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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttactagattgcaatcatgtcaacaaatgcaggcaatctgacagttacatagaaatttctacttgtggttaatttacagttttctcatttggctacagCTGCAACCCATGAGAATAAATCATTCAGCCTGATTTCTGCGGCTGATGCTCTGCTGGGTTCATCTGCCACCAAGTACAGTGCATTAGATTGCCAAAGGCC

Basic information

species Oryza sativa
transcript LOC_Os06g48650.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g48650.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G099452_T02 (Zea mays), 3'ss of exon 7
-tgttactaga--ttgcaatcatgtcaacaaatgcaggcaatctgacagttacatagaaatttctacttgtggttaatttacagttttctcatttggctacagCTGCAACCCATGAGAATAAATCATTCAGCCTGATTTCTGCGGCTGATGCTCTGCTGGGTTCATCTGCCACCAAGTACAGTGCATTAGATTGCCAAAGGCC
 || |   ||   |||  |  | |||      | | || | |||  || | ||    |  || |  |  ||||||| || ||| |||||||||     |||||||||||| |||| |||||  || || |||||||||||||| ||||||||||| ||||| |||||||| | |||||||||||||||||| || || |||||
gtggtggaagcctttgacactaggtctgttt-ttctggtattctatcaataacccttatgttccagccagtggtta-ttgacaattttctcatacaa-tacagCTGCAACACATGGGAATATGTCGTTTAGCCTGATTTCTGCAGCTGATGCTCTTCTGGGCTCATCTGCAAGCAAGTACAGTGCATTAGACTGTCAGAGGCC

upper sequence: LOC_Os06g48650.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G114394_T02 (Zea mays), 3'ss of exon 7
tgttactagattgca-atcatgtc-aacaaatgcaggcaatctgacagttacatagaaatttctacttgtggttaatttacagttttctcatttggctacagCTGCAACCCATGAGAATAAATCATTCAGCCTGATTTCTGCGGCTGATGCTCTGCTGGGTTCATCTGCCACCAAGTACAGTGCATTAGATTGCCAAAGGCC
  ||   || |   |    || |   |    | | || | |||  || | ||    |  ||||| | |||||||| || ||| |||||||||  |  |||||||||||| |||| |||||  || |||||| |||||||||| |||||||||||  ||||||||||||| |||||||||||||||||||||||||| |||||
actttaaaggtcatatgagatatttgagtggtcctggtattctatcaataactcctatgtttctgcctgtggtta-ttgacaattttctcatacga-tacagCTGCAACACATGGGAATATGTCGTTCAGCTTGATTTCTGCAGCTGATGCTCTATTGGGTTCATCTGCAACCAAGTACAGTGCATTAGATTGCCAGAGGCC
















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|66913003|gb|CX099851.1|CX099851
EST:     TCATTTGGTGCTAGGAAATGGGAAACTTCTTCCTGGACTTGGTGTATCAC                         CTGCAACCCATGAGAATAAATCATTCAGCCTGATTTCTGCGGCTGATGCTC
genomic: TCATTTGGTGCTAGGAAATGGGAAACTTCTTCCTGGACTTGGTGTATCACgtaagttctg ... ttggctacagCTGCAACCCATGAGAATAAATCATTCAGCCTGATTTCTGCGGCTGATGCTC
EST: gi|58684518|gb|CK073205.1|CK073205
EST:     TCATTTGGTGCTAGGAAATGGGAAACTTCTTCCTGGACTTGGTGTATCAC                         CTGCAACCCATGAGAATAAATCATTCAGCCTGATTTCTGCGGCTGATGCTC
genomic: TCATTTGGTGCTAGGAAATGGGAAACTTCTTCCTGGACTTGGTGTATCACgtaagttctg ... ttggctacagCTGCAACCCATGAGAATAAATCATTCAGCCTGATTTCTGCGGCTGATGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttacatagaaatttctacttgtggttaatttacagttttctcatttggctacagCTGCAACCCATGAGAATAAATCATTCAGCCTGATTTCTGCGGCTGATGCTCTGCTGGGTTCATCTGCCACCAAGTACAGTGCATTAGATTGCCAAAGGCC
                       ggttaat  putative branch site (score: 4)
                                    ttttctcattt  putative PPT
                         ttaatttacagtttt  TA-rich tract