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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttctcaaaggtagaatggggatttcacatagttctttactctctttgtccttcagcgcttagcctgttcactggcttttattcttatttcttttgcagTATATACCTTCTGTAGAAGATACAGTTCTTGGTGTTGTGGTTGACACCAAACCAGAT

Basic information

species Oryza sativa
transcript LOC_Os01g47256.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g47256.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G173989_T02 (Zea mays), 3'ss of exon 4
tcttctcaaaggtagaatggggatttcacatagttctttactctctttgtccttcagcgcttagcctgttcactggcttttat--tcttatttcttttgcagTATATACCTTCTGTAGAAGATACAGTTCTTGGTGTTGTGGTTGACACCAAACCAGAT-------------------------------------------
 | |   | |    | || | |   ||   |  | | |   | || |  | |  ||| | | || |   | | |    || ||  |||| ||| |||| |||||||||||||||||||||||||| ||||||||| ||||||| ||||||||||||||                                            
-cgtgggagactgcggatagtgtagtctgttcctccctatttatcgtgattcagcagtgatcagtc-acttattcatgttcatggtcttcttttttttacagTATATACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGACGTAAGTATACATTTATATTCAGGAGTATGTGAGTTGATACTTG

upper sequence: LOC_Os01g47256.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G540589_T01 (Zea mays), 3'ss of exon 2
tcttctcaaaggtagaatggg-gatttcacatagttctttactctctttgtccttcagcgcttagcctgttcactggcttttattcttatt----tcttttgcagTATATACCTTCTGTAGAAGATACAGTTCTTGGTGTTGTGGT--TGACACCA-AACCAGAT
   ||| ||  |||   |||| || |    ||||| ||  | ||| ||   || ||   |    |  | ||  | | |  |||||||| ||    | |||||||||||||||||| ||||||||||||||||||||||  |||  |  ||       ||||| | 
---tcttaactgtaacgtgggagactgtggatagtgct--agtctgttccaccctcttggtcatgtgttttagcagccacttattcttgttcttcttttttgcagTATATACCTTATGTAGAAGATACAGTTCTTGGTACTGTCATACTGTGGTTGGAACCAAAC

upper sequence: LOC_Os01g47256.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G173989_T01 (Zea mays), 3'ss of exon 4
tcttctcaaaggtagaatggggatttcacatagttctttactctctttgtccttcagcgcttagcctgttcactggcttttat--tcttatttcttttgcagTATATACCTTCTGTAGAAGATACAGTTCTTGGTGTTGTGGTTGACACCAAACCAGAT
 | |   | |    | || | |   ||   |  | | |   | || |  | |  ||| | | || |   | | |    || ||  |||| ||| |||| |||||||||||||||||||||||||| ||||||||| ||||||| |||||||||||||| 
-cgtgggagactgcggatagtgtagtctgttcctccctatttatcgtgattcagcagtgatcagtc-acttattcatgttcatggtcttcttttttttacagTATATACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGAC

upper sequence: LOC_Os01g47256.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G802854_T01 (Zea mays), 3'ss of exon 4
tcttctcaaaggtagaatggggatttcaca--tagttctttactctct-ttgtccttcagcgcttagc--ctgttcactggcttttattcttat-ttcttttgcagTATATACCTTCTGTAGAAGATACAGTTCTTGGTGTTGTGGTTGACACCAAACCAGAT
          || ||| |  ||||     |    |||| |  |||| | ||||  ||||||  | | |      | | |    || ||  |  | || ||||  |||||| |||||||||||||||||| ||||||||| ||||||| |||||||||||||| 
------acgtgggagactccggatagtgtagtctgttcctccctctttattgtgtttcagcagtgatcagtcacttattcatgttcatggtcttctttttttatagTATAAACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGAC

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|58653630|gb|CK042310.1|CK042310
EST:     TACGGCTTTCGAAGCCCAGCAAATACTGGGTCGAGAGCTCGCAGAAGAGG                         TATATACCTTCTGTAGAAGATACAGTTCTTGGTGTTGTGGTTGACACCAAA
genomic: TACGGCTTTCGAAGCCCAGCAAATACTGGGTCGAGAGCTCGCAGAAGAGGgtgagcgctc ... tcttttgcagTATATACCTTCTGTAGAAGATACAGTTCTTGGTGTTGTGGTTGACACCAAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtccttcagcgcttagcctgttcactggcttttattcttatttcttttgcagTATATACCTTCTGTAGAAGATACAGTTCTTGGTGTTGTGGTTGACACCAAACCAGAT
                               cttttattcttatttc  CT-rich tract
                                ttttattcttatttct  TA-rich tract