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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcgtctcctccctgtagctccgtgctgttcgcctgcgcgcacagcagctcgtctcgtaagtgaattgacctcttctcgctgatgtgattttggtggactactcgatctctgcgtggttttttagGGTATACCGAGGTGAGGGGGAGGGTCACCGGCCTCGCTCCGGGCCTCCATGGCTTCCACATCCACTCCTTTGGCGACACCACCAACGGCTGCAACTCTAC

Basic information

species Oryza sativa
transcript LOC_Os03g11960.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g11960.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G891739_T01 (Zea mays), 3'ss of exon 1
gtacgcgtctcctccctgtagctccgtgctgttcgcctgcgcgcacagcagctcgtctcgtaagtgaattgacctcttctcgctgatgtgattttggtggactactcgatctctgcgtggt--tttttagGGTATACCGAGGTGAGGGGGAGGGTCACCGGCCTCGCTCCGGGCCTCCATGGCTTCCACATCCACTCCTTTGGCGACACCACCAACGGCTGCAACTCTAC
                                  |    ||| | |   |||||   |  |  |||   |  ||| |  ||       |  |  |     ||  |||| || ||     ||   |   |||||| |||||||||||||| | |||||| ||| |  |||||||    ||||| ||||||||||||  ||| |||||||| ||||| ||||||||||| ||
----------------------------------gtagccgctctctcgagctctctttatctgtg---ttccctatgttcatcagaat--tcctaccttacctctcgctcgctctcctgtggctgccagGGTACACCGAGGTGAGGGGCAAGGTCACGGGCTTGACTCCGGGAAGGCATGGATTCCACATCCACGTCTTCGGCGACACTACCAATGGCTGCAACTCAAC
















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|86901830|gb|CI298477.1|CI298477
EST:     CAACAGCGCGGTCGCCGGCGCCCTCCACTTCTTCCAGGACCCCTCCACCG                         GGTATACCGAGGTGAGGGGGAGGGTCACCGGCCTCGCTCCGG
genomic: CAACAGCGCGGTCGCCGGCGCCCTCCACTTCTTCCAGGACCCCTCCACCGgtacgcgtct ... ggttttttagGGTATACCGAGGTGAGGGGGAGGGTCACCGGCCTCGCTCCGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttctcgctgatgtgattttggtggactactcgatctctgcgtggttttttagGGTATACCGAGGTGAGGGGGAGGGTCACCGGCCTCGCTCCGGGCCTCCATGGCTTCCACATCCACTCCTTTGGCGACACCACCAACGGCTGCAACTCTAC
       cgctgat  putative branch site (score: 4)
                                               tttttt  putative PPT
                                               tttttta  TA-rich tract