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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttaatgctctgttaggttcgaagtattgacatatctatgtcatgtgacttacattccagttcatgtatcagttatttccacgttatgctaaaattttggtgtctagtgcttgagcatttccaacagtttttcctgcatggttgcatgtactgcagGCTGATGTTCTGTACAAGCTTATTGGGGAATCTGCTGGGCTTAAGGGAGATGGCTCTGAGATTATCCTTGACTTGTTCTGTGGAACCGGAACCATTGGTC

Basic information

species Oryza sativa
transcript LOC_Os01g09750.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g09750.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G115198_T02 (Zea mays), 3'ss of exon 5
gtttgttaatgctctgttaggttcgaagtattgacatatctatgtcatgtgacttacattccagttcatgtatcagttatttccacgttatgctaaaattttggtgtctagtgcttgagcatttccaacagtttttcctgcatggttgcatgtactgcagGCTGATGTTCTGTACAAGCTTATTGGGGAATCTGCTGGGCTTAAGGGAGATGGCTCTGAGATTATCCTTGACTTGTTCTGTGGAACCGGAACCATTGGTC
                                              ||       | |  |||||  ||| |  |  |          | ||  |  || |   |  || ||| || |  || |     ||   |  |       ||  |  |  |||||||||||||||| |||||||||||||  || |||||||||||||| |||||||||||||| ||| | |||||  |||| |||||||| |||||||||||| 
--------------------------------------------gtatagatgagaaagaccagtaaatggaaaaaatga------actttgaaatgatgtcccttcctggtgtttaatgatctg----agccctctcc------tttgacttcttgcagGCTGATGTTCTTTACAAGCTTATTGAAGATTCTGCTGGGCTTAAAGGAGATGGCTCTGAAATTGTTCTTGATCTGTTTTGTGGAACTGGAACCATTGGTT

upper sequence: LOC_Os01g09750.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT3G21300.1 (Arabidopsis thaliana), 3'ss of exon 6
gtttgttaatgctctgttaggttcgaagtattgacatatctatgtcatgtgacttacattccagttcatgtatcagttatttccacgttatgctaaaattttggtgtctagtgcttgagcatttccaacagtttttcctgcatggttgcatgtactgcagGCTGATGTTCTGTACAAGCTTATTGGGGAATCTGCTGGGCTTAAGGGAGATGGCTCTGAGATTATCCTTGACTTGTTCTGTGGAACCGGAACCATTGGTC
                                                                     ||||  | ||   | | |  |         |||       |   | | |  ||  | |   |||     |  |  | ||       || ||||||| ||| | || |||||||||| |||||||||||| ||||| ||||||||||| ||  |  | || ||  | ||||||||||| || ||||| || |
---------------------------------------------------------------------gtatatggtaccactaagcaacatggtttcttttacactcaaaacatta--atcacaacttgttgaaaataaaatggtgttcactgtgtagGCTGAAGTTTTATATAAGCTTATTGAGGAATCTGCTGGACTTAAAGGAGATGGCTCAGAAGTCGTGCTCGATCTTTTCTGTGGAACTGGTACCATAGGCC

upper sequence: LOC_Os01g09750.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv09s0002g02670.t01 (Vitis vinifera), 3'ss of exon 6
gtttgttaatgctctgttaggttcgaagtattgacatatctatgtcatgtgacttacattccagttcatgtat-cagttatttccacgttatgctaaaattttggtgtctag-tgcttgagcatttcc-aacagtttttcctgcatggttgcatgtactgcagGCTGATGTTCTGTACAAGCTTATTGGGGAATCTGCTGGGCTTAAGGGAGATGGCTCTGAGATTATCCTTGACTTGTTCTGTGGAACCGGAACCATTGGTC
                     | |    |  ||| || |  ||||  ||| |  | ||| |  |||    ||| | ||   |      |    ||  | |||   | ||||| |  |||    || |   | ||    | ||  | |  |  ||    | ||||| || || ||||| || ||||| |  || | |||||| ||||  || || |||||||| ||| | |||||| |||| |||||||| |||||||||||||
------------------gtatgctgcatgatgaaat-tgaatgtactgtcagct-catgctggttttgatattctgtccctatagtctctcactttagtttcc-tatctagctttttggatgttccttgatagcaaattct--aagactttataatgttcagGCAGAGGTGCTGTATAAACTTATAGAAGATTGTGCTGGTCTTAGAGGTGACGGCTCTGAAATTGTTCTTGACCTGTTTTGTGGAACTGGAACCATTGGTC

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|27548300|gb|CA766414.2|CA766414
EST:     TTACATTCCAGATATCTGCCAACTCCTTTTTCCAGACTAATACAAAACAG                         GCTGATGTTCTGTACAAGCTTATTGGGGAATCTGCTGGGCTTAAGGGAGAT
genomic: TTACATTCCAGATATCTGCCAACTCCTTTTTCCAGACTAATACAAAACAGgtttgttaat ... tgtactgcagGCTGATGTTCTGTACAAGCTTATTGGGGAATCTGCTGGGCTTAAGGGAGAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctagtgcttgagcatttccaacagtttttcctgcatggttgcatgtactgcagGCTGATGTTCTGTACAAGCTTATTGGGGAATCTGCTGGGCTTAAGGGAGATGGCTCTGAGATTATCCTTGACTTGTTCTGTGGAACCGGAACCATTGGTC
                        agttttt  TA-rich tract