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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatattgttctctttatggttcttagatttgtggtgcctactgtgtgtgcaggtatgttggcactccataactaattgtttttgtcttccattcttgtacagTCAATCATAAGAGCTTACGGACGGGTTGACCCAGACGGTTCGCGCTATTTACTTGGTGATAATGCAGGCATATTGCATTTACTTGTCCTTACCCATGAAC

Basic information

species Oryza sativa
transcript LOC_Os05g51480.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g51480.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G402002_T01 (Zea mays), 3'ss of exon 9
gtaatatattgttctctttatggttcttagatttgtggtgcctactgtgtgt--gcaggtatgttggc-actcca----taac-taattgtttttgtctt------ccattcttgtacagTCAATCATAAGAGCTTACGGACGGGTTGACCCAGACGGTTCGCGCTATTTACTTGGTGATAATGCAGGCATATTGCATTTACTTGTCCTTACCCATGAAC
||||| | |||    | |     |  ||   ||||||||||| |||   |||  |  ||||   |||| || | |    |||| ||||| ||||   |||        |||  |   ||||| ||||| |||||||| ||||||||||||||||| ||||| || |||||||| ||||||||| | || || ||||||||||||||||||||||||||||
gtaatctcttgcctacatctctttatttttctttgtggtgccaacttcatgttggttggtaccgtggctacactaattctaacataattcttttctccttgattactgatttcttggcagTCCATCATCAGAGCTTATGGACGGGTTGACCCAGATGGTTCTCGATATTTACTCGGTGATAATACTGGAATTTTGCATTTACTTGTCCTTACCCATGAAC
















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|86904800|gb|CI310593.1|CI310593
EST:     TAGTTTACTGCAATGCCAACTCTACATTTAGAGCTATACCTATCAAACAG                         TCAATCATAAGAGCTTACGGACGGGTTGACCCAGACGGTTCGCGCTATTTA
genomic: TAGTTTACTGCAATGCCAACTCTACATTTAGAGCTATACCAATCAAACAGgtaatatatt ... tcttgtacagTCAATCATAAGAGCTTACGGACGGGTTGACCCAGACGGTTCGCGCTATTTA
EST: gi|29669278|gb|CB665553.1|CB665553
EST:     TAGTTTACTGCAATGCCAACTCTACATTTAGAGCTATACCAATCAAACAG                         TCAATCATAAGAGCTTACGGACGGGTTGACCCAGACGGTTCGCGCTATTTA
genomic: TAGTTTACTGCAATGCCAACTCTACATTTAGAGCTATACCAATCAAACAGgtaatatatt ... tcttgtacagTCAATCATAAGAGCTTACGGACGGGTTGACCCAGACGGTTCGCGCTATTTA
EST: gi|86894503|gb|CI308252.1|CI308252
EST:     TAGTTTACTGCAATGCCAACTCTACATTTAGAGCTATACCAATCAAACAG                         TCAATCATAAGAGCTTACGGACGGGTTGACCCAGACGGTTCGCGCTATTTA
genomic: TAGTTTACTGCAATGCCAACTCTACATTTAGAGCTATACCAATCAAACAGgtaatatatt ... tcttgtacagTCAATCATAAGAGCTTACGGACGGGTTGACCCAGACGGTTCGCGCTATTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaggtatgttggcactccataactaattgtttttgtcttccattcttgtacagTCAATCATAAGAGCTTACGGACGGGTTGACCCAGACGGTTCGCGCTATTTACTTGGTGATAATGCAGGCATATTGCATTTACTTGTCCTTACCCATGAAC
                      aactaat  putative branch site (score: 2)
                            ttgtttttgtcttcca  CT-rich tract
                    ataactaattgttttt  TA-rich tract