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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctacttttcctctattttcttctccgtacttcacagaagtaaaataataatattctactcaaagtactgaaccttttgtcctttgtatttttttctatagGAAGAAGTGCAAGCTGATAGTGAAAGTGATGATGAAGACCAACAAATCTACAATCCTCTTAAGTTGCCGATGGGTTGGGACGGCAAACCTATACCCTATT

Basic information

species Oryza sativa
transcript LOC_Os03g50850.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g50850.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G178227_T02 (Zea mays), 3'ss of exon 9
-ctacttttcctctattttcttctccgtacttcacagaagtaaaataataatattctactcaaagtactgaaccttttgtcctttgtattt---ttttctatagGAAGAAGTGCAAGCTGATAGTGAAAGTGATGATGAAGACCAACAAATCTACAATCCTCTTAAGTTGCCGATGGGTTGGGACGGCAAACCTATACCCTATT
  |  | ||   | | ||   |     || |       |     ||   | ||  |||||   |||  |  | ||  || | | | ||| |   |||||||||||| || || |||| ||| | ||| |||||||| ||||| |||||||||||||||||||| |||||||||||||||||||| ||||||||||| ||||| |
tatgatcttataccacttggctgaaaatagtatttttca--tgcatggaagtaaactactt--agtttttcaactactggcttatatatatgtattttctatagGAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAGCAACAAATCTACAATCCTCTCAAGTTGCCGATGGGTTGGGATGGCAAACCTATCCCCTACT

upper sequence: LOC_Os03g50850.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv16s0098g00320.t01 (Vitis vinifera), 3'ss of exon 9
-ctacttttcctctattttcttctccgtacttca-caga-agtaaaataataatattctactcaaagtactgaaccttttgtcctttgtatttttttctatagGAAGAAGTGCAAGCTGATAGTGAAAGTGATGATGAAGACCAACAAATCTACAATCCTCTTAAGTTGCCGATGGGTTGGGACGGCAAACCTATACCCTATT
  | |||||  | | | || || || | | |  | || | | |   ||    || |  |||      || | ||| ||| |   |    |||||       |||||||||| ||||| || |  |||||||||||||| || || || ||||| |||||||| |||||||| ||||| ||||| || || ||||| || || |
ctttcttttattttttatttttatctgcattgtatcatacactgccatttgcatgtcttacctctgatagtcaacgtttggatttggaaattttga---gcagGAAGAAGTACAAGCAGACACCGAAAGTGATGATGAGGAGCAGCAGATCTATAATCCTCTCAAGTTGCCAATGGGCTGGGATGGGAAGCCTATTCCTTACT
















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|13420528|gb|AU174618.1|AU174618
EST:     AGAAGAAGCTGACTCTCACATATGAAGAAATGGAAGCAGAACGAGAAGAG                         GAAGAAGTGCAAGCTGATAGTGAAAGTGATGATGAAGACCAACAAATCTAC
genomic: AGAAGAAGCTGACTCTCACATATGAAGAAATGGAAGCAGAACGAGAAGAGgtaatctgca ... ttttctatagGAAGAAGTGCAAGCTGATAGTGAAAGTGATGATGAAGACCAACAAATCTAC
EST: gi|4714942|gb|AU056059.1|AU056059
EST:     AGAAGAAGCTGACNCTCACATATGAAGANATGGAAGCAGAACGAGAAG-G                         GAAGAAGTGCAAGCTGNTAGTGAAAGTGATGATGAAGACCAACAAAATCTA
genomic: AGAAGAAGCTGACTCTCACATATGAAGAAATGGAAGCAGAACGAGAAGAGgtaatctgca ... ttttctatagGAAGAAGTGCAAGCTGATAGTGAAAGTGATGATGAAGACCAACAAA-TCTA
EST: gi|29625135|gb|CB630146.1|CB630146
EST:     AGAAGAAGCTGACTCTCACATATGAAGAAATGGAAGCAGAACGAGAAGAG                         GAGGAAGTGCAAGCTGATAGTGAAAGTGATGATGAAGACCAACAAATCTAC
genomic: AGAAGAAGCTGACTCTCACATATGAAGAAATGGAAGCAGAACGAGAAGAGgtaatctgca ... ttttctatagGAAGAAGTGCAAGCTGATAGTGAAAGTGATGATGAAGACCAACAAATCTAC
EST: gi|29664559|gb|CB660834.1|CB660834
EST:     AGAAGAAGCTGACTCTCACATATGAAGAAATGGAAGCAGAACGAGAAGAG                         GAAGAAGTGCAAGCTGATAGTGAAAGTGATGATGAAGACCAACAAATCTAC
genomic: AGAAGAAGCTGACTCTCACATATGAAGAAATGGAAGCAGAACGAGAAGAGgtaatctgca ... ttttctatagGAAGAAGTGCAAGCTGATAGTGAAAGTGATGATGAAGACCAACAAATCTAC
EST: gi|29675683|gb|CB671958.1|CB671958
EST:     AGAAGAAGCTGACTCTCACATATGAAGAAATGGAAGCAGAACGAGAAGAG                         GAAGAAGTGCAAGCTGATAGTGAAAGTGATGATGAAGACCAACAAATCTAC
genomic: AGAAGAAGCTGACTCTCACATATGAAGAAATGGAAGCAGAACGAGAAGAGgtaatctgca ... ttttctatagGAAGAAGTGCAAGCTGATAGTGAAAGTGATGATGAAGACCAACAAATCTAC
EST: gi|29664555|gb|CB660830.1|CB660830
EST:     AGAAGAAGCTGACTCTCACATATGAAGAAATGGAAGCAGAACGAGAAGAG                         GAAGAAGTGCAAGCTGATAGTGAAAGTGATGATGAAGACCAACAAATCTAC
genomic: AGAAGAAGCTGACTCTCACATATGAAGAAATGGAAGCAGAACGAGAAGAGgtaatctgca ... ttttctatagGAAGAAGTGCAAGCTGATAGTGAAAGTGATGATGAAGACCAACAAATCTAC
EST: gi|218503878|gb|FG953739.1|FG953739
EST:     AGAAGAAGCTGACTCTCACATATGAAGAAATGGAAGCAGAACGAGAAGAG                         GAGGAAGTGCAAGCTG
genomic: AGAAGAAGCTGACTCTCACATATGAAGAAATGGAAGCAGAACGAGAAGAGgtaatctgca ... ttttctatagGAAGAAGTGCAAGCTG
EST: gi|29639904|gb|CB644913.1|CB644913
EST:     AGAAGAAGCTGACTCTCACATATGAAGAAATGGAAGCAGAACGAGAAGAG                         GAAGAAGTGCAAGCTGATAGTGAAAGTGATGATGAAGACCAACAAATCTAC
genomic: AGAAGAAGCTGACTCTCACATATGAAGAAATGGAAGCAGAACGAGAAGAGgtaatctgca ... ttttctatagGAAGAAGTGCAAGCTGATAGTGAAAGTGATGATGAAGACCAACAAATCTAC

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: 59 (upstream exon), 56 (downstream exon)
Score: 18

ATCATTGTACGGACAAAGGAAAATGCAGAGAAGAAGCTGACTCTCACATATGAAGAAATGGAAGCAGAACGAGAAGAGgtaatctgca ... ttttctatagGAAGAAGTGCAAGCTGATAGTGAAAGTGATGATGAAGACCAACAAATCTACAATCCTCTTAAGTTGCCGATGGGTTGGGACGGCAAACCTATACCCTATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataatattctactcaaagtactgaaccttttgtcctttgtatttttttctatagGAAGAAGTGCAAGCTGATAGTGAAAGTGATGATGAAGACCAACAAATCTACAATCCTCTTAAGTTGCCGATGGGTTGGGACGGCAAACCTATACCCTATT
                          ccttttgtcctttgta  CT-rich tract
                                    tttgtatttttttcta  TA-rich tract