTTCACTGTCCCTCTCAAGAAGTACACCCACGAGgtccggttcc ... tttttcgcagATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
EST: gi|58604123|gb|CK014651.1|CK014651
EST:     GGCTCAGCCGCTCGTTCACTGTCCCTCTCAAGAAGTACACCCACGAG                         ATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
genomic: GGCTCAGCCGCTCGTTCACTGTCCCTCTCAAGAAGTACACCCACGAGgtccggttcc ... tttttcgcagATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
EST: gi|58676453|gb|CK065140.1|CK065140
EST:     TCGGGCTCAGCCGCTCGTTCACTGTCCCTCTCAAGAAGTACACCCACGAG                         ATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
genomic: TCGGGCTCAGCCGCTCGTTCACTGTCCCTCTCAAGAAGTACACCCACGAGgtccggttcc ... tttttcgcagATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
EST: gi|58677365|gb|CK066052.1|CK066052
EST:     TCGGGCTCAGCCGCTCGTTCACTGTCCCTCTCAAGAAGTACACCCACGAG                         ATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
genomic: TCGGGCTCAGCCGCTCGTTCACTGTCCCTCTCAAGAAGTACACCCACGAGgtccggttcc ... tttttcgcagATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
EST: gi|86496840|gb|CI139473.1|CI139473
EST:     ACACCCACGAG                         ATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
genomic: ACACCCACGAGgtccggttcc ... tttttcgcagATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
EST: gi|86593618|gb|CI264497.1|CI264497
EST:     AAGTACACCCACGAG                         ATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
genomic: AAGTACACCCACGAGgtccggttcc ... tttttcgcagATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
EST: gi|58603848|gb|CK014376.1|CK014376
EST:     CAAGAAGTACACCCACGAG                         ATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
genomic: CAAGAAGTACACCCACGAGgtccggttcc ... tttttcgcagATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
EST: gi|3768776|gb|AU032803.1|AU032803
EST:     TCGGGCTCAGCCGCTCGTTCACTGTCCCTCTCAAGAAGTACACCCACGAG                         ATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTNTTGGCGCGGCACAC
genomic: TCGGGCTCAGCCGCTCGTTCACTGTCCCTCTCAAGAAGTACACCCACGAGgtccggttcc ... tttttcgcagATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
EST: gi|38479047|gb|CF963180.1|CF963180
EST:     TCGGGCTCAGCCGCTCGTTCACTGTCCCTCTCAAGAAGTACACCCACGAG                         ATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
genomic: TCGGGCTCAGCCGCTCGTTCACTGTCCCTCTCAAGAAGTACACCCACGAGgtccggttcc ... tttttcgcagATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgcgtgatttctgttcttggatctcactgtgatgaatggattatttttcgcagATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACACTACTCCACTCCGGTTGACATCTGGTCTGTGGGCTGCATTTTTG
                      atctcac  putative branch site (score: 3)
                                          ttatttttc  putative PPT
                                    aatggattattttt  TA-rich tract