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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagtttaacagggaaagcaatttataggttaaagaagtgcttgatttgattgtgcattccttttgaaacagATTAGTGAAGAGGAGGTTTCCTTTTTGACGAAAGGGGAGGATCCATATGATGATTCTGTAATAAAAAAACTCATGCACCCAAATCTGAAACTGCTTCTTG

Basic information

species Oryza sativa
transcript LOC_Os06g12600.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g12600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G072091_T01 (Zea mays), 3'ss of exon 4
----gtaaagtttaacagggaaagcaatt-tataggttaaagaagtgcttgatttg---attgtgcattccttttgaaacagATTAGTGAAGAGGAGGTTTCCTTTTTGACGAAAGGGGAGGATCCATATGATGATTCTGTAATAAAAAAACTCATGCACCCAAATCTGAAACTGCTTCTTG
     ||   | |||         ||  | || |||  ||    ||| || |||||   ||| ||| |  ||||| ||| || | ||||||||||||||||||||| | || || || |||||||| ||||||||| | ||  |||| ||||| |||||| |||| |||||  |||||||||
gttgctattctgtaaattatggttcagctgtagaggcaaatcttgtg-ttaatttgtgcattttgcttctcttttcaaaaagGTAAGTGAAGAGGAGGTTTCCTTTCTCACAAATGGAGAGGATCCTTATGATGATGCCGTTGTAAAGAAACTTATGCACTCAAACCTGAAGTTGCTTCTTG
















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|29685992|gb|CB682267.1|CB682267
EST:     ATGCTAGAGATGGTATTCTGAGCATATGGGAAACTGCTGATGTTATCAAG                         ATTAGTGAAGAGGAGGTTTCCTTTTTGACGAAAGGGGAGGATCCATATGAT
genomic: ATGCTAGAGATGGTATACTGAGCATATGGGAAACTGCTGATGTTATCAAGgtaaagttta ... tttgaaacagATTAGTGAAGAGGAGGTTTCCTTTTTGACGAAAGGGGAGGATCCATATGAT
EST: gi|29632918|gb|CB637927.1|CB637927
EST:     ATGCTAGAGATGGTATACTGAGCATATGGGAAACTGCTGATGTTATCAAG                         ATTAGTGAAGAGGAGGTTTCCTTTTTGACGAAAGGGGAGGATCCATATGAT
genomic: ATGCTAGAGATGGTATACTGAGCATATGGGAAACTGCTGATGTTATCAAGgtaaagttta ... tttgaaacagATTAGTGAAGAGGAGGTTTCCTTTTTGACGAAAGGGGAGGATCCATATGAT
EST: gi|66917120|gb|CX103968.1|CX103968
EST:     ATGCTAGAGATGGTATACTGAGCATATGGGAAACTGCTGATGTTATCAAG                         ATTAGTGAAGAGGAGGTTTCCTTTTTGACGAAAGGGGAGGATCCATATGAT
genomic: ATGCTAGAGATGGTATACTGAGCATATGGGAAACTGCTGATGTTATCAAGgtaaagttta ... tttgaaacagATTAGTGAAGAGGAGGTTTCCTTTTTGACGAAAGGGGAGGATCCATATGAT
EST: gi|86859066|gb|CI276999.1|CI276999
EST:     ATGCTAGAGATGGTATACTGAGCATATGGGAAACTGCTGATGTTATCAAG                         ATTAGTGAAGAGGAGGTTTCCTTTTTGACGAAAGGGGAGGATCCATATGAT
genomic: ATGCTAGAGATGGTATACTGAGCATATGGGAAACTGCTGATGTTATCAAGgtaaagttta ... tttgaaacagATTAGTGAAGAGGAGGTTTCCTTTTTGACGAAAGGGGAGGATCCATATGAT
EST: gi|29685991|gb|CB682266.1|CB682266
EST:     ATGCTAGAGATGGTATACTGAGCATATGGGAAACTGCTGATGTTATCAAG                         ATTAGTGAAGAGGAGGTTTCCTTTTTGACGAAAGGGGAGGATCCATATGAT
genomic: ATGCTAGAGATGGTATACTGAGCATATGGGAAACTGCTGATGTTATCAAGgtaaagttta ... tttgaaacagATTAGTGAAGAGGAGGTTTCCTTTTTGACGAAAGGGGAGGATCCATATGAT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 73 (upstream exon), 74 (downstream exon)
Score: 27

AATTTCGTATGATCCGAATTTGAGGCTCCCACTGTGGTCATCAGCTGATGATGCTAGAGATGGTATACTGAGCATATGGGAAACTGCTGATGTTATCAAGgtaaagttta ... tttgaaacagATTAGTGAAGAGGAGGTTTCCTTTTTGACGAAAGGGGAGGATCCATATGATGATTCTGTAATAAAAAAACTCATGCACCCAAATCTGAAACTGCTTCTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaatttataggttaaagaagtgcttgatttgattgtgcattccttttgaaacagATTAGTGAAGAGGAGGTTTCCTTTTTGACGAAAGGGGAGGATCCATATGATGATTCTGTAATAAAAAAACTCATGCACCCAAATCTGAAACTGCTTCTTG
                           atttgat  putative branch site (score: 27)
                                      cattcctttt  putative PPT
            ttaaagaa  TA-rich tract