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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAGgtaaagccagtttaattgatttaaaaaaaactgacatgatatcttgagttaagtggtacatcttctcaaaacagatccaatatgttgagtgcttttcttttcaggaaaatgcattttttacttatttaccgtttcttgcag

Basic information

species Oryza sativa
transcript LOC_Os02g02690.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g02690.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G068277_T02 (Zea mays), 5'ss of exon 7
CTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAGgtaaagccagtttaattgatttaaaaaaaactgacatgatatcttgagttaagtggtacatcttctc---aaaacagatccaatatgttgagtgcttttc-ttttcaggaaaatgcatttttt--acttatttaccgtttcttgcag
|||||| ||||||||||| ||||||||||| || |||||||| |||||||| ||||| || ||||||||||| ||  |    ||| ||| |   |      || || |  | || ||| | || | || | || |    || |  |||   || ||||  |||| |||  |||||||  ||   | || ||   || |||| || | || ||||||
CTATCTGGAGCATCATCTATTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAGgtatagttaaggcaatcgatcttgtagtg---gatat-acttttttagtcatgttgcacttgttattcataagatggatttgatttgttaggtgcctttggttttcagcgaaggaccttcttgtaacatattaactgctt-ttgcag

upper sequence: LOC_Os02g02690.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G068277_T01 (Zea mays), 5'ss of exon 6
-------------------------------CTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAGgtaaagccagtttaattgatttaaaaaaaactgacatgatatcttgagttaagtggtacatcttctc---aaaacagatccaatatgttgagtgcttttc-ttttcaggaaaatgcatttttt--acttatttaccgtttcttgcag
                               |||||| ||||||||||| ||||||||||| || |||||||| |||||||| ||||| || ||||||||||| ||  |    ||| ||| |   |      || || |  | || ||| | || | || | || |    || |  |||   || ||||  |||| |||  |||||||  ||   | || ||   || |||| || | || ||||||
TATATATATATATATATTACTTTGATTCCAGCTATCTGGAGCATCATCTATTGCGTGACACTTACACCAAGGACACAGTACCAGCACTGCACAGGATCAGgtatagttaaggcaatcgatcttgtagtg---gatat-acttttttagtcatgttgcacttgttattcataagatggatttgatttgttaggtgcctttggttttcagcgaaggaccttcttgtaacatattaactgctt-ttgcag
















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|88247791|gb|CI247640.1|CI247640
EST:     TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAG                         GAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
genomic: TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAGgtaaagccag ... tttcttgcagGAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
EST: gi|89182448|gb|CI113817.1|CI113817
EST:     TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAG                         GAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
genomic: TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAGgtaaagccag ... tttcttgcagGAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
EST: gi|88481854|gb|CI419125.1|CI419125
EST:     CGGCACTACATAGGATCAG                         GAAATATTTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
genomic: CGGCACTACATAGGATCAGgtaaagccag ... tttcttgcagGAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
EST: gi|86428585|gb|CI075266.1|CI075266
EST:     TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTAAATAGGATCAG                         GAAANATTTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
genomic: TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAGgtaaagccag ... tttcttgcagGAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
EST: gi|86491300|gb|CI133933.1|CI133933
EST:     TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAG                         GAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
genomic: TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAGgtaaagccag ... tttcttgcagGAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
EST: gi|163917926|gb|EG714758.1|EG714758
EST:     TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAG                         GAAATATCTAGTAGAGGCCACAAAAGAAGCATCCAATTCTTATACTGAAGC
genomic: TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAGgtaaagccag ... tttcttgcagGAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
EST: gi|86426334|gb|CI071431.1|CI071431
EST:     TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAG                         GAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
genomic: TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAGgtaaagccag ... tttcttgcagGAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
EST: gi|86505602|gb|CI148235.1|CI148235
EST:     TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAG                         GAAATATCTAGTAGAGCCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
genomic: TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAGgtaaagccag ... tttcttgcagGAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
EST: gi|88248278|gb|CI248127.1|CI248127
EST:     TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAG                         GAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
genomic: TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAGgtaaagccag ... tttcttgcagGAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
EST: gi|86501777|gb|CI144410.1|CI144410
EST:     TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAG                         GAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
genomic: TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAGgtaaagccag ... tttcttgcagGAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
EST: gi|88227499|gb|CI226979.1|CI226979
EST:     TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAG                         GAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
genomic: TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAGgtaaagccag ... tttcttgcagGAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
EST: gi|88990699|gb|CI108086.1|CI108086
EST:     TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAG                         GAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
genomic: TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAGgtaaagccag ... tttcttgcagGAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
EST: gi|396941424|gb|HO188633.1|HO188633
EST:     TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAG                         GAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACCGAAGC
genomic: TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAGgtaaagccag ... tttcttgcagGAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
EST: gi|88245688|gb|CI245537.1|CI245537
EST:     AAGGAAACAGTACCGGCACTACATAGGATCAG                         GAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
genomic: AAGGAAACAGTACCGGCACTACATAGGATCAGgtaaagccag ... tttcttgcagGAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
EST: gi|88974820|gb|CI023114.1|CI023114
EST:     TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAG                         GAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
genomic: TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAGgtaaagccag ... tttcttgcagGAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
EST: gi|94362670|gb|CI052789.1|CI052789
EST:     TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAG                         GAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
genomic: TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAGgtaaagccag ... tttcttgcagGAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
EST: gi|86539112|gb|CI179318.1|CI179318
EST:     TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAG                         GAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
genomic: TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAGgtaaagccag ... tttcttgcagGAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
EST: gi|89167956|gb|CI109160.1|CI109160
EST:     TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAG                         GAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
genomic: TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAGgtaaagccag ... tttcttgcagGAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
EST: gi|163926568|gb|EG712432.1|EG712432
EST:     TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAG                         GAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
genomic: TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAGgtaaagccag ... tttcttgcagGAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
EST: gi|88221660|gb|CI221616.1|CI221616
EST:     TTGCGTGACACCTATACCAAGGATACAGTACCGGCACTACATAGGATCAG                         GAAATATGTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
genomic: TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAGgtaaagccag ... tttcttgcagGAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
EST: gi|88281120|gb|CI402318.1|CI402318
EST:     CATAGGATCAG                         GAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
genomic: CATAGGATCAGgtaaagccag ... tttcttgcagGAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
EST: gi|86503019|gb|CI145652.1|CI145652
EST:     TTGCGTGACACCTAGACCAAGGAAACAGTACCGGCACTACATAGGATCAG                         GAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
genomic: TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAGgtaaagccag ... tttcttgcagGAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
EST: gi|86426368|gb|CI071465.1|CI071465
EST:     TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAG                         GAAANATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC
genomic: TTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAGgtaaagccag ... tttcttgcagGAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGC

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: 45 (upstream exon), 44 (downstream exon)
Score: 2

CTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAGgtaaagccag ... tttcttgcagGAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATCTTGAGCATCATCTCTTGCGTGACACCTATACCAAGGAAACAGTACCGGCACTACATAGGATCAGgtaaagccagtttaattgatttaaaaaaaactgacatgatatcttgagttaagtggtacatcttctcaaaacagatccaatatgttgagtgcttttcttttcaggaaaatgcattttttacttatttaccgtttcttgcag

- - - - - - - - - - - - - - - - - -  AAGGAA