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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgagcagcacaatgaaggatgaataattctgtagactatcttctttgaccatctggcaggtgacacaaaccactttcttaccagGACATTAGGTATCTCATGGAGGATGTGCAAATGATGAAACCAACGGTATTTTGTGGTGTCCCTCGTGTTTATGATCGTATATACACAG

Basic information

species Oryza sativa
transcript LOC_Os11g35400.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g35400.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G104847_T01 (Zea mays), 3'ss of exon 10
gtatgagcagcacaatgaaggatgaataattctgtagactatcttctttgaccatctggcaggtgacacaaaccactt-tcttaccagGACATTAGGTATCTCATGGAGGATGTGCAAATGATGAAACCAACGGTATTTTGTGGTGTCCCTCGTGTTTATGATCGTATATACACAG
||| || |       || |   | |   | |   | || | ||||||   |   | ||| |  |||     |  |||| ||||  |||||||||||||| || ||||||||||||||| |||||||||| ||  |||| |||||||| ||||||||||||||||||||||| ||||
gtacgaactaattgttgcaatttcacagaattctttgattttcttcta-aatactgtggtac-tgaggtgtaaaacttgtctttacagGACATTAGGTACCTGATGGAGGATGTGCAAGTGATGAAACCGACAATATTCTGTGGTGTTCCTCGTGTTTATGATCGTATATATACAG
















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|58668934|gb|CK057620.1|CK057620
EST:     ATTGGATTCTGGCAAGCG                         GACATTAGGTATCTCATGGAGGATGTGCAAATGATGAAAGCCAACGGTATT
genomic: ATTGGATTCTGGCAAGCGgtatgagcag ... ttcttaccagGACATTAGGTATCTCATGGAGGATGTGCAAATGATGAAA-CCAACGGTATT
EST: gi|58659138|gb|CK047818.1|CK047818
EST:     TTGGAAACTACTGCATTTCTAAAGGAGCCTCCATTGGATTCTGGCAAGCG                         GACATTAGGTATCTCATGGAGGATGTGCAAATGATGAAACCAACGGTATTT
genomic: TTGGAAACTACTGCATTTCTAAAGGAGCCTCCATTGGATTCTGGCAAGCGgtatgagcag ... ttcttaccagGACATTAGGTATCTCATGGAGGATGTGCAAATGATGAAACCAACGGTATTT
EST: gi|58652930|gb|CK041610.1|CK041610
EST:     TTGGAAACTACTGCATTTCTAAAGGAGCCTCCATTGGATTCTGGCAAGCG                         GACATTAGGTCTCTCAGGGAGGATGTGCAAATGATGAAACCAACGGTATTT
genomic: TTGGAAACTACTGCATTTCTAAAGGAGCCTCCATTGGATTCTGGCAAGCGgtatgagcag ... ttcttaccagGACATTAGGTATCTCATGGAGGATGTGCAAATGATGAAACCAACGGTATTT
EST: gi|58609844|gb|CK037877.1|CK037877
EST:     TTGGAAACTACTGCATTTCTAAAGGAGCCTCCATTGGATTCTGGCAAGCG                         GACATTAGGTATCTCATGG
genomic: TTGGAAACTACTGCATTTCTAAAGGAGCCTCCATTGGATTCTGGCAAGCGgtatgagcag ... ttcttaccagGACATTAGGTATCTCATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtagactatcttctttgaccatctggcaggtgacacaaaccactttcttaccagGACATTAGGTATCTCATGGAGGATGTGCAAATGATGAAACCAACGGTATTTTGTGGTGTCCCTCGTGTTTATGATCGTATATACACAG
             ctttgac  putative branch site (score: 4)
                                        ccactttctt  putative PPT
                                            tttctta  TA-rich tract