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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtgctagctgcttttgattattcataagatttgattatggtgtaaatcaaatgcttagattttgacatcgggtttgctggtgcagGAAGTTCTATCAATCCCAGTGAACGAACATACCCTGAAGAAATGATTCAGACTGGGATATCTACAATTGATGTTATGAATTCTATTGCCCGTGGTCAGAA

Basic information

species Oryza sativa
transcript LOC_Os01g51380.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g51380.2 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 6
--------------gtaggtgctagctgcttttgattatt---cataagattt--gattatggtgtaaatcaaatgcttagattttgacatcgggtttgctggtg------cagGAAGTTCTATCAATCCCAGTGAACGAACATACCCTGAAGAAATGATTCAGACTGGGATATCTACAATTGATGTTATGAATTCTATTGCCCGTGGTCAGAA
               | ||| |    |    | | | | |      || ||||  || |||  |||      |||   || |||     | | |  |   || ||      ||||   ||| ||||| || ||||| || ||||||||||| || |||||||| ||||| |||||||| |||||||| ||||| |||||||| || ||||| ||
gtgcttgcactcgctttggtacaccttataatcggtaactggctgcaaaattttggaatattttgtgctatgaattgctatattcgttaaacagtctacttgatgtggcttcagGTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAACTGGAATATCTACCATTGATGTCATGAACTCTATTGCTCGAGGTCAAAA

upper sequence: LOC_Os01g51380.2 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 5
--gtaggtgctagctg---cttttgattattcataagattt--gattatggtgtaaa---tcaaatgcttagattttgacatcgggtttgctgg--tgcagGAAGTTCTATCAATCCCAGTGAACGAACATACCCTGAAGAAATGATTCAGACTGGGATATCTACAATTGATGTTATGAATTCTATTGCCCGTGGTCAGAA
  |  |    | |||     |||  | ||  |  |  || |  || |||  | ||||   | ||  | || | || | |  ||   ||  |  |    ||||   ||| |||||||| |||||||| || || ||||| || ||||||||||| || |||||||| |||||||| ||||| || || ||  | || || ||
gtgcggtcttttgcttgtcttttccactaacctcagcatcttggaatattttttaaagattgaagagatttgcttatta-gtcaatttgacatgacctcagGTGCTTCGATCAATCCAAGTGAACGGACGTATCCTGAGGAGATGATTCAGACAGGAATATCTACGATTGATGTCATGAACTCCATCGCTAGAGGACAAAA

upper sequence: LOC_Os01g51380.2 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 5
gtaggtgctagctgcttttgattattcataagatttgattatggtgtaaatcaaatgcttagattttgacatcgggtttgctggtgcagGAAGTTCTATCAATCCCAGTGAACGAACATACCCTGAAGAAATGATTCAGACTGGGATATCTACAATTGATGTTATGAATTCTATTGCCCGTGGTCAGAA
                     | || |||    ||  | | || | |  | |  |    ||||| ||                 | ||||||| || ||||| || || ||||| || ||||| |||||||||||||||||||| || || || || || |||||||| || || ||||| ||||||||
--------------------gtgatacatcttcttctact-tgatattcaactgacctctagatgttc----------------tacagGAAGCTCCATCAACCCAAGCGAACGTACGTACCCGGAAGAAATGATTCAGACTGGCATTTCGACCATCGACGTTATGAACTCCATAGCCCGAGGTCAGAA

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|58672899|gb|CK061585.1|CK061585
EST:     TATAGATAATGGCCCACCGATTTTACCAGAGGCTTACTTGGATATTTCTG                         GAAGTTCTATCAATCCCAGTGAACGAACATACCCTGAAGAAATGATTCAGA
genomic: TATAGATAATGGCCCACCGATTTTACCAGAGGCTTACTTGGATATTTCTGgtaggtgcta ... gctggtgcagGAAGTTCTATCAATCCCAGTGAACGAACATACCCTGAAGAAATGATTCAGA
EST: gi|88358211|gb|CI605136.1|CI605136
EST:     TATAGATAATGGCCCACCGATTTTACCAGAGGCTTACTTGGATATTTCTG                         GAAGTTCTATCAATCCCAGTGAACGAACATACCCTGAAGAAATGATTCANA
genomic: TATAGATAATGGCCCACCGATTTTACCAGAGGCTTACTTGGATATTTCTGgtaggtgcta ... gctggtgcagGAAGTTCTATCAATCCCAGTGAACGAACATACCCTGAAGAAATGATTCAGA
EST: gi|66915737|gb|CX102585.1|CX102585
EST:     TATAGATAATGGCCCACCGATTTTACCAGAGGCTTACTTGGATATTTCTG                         GAAGTTCTATCAATCCCAGTGAACGAACATACCCTGAAGAAATGATTCAAA
genomic: TATAGATAATGGCCCACCGATTTTACCAGAGGCTTACTTGGATATTTCTGgtaggtgcta ... gctggtgcagGAAGTTCTATCAATCCCAGTGAACGAACATACCCTGAAGAAATGATTCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgattatggtgtaaatcaaatgcttagattttgacatcgggtttgctggtgcagGAAGTTCTATCAATCCCAGTGAACGAACATACCCTGAAGAAATGATTCAGACTGGGATATCTACAATTGATGTTATGAATTCTATTGCCCGTGGTCAGAA
                             ttttgac  putative branch site (score: 3)
            taaatcaaat  TA-rich tract