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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaattattgggccgcactgtgcgcgcgcgcggccattgttgttgaatgtcgagtgtggctgctgcgccgtttgcgagtttacgcttctgggttagatgggcgagcggtgatggtgattgatgtttcttgtctcttggccacagGGCGTACGACCGCGCTGCCATCAAGTGCAATGGCAAGGATGCGGTGACGAACTTCGATCCAAGCATTTACGCCGGGGAGTTCGAGCCGCCGG

Basic information

species Oryza sativa
transcript LOC_Os04g55560.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g55560.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G174784_T02 (Zea mays), 3'ss of exon 5
gtaaaattattgggccgcactgtgcgcgcgcgcggccattgttgttgaatgtcgagtgtggctgctgcgccgtttgcgagtttacgcttctgggttagatgggcgagcggtgatggtgattgatgtttcttgtctcttggccacagGGCGTACGACCGCGCTGCCATCAAGTGCAATGGCAAGGATGCGGTGACGAACTTCGATCCAAGCATTTACGCCGGGGAGTTCGAGCCGCCGG
||||||| ||||| |||||||||| || |||| |||  || | |  ||    ||       |  ||| ||||       |  |       ||| |     | |   | ||   ||  |  |  ||| | |       ||    |||||||||||||||||| |||||||||||||| |||||||| |||||||| ||||||||||| ||||||||||||| |||| |||||||| |||
gtaaaataattggaccgcactgtgtgcccgcgaggcgtttctcg--gagcaccgccacccccctctgggccgcgaaactgactg-atggatggatgccccgtgtctgtgggattgtcgggtcgtgtgtgtgtgtgtgtgtgtgcagGGCGTACGACCGCGCGGCCATCAAGTGCAACGGCAAGGACGCGGTGACAAACTTCGATCCCAGCATTTACGCCGAGGAGCTCGAGCCGGCGG

upper sequence: LOC_Os04g55560.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G076602_T01 (Zea mays), 3'ss of exon 5
gtaaaattattgggccgcactgtgcgcgcgcgcggccattgttgttgaatgtcgagtgtggctgctgcgccgtttgcgagtttacgcttctgggttagatgggcgagcggtgatggtgattgatgtttcttgtctcttggccacagGGCGTACGACCGCGCTGCCATCAAGTGCAATGGCAAGGATGCGGTGACGAACTTCGATCCAAGCATTTACGCCGGGGAGT---TCGAGCCGCCGG
||||||| ||||| |||||||||| || |||  |||    ||| | |      |||    ||| |  |   |   ||||   |   ||  ||| |        || |      |     |   | | |||   | |  |  | |||||||||||||||||| |||||||||||||| |||||||| |||||||| ||||||||||| ||||||||||||| ||||    ||| |||| |||
gtaaaataattggaccgcactgtgtgctcgcctggcggcggttctcg------gagccccgctaccccctgggccgcgaaactg-actgatggatg----ccccgtgtctctctccctttctctctctctgtgcgcgcgcgcgcagGGCGTACGACCGCGCGGCCATCAAGTGCAACGGCAAGGACGCGGTGACAAACTTCGATCCCAGCATTTACGCCGAGGAGGAGGTCGCGCCGGCGG
















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|426926|gb|D23002.1|D23002
EST:     GTACGTCTACTTGGGGCTGTTCGACACCGAGGAGGAAGCTGCCAG                         GGCGTACGACCGCGCTGCCATCAAGTGCAATGGCAAGGATGCGGTGACGAA
genomic: GTACGTCTACTTGGGGCTGTTCGACACCGAGGAGGAAGCTGCCAGgtaaaattat ... ttggccacagGGCGTACGACCGCGCTGCCATCAAGTGCAATGGCAAGGATGCGGTGACGAA
EST: gi|29644662|gb|CB649669.1|CB649669
EST:     GTACGTCTACTTGGGGCTGTTCGACACCGAGGAGGAAGCTGCCAG                         GGCGTACGACCGCGCTGCCATCAAGTGCAATGGCAAGGATGCGGTGACGAA
genomic: GTACGTCTACTTGGGGCTGTTCGACACCGAGGAGGAAGCTGCCAGgtaaaattat ... ttggccacagGGCGTACGACCGCGCTGCCATCAAGTGCAATGGCAAGGATGCGGTGACGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggttagatgggcgagcggtgatggtgattgatgtttcttgtctcttggccacagGGCGTACGACCGCGCTGCCATCAAGTGCAATGGCAAGGATGCGGTGACGAACTTCGATCCAAGCATTTACGCCGGGGAGTTCGAGCCGCCGG
                          gattgat  putative branch site (score: 4)
                                tgtttcttgtctctt  CT-rich tract