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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttctatcctttgtttctcaatccctcctggttgcactttctcttgaggtgtataacaaccgcatgttcttatctcactgcagATTTGCTTGCATATGTTCACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTAC

Basic information

species Oryza sativa
transcript LOC_Os04g52370.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52370.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G019986_T04 (Zea mays), 3'ss of exon 11
gtatg--ttctatcctttgtttctcaatccctcctggttgcactttctct-tgaggtgtataacaaccgcatgttcttatctcactgc---------------------agATTTGCTTGCATATGTTCACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTAC
|||||  |||| ||||    || ||  ||||| | |      ||  |||  |      | ||||| | |||| || |   ||| ||                       |||| ||| |||| ||||||||| |||| || ||||| ||||| || |||||||| ||||||||||||  
gtatggtttctgtcctccacttgtcgttcccttccgccctacctccctccctccaaactgtaacagctgcatattttctcctctctctctctcgttttccccctcccctagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGT

upper sequence: LOC_Os04g52370.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G044629_T01 (Zea mays), 3'ss of exon 11
gtatg-ttctatcctttgtttctcaatccctcctggttgcactttctcttgaggtgtataacaaccgcatgttcttatctcactgcagATTTGCTTGCATATGTTCACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTAC
||||| |||||||||| | |||||  || ||   |    | ||   ||   |      |     |      || || | |   || |||| ||| |||| ||||||||| |||| || ||||| ||||| ||||||||||||||||||||||||  
gtatggttctatccttcgcttctcgttctctttcgccctccctccatccaaaaactgtt-----ctctccttttttttttttttgtagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGT
















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|3768106|gb|AU032133.1|AU032133
EST:     CTACTGAAATTAATCAGTCAACGGGACGCCTTCGTTATTGTTGGAGCAAT                         ATTTGCTTGCATATGTTCACTTTGGATTTTTTGAATCAAGTAGCANACAGC
genomic: CTACTGAAATTAATCAGTCAACGGGACGCCTTCGTTATTGTTGGAGCAATgtatgttcta ... ctcactgcagATTTGCTTGCATATGTTCACTTTGGATTTTTTGAATCAAGTAGCAAACAGC
EST: gi|88389670|gb|CI603169.1|CI603169
EST:     CTACTGAAATTAATCAGTCAACGGGACGCCTTCGTTATTGTTGGAGCAAT                         ATTTGCTTGCATATGTTCACTTTGGATTTTTTGAATCAAGTAGCAAACAGC
genomic: CTACTGAAATTAATCAGTCAACGGGACGCCTTCGTTATTGTTGGAGCAATgtatgttcta ... ctcactgcagATTTGCTTGCATATGTTCACTTTGGATTTTTTGAATCAAGTAGCAAACAGC
EST: gi|396941374|gb|HO188583.1|HO188583
EST:     CTACTGAAATTAATCAGTCAACGGGACGCCTTCGTTATTGTTGGAGCAAT                         ATTTGCTTGCATATGTTCACTTTGGATTTTTTGAATCAAGTAGCAAACAGC
genomic: CTACTGAAATTAATCAGTCAACGGGACGCCTTCGTTATTGTTGGAGCAATgtatgttcta ... ctcactgcagATTTGCTTGCATATGTTCACTTTGGATTTTTTGAATCAAGTAGCAAACAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttgcactttctcttgaggtgtataacaaccgcatgttcttatctcactgcagATTTGCTTGCATATGTTCACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTAC
                                           atctcac  putative branch site (score: 3)
                                      ttcttatctc  CT-rich tract
                       tataacaa  TA-rich tract