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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttctattcattcattcatcgcttccatttttttttctcatatatgcatcaatccatcgagatctccatgaaaaaagCATGCAAACACAGTGGGCACGGGAGCTTCTCCGACAGCGCCATGCTCAACAACGTCGTCGGCCACCTCCTGCACTCCTTCATCCTCGTCCCCTACCATGG

Basic information

species Oryza sativa
transcript LOC_Os11g01340.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g01340.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G056546_T01 (Zea mays), 3'ss of exon 1
gtatttctattcattcattcatcgcttccatttttttttctcatatatgcatcaatccatcga-gatctccatgaaaaaagCATGCAAACACAGTGGGCACGGGAGCTTCTCCGACAGCGCCATGCTCAACAACGTCGTCGGCCACCTCCTGCACTCCTTCATCCTCGTCCCCTACCATGG---
          |    | |  ||   |   || || | || || | |    ||   ||  |  | || || | |||   | |||||      |||||| || || |||||||| |||||||| | |||||||| ||| || ||||| ||||        |||||||||||||||||||||||   
---------gtgtggcgtcgatatatattatattctcttttcgtcttcctatttttcttttaacgaactacttgatgcatgcatg------cagTGGCCATGGCAGCTTCTCGGACAGCGCGACGCTCAACAGCGTGGTGGGCCATCTCC--------TTCATCCTCGTCCCCTACCATGGATG

upper sequence: LOC_Os11g01340.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G354558_T01 (Zea mays), 3'ss of exon 1
----------gtatttctattcattcattcatc--gcttccatttttttttctcatatatgcatcaat----------ccatcgagatctccatgaaaaaagCATGCAAACACAGTGGGCACGGGAGCTTCTCCGACAGCGCCATGCTCAACAACGTCGTCGGCCACCTCCTGCACTCCTTCATCCTCGTCCCCTACCATGG---
            || ||| ||| | | ||  |   | || | ||| |||   | |  ||| || | |           | |    || |    || |  | |       || |||||| || || |||||||| |||||||| | |||||||| |||||| ||||| ||||| |||||||||||||||||||| ||||||||   
gtacgtacgtcgatctctcttcctccttttgttttgttttcttttctttcggttacgtatacaacgacgacgaaatgacgacgacgaccatgttgcatgatgttgatgcacgcagTGGCCATGGCAGCTTCTCGGACAGCGCGACGCTCAACAGCGTCGTGGGCCATCTCCTTCACTCCTTCATCCTCGTCCCTTACCATGGATG
















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|55409516|gb|CV721892.1|CV721892
EST:     GCGGCGCAGGGCACCATGTTCTGGGCGCTCTTCGTCCTCGGCCACGACTG                         CATGCAAACACAGTGGGCACGGGAGCTTCTCCGACAGCGCCATGCTCAACA
genomic: GCGGCGCAGGGCACCATGTTCTGGGCGCTCTTCGTCCTCGGCCACGACTGgtatttctat ... atgaaaaaagCATGCAAACACAGTGGGCACGGGAGCTTCTCCGACAGCGCCATGCTCAACA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccatttttttttctcatatatgcatcaatccatcgagatctccatgaaaaaagCATGCAAACACAGTGGGCACGGGAGCTTCTCCGACAGCGCCATGCTCAACAACGTCGTCGGCCACCTCCTGCACTCCTTCATCCTCGTCCCCTACCATGG
                                        tctccat  CT-rich tract
     tttttttttctcatat  TA-rich tract