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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataaactttacatttgatttactacttttttcttctacattcttctgttgttgatttgtcatttcacttatgtcaatttttcttttcaactattgcccagGCGTACTATTAAATCATTCATCCAAGGATTTCTGCCAGGAATTGCTCTGAAGATTTTCCTTATATTGCTCCCTAGCATATTAATGTTTATGTCTAAAGTT

Basic information

species Oryza sativa
transcript LOC_Os01g35050.3
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G064189_T01 (Zea mays), 3'ss of exon 1
ataaactttacatttgatttactacttttt--tcttctacattcttc-tgttgttgatttgtcatttcacttatgtcaatttttcttttcaactattgcccagGCGTACTATTAAATCATTCATCCAAGGATTTCTGCCAGGAATTGCTCTGAAGATTTTCCTTATATTGCTCCCTAGCATATTAATGTTTATGTCTAAAGTT
  || |   | ||| || ||  | ||||||  |||  || | |   | ||||  | || | | |   |  |||  | |||| |  |||||   | ||   ||||| |||||||||||||||||||||||| || || || ||||||||||||||||| ||||||||||||||||| ||||||||||||||||||||||| |||
ccaagccccaaattggaattttttctttttactctgttataatgggcatgtttcttatctctgaaaccttttagttgaattgtatttttc---ttttcttcagGCATACTATTAAATCATTCATCCAAGGTTTCCTTCCGGGAATTGCTCTGAAGATCTTCCTTATATTGCTCCCAAGCATATTAATGTTTATGTCTAAGGTT

upper sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G021194_T01 (Zea mays), 3'ss of exon 8
-ataaactttacatttgatttactacttttt--tcttctacattcttc-tgttgttgatttgtcatttcacttatgtcaatttttcttttcaactattgcccagGCGTACTATTAAATCATTCATCCAAGGATTTCTGCCAGGAATTGCTCTGAAGATTTTCCTTATATTGCTCCCTAGCATATTAATGTTTATGTCTAAAGTT
   || | | | ||| || ||  | ||||||  |||  || | |   | ||||  | || | | |   |  |||  | || | || |||    || ||   ||||| |||||||||||||||||||||||| || || || ||||||||||||||||| ||||||||||||||||| ||||||||||||||||||||||| |||
accaagcctcaaattggaattgtttctttttactctgttataatgggcatgtttcttatctctgaaaccttttagttgaactgtttttt----cttttcttcagGCATACTATTAAATCATTCATCCAAGGTTTCCTTCCGGGAATTGCTCTGAAGATCTTCCTTATATTGCTCCCAAGCATATTAATGTTTATGTCTAAGGTT
















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|66923753|gb|CX110601.1|CX110601
EST:     ATTGAAGGGATTGAGAAGGCAGCTCCATTTCTGAAGCCTTTGATTGAAAT                         GCGTACTATTAAATCATTCATCCAAGGATTTCTGCCAGGAATTGCTCTGAA
genomic: ATTGAAGGGATTGAGAAGGCAGCTCCATTTCTGAAGCCTTTGATTGAAATgtacgtgcat ... tattgcccagGCGTACTATTAAATCATTCATCCAAGGATTTCTGCCAGGAATTGCTCTGAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgttgatttgtcatttcacttatgtcaatttttcttttcaactattgcccagGCGTACTATTAAATCATTCATCCAAGGATTTCTGCCAGGAATTGCTCTGAAGATTTTCCTTATATTGCTCCCTAGCATATTAATGTTTATGTCTAAAGTT
   tgttgat  putative branch site (score: 4)
                               tttttcttttcaact  putative PPT
                             aatttttcttttcaa  TA-rich tract