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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatagagtgcacaaatattgattagtgtaatcctgaatcttcccatcagaaacacaggctggagaagtatattcttcagattgatcgaacatatttatttgttatatgccattgcaatctttgcctataattttaaattttcgattcattcctaaacaactgctgtattgcagTCTGGCCACAACATCGAAAAAGTCAGAGAAAAAATGGGAGAGCTGATAAAGCAAATGGTCAACATCTATTCTCTTCCAAAACTTCTCCCATACATTTTGG

Basic information

species Oryza sativa
transcript LOC_Os01g60040.2
intron # 36
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 36
lower sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 36
gtacatagagtgcacaaatattgattagtgtaatcctgaatcttcccatcagaaacacaggctggagaagtatattcttcagattgatcgaacatatttatttgttatatgccattgcaatctttgcctataattttaaattttcgattcattcctaaacaa-ctgctgtattgcagTCTGGCCACAACATCGAAAAAGTCAGAGAAAAAATGGGAGAGCTGATAAAGCAAATGGTCAACATCTATTCTCTTCCAAAACTTCTCCCATACATTTTGG
                                                                                                  ||    |  ||    | ||||   ||    | | ||  ||  ||    || || || | | |||  | ||||  |||||||||| || ||||| ||||||||||| ||||||||||| |||||||||||||||||| ||||||| || |||||||| |||||  | || || ||  | |
-------------------------------------------------------------------------------------------------gtacggttagtacaaaaatgcatatttgatgtgttatcatag-ttcataatacaatcatgaccaaattactgttctgcagTCTGGTCATAACATTGAAAAAGTCAGGGAAAAAATGGGGGAGCTGATAAAGCAAATGATCAACATTTACTCTCTTCCCAAACTAATTCCCTATATACTTG

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 36
lower sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 18
gtacatagagtgcacaaatattgattagtgtaatcctgaatcttcccatcagaaacacaggctggagaagtatattcttcagattgatcgaacatatttatttgttatatgccattgcaatctttgcctataattttaaattttcgattcattcctaaacaactgctgtattgcagTCTGGCCACAACATCGAAAAAGTCAGAGAAAAAATGGGAGAGCTGATAAAGCAAATGGTCAACATCTATTCTCTTCCAAAACTTCTCCCATACATTTTGG
                                                                                             ||  ||| |    |  |||   |   || | |   ||| || ||  || ||  | ||||  | |||    | ||||  |||||||||| || ||||| ||||||||||| ||||||||||| || ||||||||||||||||||||||| ||||||||||| ||| | || || || ||| | |
-------------------------------------------------------------------------------------------gtatgattagtccaaaagtgcatattggatgtgt---tatcatatttcatattacaatcatgaccaaat---tcctgttctgcagTCTGGTCATAACATTGAAAAAGTCAGGGAAAAAATGGGGGATCTGATAAAGCAAATGGTCAACATTTATTCTCTTCCCAAATTACTTCCCTATATTCTTG
















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|88665316|gb|CI711114.1|CI711114
EST:     TGTTAACAGAAGCTGAAGCTGCAATTTTCCTTCCATGTCTTATGGAGAAG                         TCTGGCCACAACATCGAAAAAGTCAGAGAAAAAATGGGAGAGCTGATAAAG
genomic: TGTTAACAGAAGCTGAAGCTGCAATTTTCCTTCCATGTCTTATGGAGAAGgtacatagag ... tgtattgcagTCTGGCCACAACATCGAAAAAGTCAGAGAAAAAATGGGAGAGCTGATAAAG
EST: gi|88664232|gb|CI673700.1|CI673700
EST:     TGTTAACAGAAGCTGAAGCTGCAATTTTCCTTCCATGTCTTATGGAGAAG                         TCTGGCCACAACATCGAAAAAGTCAGAGAAAAAATGGGAGAGCTGATAAAG
genomic: TGTTAACAGAAGCTGAAGCTGCAATTTTCCTTCCATGTCTTATGGAGAAGgtacatagag ... tgtattgcagTCTGGCCACAACATCGAAAAAGTCAGAGAAAAAATGGGAGAGCTGATAAAG
EST: gi|88592754|gb|CI710878.1|CI710878
EST:     TGTTAACAGAAGCTGAAGCTGCAATTTTCCTTCCATGTCTTATGGAGAAG                         TCTGGCCACAACATCGAAAAAGTCAGAGAAAAAATGGGAGAGCTGATAAAG
genomic: TGTTAACAGAAGCTGAAGCTGCAATTTTCCTTCCATGTCTTATGGAGAAGgtacatagag ... tgtattgcagTCTGGCCACAACATCGAAAAAGTCAGAGAAAAAATGGGAGAGCTGATAAAG
EST: gi|396941288|gb|HO188497.1|HO188497
EST:     TGTTAACAGAAGCTGAAGCTGCAATTTTCCTTCCATGTCTTATGGAGAAG                         TCTGGCCACAACATCGAAAAAGTCAGAGAAAAAATGGGAGAGCTGATAAAG
genomic: TGTTAACAGAAGCTGAAGCTGCAATTTTCCTTCCATGTCTTATGGAGAAGgtacatagag ... tgtattgcagTCTGGCCACAACATCGAAAAAGTCAGAGAAAAAATGGGAGAGCTGATAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgcctataattttaaattttcgattcattcctaaacaactgctgtattgcagTCTGGCCACAACATCGAAAAAGTCAGAGAAAAAATGGGAGAGCTGATAAAGCAAATGGTCAACATCTATTCTCTTCCAAAACTTCTCCCATACATTTTGG
                               tcctaaa  putative branch site (score: 2)
       tataattttaaatttt  TA-rich tract