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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_Os01g53880.1
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|29675173|gb|CB671448.1|CB671448
EST:     CATGGTGCTCCTGCTACACCTGCGCGCAACAGACCACAGACCCAGGGAAG                         AGGAGCTGCAGCACCAGTGGTTGGTTGGCCTCCAATTCGATCCTTCAGGAG
genomic: CATGGTGCTCCTGCTACACCTGCGCGCAACAGACCACAGACCCAGGGAAGgtactgatag ... ctgtttgtagAGGAGCTGCAGCACCAGTGGTTGGTTGGCCTCCAATTCGATCCTTCAGGAG
EST: gi|4715020|gb|AU056137.1|AU056137
EST:     ATGGGTGCTCCTGCTACACCTGCGCGCAACAGACCACAGACCCAGGGAGG                         AGGAGCTGCAGCACCAGTGGTTGGTTGGCCTCCAATTCGATCCTTCAGGAG
genomic: ATGG-TGCTCCTGCTACACCTGCGCGCAACAGACCACAGACCCAGGGAAGgtactgatag ... ctgtttgtagAGGAGCTGCAGCACCAGTGGTTGGTTGGCCTCCAATTCGATCCTTCAGGAG
EST: gi|58695140|gb|CK083827.1|CK083827
EST:     CATGGTGCTCCTGCTACACCTGCGCGCAACAGACCACAGACCCAGGGAAG                         AGGAGCTGCAGCACCAGTGGTTGGTTGGCCTCCAATTCGATCCTTCAGGAG
genomic: CATGGTGCTCCTGCTACACCTGCGCGCAACAGACCACAGACCCAGGGAAGgtactgatag ... ctgtttgtagAGGAGCTGCAGCACCAGTGGTTGGTTGGCCTCCAATTCGATCCTTCAGGAG
EST: gi|4714667|gb|AU055784.1|AU055784
EST:     ATGGTGCTCCCTGCTACACC-GCGCGCAACAGACCACAGACCCAGGGAAG                         AGGAGCTGCAGCACCAGTGGTTGGTTGGCCTCCAATTCGATCCTTCAGGAG
genomic: ATGGTGCT-CCTGCTACACCTGCGCGCAACAGACCACAGACCCAGGGAAGgtactgatag ... ctgtttgtagAGGAGCTGCAGCACCAGTGGTTGGTTGGCCTCCAATTCGATCCTTCAGGAG
EST: gi|29675175|gb|CB671450.1|CB671450
EST:     CATGGTGCTCCTGCTACACCTGCGCGCAACAGACCACAGACCCAGGGAAG                         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