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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attaaattattttaactattttattttattaatattatgcaatcatttatctcgatggcctttcagagacgaactcaccagttttctaacctgtttgtagAGGAGCTGCAGCACCAGTGGTTGGTTGGCCTCCAATTCGATCCTTCAGGAGAAACCTTGCTAGTAGTAGTTCATCCAAACATTCCCCTGAACCACAAAAT

Basic information

species Oryza sativa
transcript LOC_Os01g53880.6
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g53880.7 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA07G01800.1 (Glycine max), 3'ss of exon 1
attaaattattttaactattttattttattaatattatgcaatcatttatctcgatggcctttcagagacgaactcaccagttttctaacctgtttgtagAGGAGCTGCAGCA---CCAGTGGTTGGTTGGCCTCCAATTCGATCCTTCAGGAGAAACCTTGCTAGTAGTAGTTCATCCAAACATTCCCCTGAACCACAAAAT--
 |   || ||| | | |||  | || | ||  ||   |        |||| |  |  |  | ||   | | ||||     ||       ||       |   || ||||  ||   ||||| || ||||||||||||||||| ||||||||||  ||| |||| ||| | ||  | || ||   |     |   |  |    |  
-tgtgatgattctga-tatgcttttgtcttcttagggtagtgcttgttatttttactgtttatccatgcctaactt-tttgtacatgggcccaccaaaaacagAACTGCTTCAGGTCCAGTAGTGGGTTGGCCTCCAATTCGTTCCTTCAGGAAGAACATTGCAAGTGGAAGCACTTCTAAT--TCTAAGTTGCCTTCTGGGTCC
















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|29672643|gb|CB668918.1|CB668918
EST:     CATGGTGCTCTTGCTACACTTGCGCGCAACAGACCACAGACCCAGGGAAG                         AGGAGCTGCAGCACCAGTGGTTGGTTGGCCTCCAATTCGATCCTTCAGGAG
genomic: CATGGTGCTCCTGCTACACCTGCGCGCAACAGACCACAGACCCAGGGAAGgtactgatag ... ctgtttgtagAGGAGCTGCAGCACCAGTGGTTGGTTGGCCTCCAATTCGATCCTTCAGGAG
EST: gi|29643256|gb|CB648263.1|CB648263
EST:     AGACCCAGGGAAG                         AGGAGCTGCAGCACCAGTGGTTGGTTGCCCTCCAATTCGATCCTTCAGGAG
genomic: AGACCCAGGGAAGgtactgatag ... ctgtttgtagAGGAGCTGCAGCACCAGTGGTTGGTTGGCCTCCAATTCGATCCTTCAGGAG
EST: gi|58695140|gb|CK083827.1|CK083827
EST:     CATGGTGCTCCTGCTACACCTGCGCGCAACAGACCACAGACCCAGGGAAG                         AGGAGCTGCAGCACCAGTGGTTGGTTGGCCTCCAATTCGATCCTTCAGGAG
genomic: CATGGTGCTCCTGCTACACCTGCGCGCAACAGACCACAGACCCAGGGAAGgtactgatag ... ctgtttgtagAGGAGCTGCAGCACCAGTGGTTGGTTGGCCTCCAATTCGATCCTTCAGGAG
EST: gi|29639753|gb|CB644762.1|CB644762
EST:     CATGGTGCTCNTGCTACACCTGCGCGCAACAGACCACAGACCCAGGGAAG                         AGGAGCTGCAGCACCAGTGGTTGGTTGGCCTCCAATTCGATCCTTCAGGAG
genomic: CATGGTGCTCCTGCTACACCTGCGCGCAACAGACCACAGACCCAGGGAAGgtactgatag ... ctgtttgtagAGGAGCTGCAGCACCAGTGGTTGGTTGGCCTCCAATTCGATCCTTCAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatctcgatggcctttcagagacgaactcaccagttttctaacctgtttgtagAGGAGCTGCAGCACCAGTGGTTGGTTGGCCTCCAATTCGATCCTTCAGGAGAAACCTTGCTAGTAGTAGTTCATCCAAACATTCCCCTGAACCACAAAAT
                                      ttctaac  putative branch site (score: 1)
                                            cctgttt  CT-rich tract
                                    ttttctaa  TA-rich tract