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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactctcaaaactcctgaaaagtatgattggaaaagatctatgaatcgcatagcaggaaatgaaatctcacatatcctctttctctccaatttcggacagGGAACAAGGCTTGGCAGTTCTGATCCTAAGGGATGCTTCA

Basic information

species Oryza sativa
transcript LOC_Os08g10600.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g10600.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G155729_T01 (Zea mays), 3'ss of exon 3
gtactctcaaaactcctgaaaa----gtatgatt-ggaaaagatctatga---atcgcatagcaggaaatgaaat-ctcacatatcctctt------tctctccaatttcggacagGGAACAAGGCTTGGCAGTTCTGATCCTAAGGGATGCTTCA
||| |||   |    || | |      | || ||  |      || ||      |   || | | || |  |||  |||| |||   |  |      | |   ||| |  |||||||| || ||||||||||||||||| || |||||||| ||||
gtattctaggactcacttagattgctatgtggttcagtggttgtccatattatgttttatggtatgatagaaaacgctcatatactttgctatttgtttttatcaactggggacagGGGACTAGGCTTGGCAGTTCTGACCCCAAGGGATGTTTCA

upper sequence: LOC_Os08g10600.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G155729_T02 (Zea mays), 3'ss of exon 3
gtactctcaaaactcctgaaaa----gtatgatt-ggaaaagatctatga---atcgcatagcaggaaatgaaat-ctcacatatcctctt------tctctccaatttcggacagGGAACAAGGCTTGGCAGTTCTGATCCTAAGGGATGCTTCA------------------------------------------------------------
||| |||   |    || | |      | || ||  |      || ||      |   || | | || |  |||  |||| |||   |  |      | |   ||| |  |||||||| || ||||||||||||||||| || |||||||| ||||                                                            
gtattctaggactcacttagattgctatgtggttcagtggttgtccatattatgttttatggtatgatagaaaacgctcatatactttgctatttgtttttatcaactggggacagGGGACTAGGCTTGGCAGTTCTGACCCCAAGGGATGTTTCAGTAAGTCTTCCCACCCAAGCCATTGAATTTTAGTTTTGCTTTCTTCAATTAGTGCTATGA
















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|218500747|gb|FG962718.1|FG962718
EST:     AAGCCATTTCAGAGGGGAAATTGG-TG--GTCCTTTTGGCTGGTGGTCAG                         GCAACAAGGCTTGGCAGTTCTGATCCTAAGGGATGCTTCA
genomic: AAGCCATTTCAGAGGGGAAATTGGCTGTTGTCCTTTTGGCTGGTGGTCAGgtactctcaa ... tttcggacagGGAACAAGGCTTGGCAGTTCTGATCCTAAGGGATGCTTCA
EST: gi|29616664|gb|CB621676.1|CB621676
EST:     AAGCCATTTCAGAGGGGAAATTGGCTGTTGTCCTTTTGGCTGGTGGTCAG                         GGAACAAGGCTTGGCAGTTCTGATCCTAAGGGATGCTTCA
genomic: AAGCCATTTCAGAGGGGAAATTGGCTGTTGTCCTTTTGGCTGGTGGTCAGgtactctcaa ... tttcggacagGGAACAAGGCTTGGCAGTTCTGATCCTAAGGGATGCTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgcatagcaggaaatgaaatctcacatatcctctttctctccaatttcggacagGGAACAAGGCTTGGCAGTTCTGATCCTAAGGGATGCTTCA
                   atctcac  putative branch site (score: 3)
                           tatcctctttctctcc  CT-rich tract
            aaatgaaat  TA-rich tract