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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtacccctcgtcttcaaatcaactcaatatatgcaccaattagttctcacatctttaggatggcactaagatcacttgagtatgatcttggccatgtaagatgacagtaagattatttgaatttgatcctgacaatgtaatgttttttttggcagGTGAAGCTGCCGTTCTTCGTGCTGCACGGCGACGCCGACACGGTGACGGACCCGGAGGTGAGCCGGGCGCTGTACGAGCGCGCCGCCAGCGCCGACAAGG

Basic information

species Oryza sativa
transcript LOC_Os01g21310.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g21310.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G080320_T02 (Zea mays), 3'ss of exon 7
gtatgtacccctcgtcttcaaatcaactcaatatatgcaccaattagttctcacatctttaggatg-gcactaagatcacttgagtatgatcttggccatgtaagatgacagtaagattatttgaatttgatcctgacaatgtaatgttttttttggcagGTGAAGCTGCCGTTCTTCGTGCTGCACGGCGACGCCGACACGGTGACGGACCCGGAGGTGAGCCGGGCGCTGTACGAGCGCGCCGCCAGCGCCGACAAGG
                                                             | | |  |||     | || |||| |   |||   ||  ||  |  | | |            | | || | ||||       ||||||      |||||||| ||||||||||||||| ||||||||||| |||||||||||||||||||||||||||||||| ||||||||||||||  | ||||||||||||||| 
-------------------------------------------------------------gtacgtacacccgtcttacgtgagca--gtctaaacc-cgtccgtcgtcggcgcaggag---aactctggttctga-------atgtttgggc--gcagGTGACGCTGCCGTTCTTCGTCCTGCACGGCGAGGCCGACACGGTGACGGACCCGGAGGTGAGCCGCGCGCTGTACGAGCGTTCGGCCAGCGCCGACAAGA

upper sequence: LOC_Os01g21310.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv07s0005g00510.t01 (Vitis vinifera), 3'ss of exon 7
gtatgtacccctcgtcttcaaatcaactcaatatatgcaccaattagttctcacatctttaggatggcactaagatcacttgagtatgatcttggccatgtaagatgacagtaagattatttgaatttgatcctgacaatgtaatgttttttttggcagGTGAAGCTGCCGTTCTTCGTGCTGCACGGCGACGCCGACACGGTGACGGACCCGGAGGTGAGCCGGGCGCTGTACGAGCGCGCCGCCAGCGCCGACAAGG
||   | ||  || |||||   |    |||| | || ||  |  || |            ||||  ||| ||     |    |  ||   ||     || |  |||  |       |||| |        |  |||     | | ||  |||||||||||| |   |||| ||||| |||||||||||||| || || || ||||| ||||| || ||||||||||| ||||| |  |  |||   |||   |||||| 
gtcattgcctttcttcttctt-tggtgtcaacacatacataagataatc-----------aggacagcattacaggaaacaaaagat--cctcattgattttggatttcccc----ttatct--ccccagtgttgat----tgaggtggtttttggcagGTTACATTGCCATTCTTTGTGCTGCACGGCGAGGCAGATACAGTGACTGACCCAGACGTGAGCCGGGCACTGTATGGACAAGCCAGTAGCAGAGACAAGA
















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|88444707|gb|CI694944.1|CI694944
EST:     TTGAGATGCTCAGGACCAGCATGTACGTAGAGGACAGCTTGTCCAAG                         GTGAAGCTGCCGTTCTTCGTGCTGCACGGCGACGCCGACACGGTGACGGAC
genomic: TTGAGATGCTCAGGACCAGCATGTACGTAGAGGACAGCTTGTCCAAGgtatgtaccc ... tttttggcagGTGAAGCTGCCGTTCTTCGTGCTGCACGGCGACGCCGACACGGTGACGGAC
EST: gi|88379080|gb|CI681912.1|CI681912
EST:     TTGAGATGCTCAGGACCAGCATGTACGTAGAGGACAGCTTGTCCAAG                         GTGAAGCTGCCGTTCTTCGTGCTGCACGGCGACGCCGACACGGTGACGGAC
genomic: TTGAGATGCTCAGGACCAGCATGTACGTAGAGGACAGCTTGTCCAAGgtatgtaccc ... tttttggcagGTGAAGCTGCCGTTCTTCGTGCTGCACGGCGACGCCGACACGGTGACGGAC
EST: gi|58596166|gb|CK006694.1|CK006694
EST:     CACTTGAGATGCTCAGGACCAGCATGCACGTAGAGGACAGCTTGTCCAAG                         GTGAAGCTGCCGTTCTTCGTGCTGCACGGCGACGCCGACACGGTGACGGAC
genomic: CACTTGAGATGCTCAGGACCAGCATGTACGTAGAGGACAGCTTGTCCAAGgtatgtaccc ... tttttggcagGTGAAGCTGCCGTTCTTCGTGCTGCACGGCGACGCCGACACGGTGACGGAC
EST: gi|88338092|gb|CI677080.1|CI677080
EST:     TTGAGATGCTCAGGACCAGCATGTACGTAGAGGACAGCTTGTCCAAG                         GTGAAGCTGCCGTTCTTCGTGCTGCACGGCGACGCCGACACGGTGACGGAC
genomic: TTGAGATGCTCAGGACCAGCATGTACGTAGAGGACAGCTTGTCCAAGgtatgtaccc ... tttttggcagGTGAAGCTGCCGTTCTTCGTGCTGCACGGCGACGCCGACACGGTGACGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgacagtaagattatttgaatttgatcctgacaatgtaatgttttttttggcagGTGAAGCTGCCGTTCTTCGTGCTGCACGGCGACGCCGACACGGTGACGGACCCGGAGGTGAGCCGGGCGCTGTACGAGCGCGCCGCCAGCGCCGACAAGG
                          tcctgac  putative branch site (score: 2)
                                        tgtttttttt  putative PPT
       taagattatttgaatt  TA-rich tract