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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgtgatagggaaaataacaagacatctgcaactatatgcttcatattgcatctacccactatacctaaccagcctccatggttgcttgttcttttcagTAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAAATCCCTGTGTGGTGTGGTGTTCTGATAACTGGACTCAGCACTCTGATGCTACTGTTACTACA

Basic information

species Oryza sativa
transcript LOC_Os06g46310.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g46310.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G069198_T05 (Zea mays), 3'ss of exon 6
tttgtgatagggaaaataacaagacatctgcaactatatgcttcatattgcatctacccactatacctaaccagcctccatggttgcttgttcttttcagTAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAAATCCCTGTGTGGTGTGGTGTTCTGATAACTGGACTCAGCACTCTGATGCTACTGTTACTACA
| | ||  |    |    |  | ||| | |   || |  |||| || ||| ||   ||    ||  || | || |    ||||  | ||  |||||  |||||||||||||||||||||| | |||||||| || | |||||| || |||||||||||||| |||||||||||||||||||| |||||  | || || ||
tgtctgtcaaactagcagatcacacaaccgattcttttagctttatgttgaattctccagtaatttcttatcaactaagatggcggtttactctttgtagTAATTGGAACTGCTTTTGCTCTAAACATGCTGTTCAGAATCCCAGTATGGTGTGGTGTTCTAATAACTGGACTCAGCACTCTAATGCTCTTATTGCTGCA

upper sequence: LOC_Os06g46310.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G069198_T04 (Zea mays), 3'ss of exon 6
tttgtgatagggaaaataacaagacatctgcaactatatgcttcatattgcatctacccactatacctaaccagcctccatggttgcttgttcttttcagTAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAAATCCCTGTGTGGTGTGGTGTTCTGATAACTGGACTCAGCACTCTGATGCTACTGTTACTACA----------
                                    || |||| || ||| ||   ||    ||  || | || |    ||||  | ||  |||||  |||||||||||||||||||||| | |||||||| || | |||||| || |||||||||||||| |||||||||||||||||||| |||||  | || || ||          
------------------------------------ta-gctttatgttgaattctccagtaatttcttatcaactaagatggcggtttactctttgtagtaattggaactgcttttgctctaaacatgctgttcagAATCCCAGTATGGTGTGGTGTTCTAATAACTGGACTCAGCACTCTAATGCTCTTATTGCTGCAGCAATATGGG

upper sequence: LOC_Os06g46310.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA15G00590.1 (Glycine max), 3'ss of exon 5
tttgtgatagggaaaataacaagacatctgcaactatatgcttcatattgcatctacccactatacctaaccagcctcca-tggttgcttgttctttt-cagTAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAAATCCCTGTGTGGTGTGGTGTTCTGATAACTGGACTCAGCACTCTGATGCTACTGTTACTACA
     | |    |||  ||| | |  | | ||  | | |  |    |||   | || |  ||||   |    | | |  | |  ||  |||| |   | |||||||||| || || ||||| |||||||||||||| || || ||||| |||  |||||||||  | || |||||||||||  |||| ||  |   | ||||
--ctagtttttaaaacaaaccataactttccatttcttttttctgcattctctttaacttctatttatcttaatcttgaaattttttattgtacacatgcagTAATTGGGACAGCCTTTGCATTGAACATGCTCTTCAACATACCTGTTTGGATTGGTGTTCTTCTGACAGGACTCAGCACATTGATCCTCTTAGCATTACA

upper sequence: LOC_Os06g46310.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G44710.1 (Glycine max), 3'ss of exon 4
tttgtgatagggaaaataacaagacatctgcaactatatgcttcatattgcatctacccactatacctaaccagcctccatggttgc--ttgttctttt-cagTAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAAATCCCTGTGTGGTGTGGTGTTCTGATAACTGGACTCAGCACTCTGATGCTACTGTTACTACA
     | |    |||  ||||  || | | ||  | | |  |    |||   | || |   |||   |    | | |  ||  ||    |||| |   | |||||||||| || || ||||| |||||||||||||| || || ||||| |||  |||||||||  | || |||||||||||  |||||||  |   | | ||
--ctaggttttaaaacaaacataac-tttccatttcttttttctgcattctctttaacttttatttatcttaatcttgaatttttttcattgtacacatacagTAATTGGGACAGCCTTTGCATTGAACATGCTCTTCAACATACCTGTTTGGATTGGTGTTCTTCTGACAGGACTCAGCACATTGATGCTCTTAGCATTGCA

upper sequence: LOC_Os06g46310.3 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv09s0070g00210.t01 (Vitis vinifera), 3'ss of exon 6
tttgtgatagggaaaataacaagacatctgca--actatatgcttcatattgcatctacccactat--acctaaccagcctccatggttgcttgttcttttcagTAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAAATCCCTGTGTGGTGTGGTGTTCTGATAACTGGACTCAGCACTCTGATGCTACTGTTACTACA
 |  || |     || |  ||     ||| ||  | |||   ||| || |  |||  ||      |  |||||  | |  | | ||  || ||  | ||| |||| |||||||| || ||||| |||||||||||||| || || ||||||||||||||||||||  | || || || || ||  || | || ||     ||||
-taatggtttcttaagtg-catcctctcttcattattattaacttgatgtgtcatgcacatttcttcaacctattctgatttc-tgcatgttt-ctttttccagTGATTGGAACAGCCTTTGCATTGAACATGCTCTTCAATATTCCTGTGTGGTGTGGTGTTCTTCTTACAGGGCTTAGTACATTGGTTCTTCTAGCTTTACA

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|33653430|gb|CF276044.1|CF276044
EST:     ATTATGGATTCTTGCGGAACTAGCTGTAGTTGCATGCGACATTCCTGAAG                         TAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAA-TCCCTG
genomic: ATTATGGATTCTTGCGGAACTAGCTGTAGTTGCATGCGACATTCCTGAAGgtaccagagt ... ttcttttcagTAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAAATCCCTG
EST: gi|29664628|gb|CB660903.1|CB660903
EST:     ATTATGGATTCTTGCGGAACTAGCTGTAGTTGCATGCGACATTCCTGAAG                         TAATTGGAACTGCTTATGCTTTGAACATGCTCTTTAAAATCCCTGTGTGGT
genomic: ATTATGGATTCTTGCGGAACTAGCTGTAGTTGCATGCGACATTCCTGAAGgtaccagagt ... ttcttttcagTAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAAATCCCTGTGTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgcatctacccactatacctaaccagcctccatggttgcttgttcttttcagTAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAAATCCCTGTGTGGTGTGGTGTTCTGATAACTGGACTCAGCACTCTGATGCTACTGTTACTACA
                   acctaac  putative branch site (score: 2)
                                      ttgcttgttcttttc  putative PPT
                                             ttctttt  TA-rich tract