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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaaaagaatatgatcgtttctttggtttgagtattaatggggttaagtacagtattagctaatgcaatcttgttggtttattgttttcattaattggatggattcttcacttgttgtccttcagTACCATTGGCCGTGCTGCATTCACTGGGAATCATCAATGGATTGTCCATGAAACTGCCAATGATCACGGGCTCAGATCCGAG

Basic information

species Oryza sativa
transcript LOC_Os12g06335.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g06330.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G069408_T01 (Zea mays), 3'ss of exon 2
gtaagcaaaagaatatgatcgtttctttggtttgagtattaatggg-gttaagtacagtattagctaatgcaatcttgttggtttattgttttcattaattggatggattcttcacttgttgtccttcagTACCATTGGCCGTGCTGCATTCACTGGGAATCATCAATGGATTGTCCATGAA------ACTGCCAATGATCACGGGCTCAGATCCGAG
|||||||   |||| |    ||||   | |||  ||| || || |    ||||| |             |  |  ||     |||  || | |   ||  || ||| || ||   |||||  | |||||||||||||||||||||||| |||||||| |||||||||||||||||||||||       ||||||| |||||||   |||||| | |||
gtaagca--ggaattt---tgttttgcttgttacagtgttcatagctaataagtgcttcggcgttgttggagaagttcaaactttgctgatgtatgta--tgtatgtatgctgtgcttgt-attcttcagTACCATTGGCCGTGCTGCTTTCACTGGAAATCATCAATGGATTGTCCATGATCCTGCCACTGCCAGTGATCACAATCTCAGACCGGAG

upper sequence: LOC_Os12g06330.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G031656_T02 (Zea mays), 3'ss of exon 3
gtaagcaaaagaatatgatcgtttctttggtttgagtattaatggggttaagtacagtattagctaatgcaatcttgttggtttattgttttcattaattggatggattcttcacttgttgtccttcagTACCATTGGCCGTGCTGCATTCACTGGGAATCATCAATGGATTGTCCATGAAACTGCCAATGATCACGGGCTCAGATCCGAG
           |  | ||   || ||||| ||   |    ||||   |||  |  | ||   |||   ||  | |||  |   |      || | | || | ||| || ||   |||||  | |||||||||||||||||||||||| ||||| || |||||||||||||||||||||||  ||||||||||||||   |||||| |||||
--------gtaagcaggaattttgctttgctt---gctacaatgttcttagct--aataagtgcttcggcg-ttttggagaagttcaagctttactgat-gtatgtatgctatgcttgt-attcttcagTACCATTGGCCGTGCTGCTTTCACCGGAAATCATCAATGGATTGTCCATGATCCTGCCAATGATCACAATCTCAGACCCGAG
















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|58673730|gb|CK062416.1|CK062416
EST:     ACGCTTGTTAGGAAGATCATGGCCTCGCAGGTTCATGTTGTTGGAGAAGG                         TACCATTGGCCGTGCTGCATTCACTGGGAATCATCAATGGATTGTCCATGA
genomic: ACGCTTGTTAGGAAGATCATGGCCTCGCAGGTTCATGTTGTTGGAGAAGGgtaagcaaaa ... tgtccttcagTACCATTGGCCGTGCTGCATTCACTGGGAATCATCAATGGATTGTCCATGA
EST: gi|58654584|gb|CK043264.1|CK043264
EST:     ACGCTTGTTAGGAAGATCATGGCCTCGCAGGTTCATGTTGTTGGAGAAGG                         TACCATTGGCCGTGCTGCATTCACTGGGAATCATCAATGGATTGTCCATGA
genomic: ACGCTTGTTAGGAAGATCATGGCCTCGCAGGTTCATGTTGTTGGAGAAGGgtaagcaaaa ... tgtccttcagTACCATTGGCCGTGCTGCATTCACTGGGAATCATCAATGGATTGTCCATGA
EST: gi|58656374|gb|CK045054.1|CK045054
EST:     ACGCTTGTTAGGAAGATCATGGCCTCGCAGGTTCATGTTGTTGGAGAAGG                         TACCATTGGCCGTGCTGCATTCACTGGGAATCATCAATGGATTGTCCATGA
genomic: ACGCTTGTTAGGAAGATCATGGCCTCGCAGGTTCATGTTGTTGGAGAAGGgtaagcaaaa ... tgtccttcagTACCATTGGCCGTGCTGCATTCACTGGGAATCATCAATGGATTGTCCATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttggtttattgttttcattaattggatggattcttcacttgttgtccttcagTACCATTGGCCGTGCTGCATTCACTGGGAATCATCAATGGATTGTCCATGAAACTGCCAATGATCACGGGCTCAGATCCGAG
                  cattaat  putative branch site (score: 3)
                                            ttgtccttc  putative PPT
       tttattgttttcatta  TA-rich tract