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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtcagattgtctctacaacgagatttcttgttttagtcctttccagacccttaaatggtgttctcatctaactttctacagtatgctgttctactatgcagGAATCAAGAAGTAACTGGATTGGTATTACAAGGGCTCTACAGCTTATAGTTGATGTAAATGATACTGCAAA

Basic information

species Oryza sativa
transcript LOC_Os04g14654.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g14654.3 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G003734_T01 (Zea mays), 3'ss of exon 17
gttagtcagattgtctctacaacgagatttcttgttttagtcctttccagacccttaaatggtgttctcatct--------aactttctacagtatgctgttctactatgcagGAATCAAGAAGTAACTGGATTGGTATTACAAGGGCTCTACAGCTTATAGTTGATGTAAATGATACTGCAAA
||||||||| || |   |   ||   | |  ||  || |||| | |   |  |||| | || |||| || | |        ||  ||  |    ||  || |  ||||  |||||||||||||| || ||| ||||||||||||| || || |||||||||||||| ||||||||||| |||||
gttagtcag-ttttgagtgtcactgaactgttt-cttcagtcatctgtggttccttcagtgttgttttcttttgccttcataatctttaatgacatattgctgcactacccagGAATCAAGAAGCAATTGGGTTGGTATTACAAGAGCACTGCAGCTTATAGTTGACGTAAATGATACAGCAAA
















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|163929156|gb|EG710989.1|EG710989
EST:     ACATGCCCTTGTTATACAATCTGGAAAAGGCTGGCCTATTTAAGCGCCAG                         GAATCAAGAAGTAACTGGATTGGTATTACAAGGGCTCTACAGCTTATAGTT
genomic: ACATGCCCTTGTTATACAATCTGGAAAAGGCTGGCCTATTTAAGCGCCAGgttagtcaga ... tactatgcagGAATCAAGAAGTAACTGGATTGGTATTACAAGGGCTCTACAGCTTATAGTT
EST: gi|66928780|gb|CX115628.1|CX115628
EST:     ACATGCCCTTGTTATACAATCTGGAAAGGG-TGGNCTATTTAAGCGCCAG                         GAATCA-GAAGTACCTG-AGTGGT-TTACA-GGGCTCTA
genomic: ACATGCCCTTGTTATACAATCTGGAAAAGGCTGGCCTATTTAAGCGCCAGgttagtcaga ... tactatgcagGAATCAAGAAGTAACTGGATTGGTATTACAAGGGCTCTA
EST: gi|163917728|gb|EG711274.1|EG711274
EST:     ACATGCCCTTGTTATACAATCTGGAAAAGGCTGGCCTATTTAAGCGCCAG                         GAATCAAGAAGTAACTGGATTGGTATTACAAGGGCTCTACAGCTTATAGTT
genomic: ACATGCCCTTGTTATACAATCTGGAAAAGGCTGGCCTATTTAAGCGCCAGgttagtcaga ... tactatgcagGAATCAAGAAGTAACTGGATTGGTATTACAAGGGCTCTACAGCTTATAGTT
EST: gi|28298184|gb|CB238414.1|CB238414
EST:     ACATGCCCTTGTTATACAATCTGGAAAAGGCTGGCCCATTTAAGCGCCAG                         GAATCAAGAAGTAACTGGATTGGTATTACAAGGGCTCTACAGCTTATAGTT
genomic: ACATGCCCTTGTTATACAATCTGGAAAAGGCTGGCCTATTTAAGCGCCAGgttagtcaga ... tactatgcagGAATCAAGAAGTAACTGGATTGGTATTACAAGGGCTCTACAGCTTATAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acccttaaatggtgttctcatctaactttctacagtatgctgttctactatgcagGAATCAAGAAGTAACTGGATTGGTATTACAAGGGCTCTACAGCTTATAGTTGATGTAAATGATACTGCAAA
                   atctaac  putative branch site (score: 2)
                                       ctgttct  putative PPT
                      taacttt  TA-rich tract