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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgctgactagcaattatatttactctgtacctcatagggagaatactactgcttctaatatgtgtatcaacagGTCGTGTATGCTATCTTGCATCGACAAGAGGTATTTCAGCCATTCAAAAACCATCCCCGCTTCAATGAATTGCTTGAGAATATTTACACA

Basic information

species Oryza sativa
transcript LOC_Os01g56630.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56630.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G079389_T01 (Zea mays), 3'ss of exon 13
gtatgtgctgactagcaattatatttactctgtacctcatagggagaatactactgcttctaatatgtgtatcaacagGTCGTGTATGCTATCTTGCATCGACAAGAGGTATTTCAGCCATTCAAAAACCATCCCCGCTTCAATGAATTGCTTGAGAATATTTACACA
||||||  || |  ||| ||   ||||||         | |||  || ||  ||||||      |  | | || |||||| ||||||||| | ||||||||||||||||| ||| ||||||| ||||||||||| || |||| |||| |||||||||| || ||||||
gtatgtattggcctgcagttcagtttactgg-------acaggaggactagcactgct-----aacatttttctacagGTTGTGTATGCTGTATTGCATCGACAAGAGGTGTTTGAGCCATTTAAAAACCATCCACGTTTCAGTGAACTGCTTGAGAACATATACACA

upper sequence: LOC_Os01g56630.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G078576_T04 (Zea mays), 3'ss of exon 13
gtatgtgctgactagcaattatatttactctgtacctcatagggagaatactactgcttctaatatgtgtatcaacagGTCGTGTATGCTATCTTGCATCGACAAGAGGTATTTCAGCCATTCAAAAACCATCCCCGCTTCAATGAATTGCTTGAGAATATTTACACA
||||||  || |  ||||||   ||||||          |     || ||  ||||||||||| || | | |  |||||| || |||||| | ||||||||||||||||| ||| ||||||| ||||| ||||| || || |||||| |||||||||| || ||||| 
gtatgtattggcctgcaattcagtttact----------tgacaggactagcactgcttctaacatttttgt--acagGTTGTATATGCTGTATTGCATCGACAAGAGGTTTTTGAGCCATTTAAAAATCATCCACGTTTTAATGAACTGCTTGAGAACATATACACT

upper sequence: LOC_Os01g56630.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA10G38920.2 (Glycine max), 3'ss of exon 13
-------------------------------------------gtatgtgctgactagcaatt-atatttactctgtacctcatagggagaatactactg-cttctaatatgtgtatcaacagGTCGTGTATGCTATCTTGCATCGACAAGAGGTATTTCAGCCATTCAAAAACCATCCCCGCTTCAATGAATTGCTTGAGAATATTTACACA
                                            ||| |  |     | |||  | ||||||  |  | |   | |     ||  |||||  ||||  | ||  |     ||||| |||||||| ||  ||||  | || || || |||||||||||||| || ||||| |||||||||||| || |||| || ||||| || 
gtaaatgatcttgattgactgagaagatttatcatgcctatttttatctagtttgctgtaatagaaatttacattacaaccttttgcatctatcttactgatttcttgtgtgactgg-ggcagGTAGTGTATGCAATAATGCACAGGCAGGAAGTCTTTCAGCCATTCAAGAATCATCCACGCTTCAATGAACTGATTGATAACATTTATACT

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|58684083|gb|CK072770.1|CK072770
EST:     TAGAAATCATCAATGCAATTCTTACATATGCATTGCCTAGAAATCCTGAG                         GTCGTGTATGCTATCTTGCATCGACAAGAGGTATTTCAGCCATTCAAAAAC
genomic: TAGAAATCATCAATGCAATTCTTACATATGCATTGCCTAGAAATCCTGAGgtatgtgctg ... gtatcaacagGTCGTGTATGCTATCTTGCATCGACAAGAGGTATTTCAGCCATTCAAAAAC
EST: gi|426809|gb|D22882.1|D22882
EST:     TAGAAATCATCAATGCAATTCTTACATATGCATTGCCTAGAAATCCTGAG                         GTCGTGTATGCTATCTTGCATCGACAAGAGGTATTTCAGCCATTCAAAAAC
genomic: TAGAAATCATCAATGCAATTCTTACATATGCATTGCCTAGAAATCCTGAGgtatgtgctg ... gtatcaacagGTCGTGTATGCTATCTTGCATCGACAAGAGGTATTTCAGCCATTCAAAAAC
EST: gi|58678344|gb|CK067031.1|CK067031
EST:     TAGAAATCATCAATGCAATTCTTACATATGCATTGCCTAGAAATCCTGAG                         GTCGTGTATGCTATCTTGCATCGACAAGAGGTATTTCAGCCATTCAAAAAC
genomic: TAGAAATCATCAATGCAATTCTTACATATGCATTGCCTAGAAATCCTGAGgtatgtgctg ... gtatcaacagGTCGTGTATGCTATCTTGCATCGACAAGAGGTATTTCAGCCATTCAAAAAC
EST: gi|29639051|gb|CB644060.1|CB644060
EST:     TAGAAATCATCAATGCAATTCTTACATATGCATTGCCTAGAAATCCTGAG                         GTCGTGTATGCTATCTTGCATCGACAAGAGGTATTTCAGCCATTCAAAAAC
genomic: TAGAAATCATCAATGCAATTCTTACATATGCATTGCCTAGAAATCCTGAGgtatgtgctg ... gtatcaacagGTCGTGTATGCTATCTTGCATCGACAAGAGGTATTTCAGCCATTCAAAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttactctgtacctcatagggagaatactactgcttctaatatgtgtatcaacagGTCGTGTATGCTATCTTGCATCGACAAGAGGTATTTCAGCCATTCAAAAACCATCCCCGCTTCAATGAATTGCTTGAGAATATTTACACA
                                  ttctaat  putative branch site (score: 2)
                                  ttctaatat  TA-rich tract