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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttttgcattcgtacttgagaaaagtatactatctaaagtttatagagctaaggccagagtattttttttaaatgctattagGTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACTAAAAAGCTTGAGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTG

Basic information

species Oryza sativa
transcript LOC_Os03g20100.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g20100.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G862107_T01 (Zea mays), 3'ss of exon 4
gtattttttgcattcgtacttgagaaaagtatactatctaaagtttatagagctaaggccagagtattttttttaaatgctattagGTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACTAAAAAGCTTGAGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTG
||||| |  ||  | || ||||       |    |||| | | || || |||||||  |||  | ||| | ||     |||  ||||||||||| || ||||||||||||||||||||||| || || ||||||||||| ||||||||||| ||||||||||||||||| |||||||| |||||||
gtattgtg-gctgtggttcttggttgttatgccatatccatacttaatggagctaacaccaatgaattctgtt-----gcttatagGTTATGATACTGAGCCATGACCGTGAAAGAGGCCGAGTCAGCCTTTCTACTAAGAAGCTTGAGCCAACACCTGGTGACATGATCCGCAATCCCAAGCTTG

upper sequence: LOC_Os03g20100.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA09G03660.1 (Glycine max), 3'ss of exon 4
gtattttttgcattcgtacttgagaaaa-gtatactatctaaagtttatagagctaaggccagagt---attttttttaa-atgctattagGTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACTAAAAAGCTTGAGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTG
        |  |    |  |     |   |  || |  ||     | | |||  | | |    | |   || |  ||||  ||    |||||| |||||  |||| |||||||| || |||||  | || |||||||| || || ||| | || || ||||||||||||||||||||||||||||||||||
-------gtaaacctatgataagctatgtgagtatttgcttggaatcacagatgttatgtggaaattaaatctaatttattatttggttagGTGATGATCTTAAGTCATGACCGAGAGAGAGGAAGGGTAAGTCTTTCCACAAAGAAGTTGGAACCCACACCTGGTGACATGATTCGCAATCCAAAGCTTG

upper sequence: LOC_Os03g20100.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA15G14550.1 (Glycine max), 3'ss of exon 4
gtattttttgcattcgtacttgagaaaagta-tactatctaaagtttatagagctaa---ggccagagtattttttttaa-atgctattagGTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACTAAAAAGCTTGAGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTG
        |  | |  | ||     |    | || |  ||     | | |||  | |   || || |  || || ||||  ||    |||||| |||||  |||| |||||||| || ||||| || || |||||||| || || ||| | || || || |||||||||||||||||||||||||||||||
-------gtaaacttatgctaagctatgccagtatttgcttggaatcacagatgtcatgtggacataaaatcttgtttattatttggttagGTGATGATCTTAAGTCATGACCGAGAGAGAGGACGAGTAAGTCTTTCCACAAAGAAGTTGGAACCCACGCCTGGTGACATGATTCGCAATCCAAAGCTTG

upper sequence: LOC_Os03g20100.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA17G04190.1 (Glycine max), 3'ss of exon 4
gtattttttgcattcgtacttgagaaaagtatactatctaaagtttatagagctaaggccagagtattttttttaaatgctattagGTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACTAAAAAGCTTGAGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTG
      ||  | |   |   ||  |   | ||  |  |  |   |  | ||  |||    |    |  ||| |||  || |  ||||| |||||  ||||||||||||| || ||||| || || |||||||| ||||| ||| | ||||| |||||||| |||||||||||||||||||||||||
-----gttaacctatattaatgttatgtggatgtttgcctagactcttggacataaaa--atctcaagtttcttatttgtt--tagGTGATGATCTTAAGCCATGACCGAGAGAGAGGTCGAGTAAGTCTTTCCACTAAGAAGTTAGAGCCCACACCTGGAGACATGATTCGCAATCCAAAGCTTG

upper sequence: LOC_Os03g20100.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv05s0077g00450.t01 (Vitis vinifera), 3'ss of exon 4
-----------gtattttttgcattc-gtacttgagaaaagtatactatctaaagtttatagagctaaggccagagtatttt---ttttaaatgctattagGTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACTAAAAAGCTTGAGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTG
            |||  | |  || | ||     |      |  |||  ||| || | |   |    | |      | ||||   |||    |||| | |||||||||| || ||||| |||||||| ||||||||||| ||||| || ||||| ||| | || || || ||||| |||||||||||||||||||||||||
gtttgcctataatatactgtcaatactgtcaccaaatttcttccactccctacagataaataaatgtatgtatttattttttgtgtttctcttgctgt-agGTTATGATCCTGAGCCACGACCGTGAGAGAGGCCGTGTAAGTCTCTCAACTAAGAAGTTAGAACCTACCCCTGGAGACATGATTCGCAATCCAAAGCTTG

upper sequence: LOC_Os03g20100.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S32_313V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------------------------------------------------------------------------------gtattttttgcattcgtacttgagaaaagtatact--atctaaagtttatagagctaaggccag--agtattttttttaaatgctatt----agGTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACTAAAAAGCTTGAGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTG
                                                                                               || || ||| | |||||   | |||   |   |||  || |     |  ||  | |  | |     | ||   | | |   ||  |||    |||| |||||| | || || ||    || ||||||||| ||||| | || || || ||||||||||| ||||||||||||||| | ||||||||| |  | |
gtacttagtcttaccagtctttgtagaagtgaatggtgtttagtccgtgcacatggatcttcacgaactatcacgcatgttgacataagttgattgtcttctttcc-ttcgtttataagacttgatgacttcatatgtgagtggtaaggatgtgtcttaccattaacatgtcttgttgtgattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACCAAGAAGCTTGAGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGG

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|86546307|gb|CI186513.1|CI186513
EST:     TGCGGACATCTCGACAGTTCTGCAACCAGGAGATACGCTCAAG                         GTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACT
genomic: TGCGGACATCTCGACAGTTCTGCAACCAGGAGATACGCTCAAGgtattttttg ... atgctattagGTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACT
EST: gi|18388863|gb|BM422061.1|BM422061
EST:     CCCGTGTT-CCGACATCTCGACAGTTCTGCAACCAGGAGATACGCTCAAG                         GTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACT
genomic: -CCGTGTTGCGGACATCTCGACAGTTCTGCAACCAGGAGATACGCTCAAGgtattttttg ... atgctattagGTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACT
EST: gi|218483682|gb|FG943816.1|FG943816
EST:     ACCGTGTTGCGGACATCTCGACAGTTCTGCAACCAGGAGATACGCTCAAG                         GTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACT
genomic: ACCGTGTTGCGGACATCTCGACAGTTCTGCAACCAGGAGATACGCTCAAGgtattttttg ... atgctattagGTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACT
EST: gi|29638067|gb|CB643076.1|CB643076
EST:     ACCGTGTTGCGGACATCTCGACAGTTCTGCAACCAGGAGATACGCTCAAG                         GTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACT
genomic: ACCGTGTTGCGGACATCTCGACAGTTCTGCAACCAGGAGATACGCTCAAGgtattttttg ... atgctattagGTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACT
EST: gi|29662710|gb|CB658985.1|CB658985
EST:     ACCGTGTTGCGGACATCTCGACAGTTCTGCAACCAGGAGATACGCTCAAG                         GTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACT
genomic: ACCGTGTTGCGGACATCTCGACAGTTCTGCAACCAGGAGATACGCTCAAGgtattttttg ... atgctattagGTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACT
EST: gi|29660922|gb|CB657197.1|CB657197
EST:     ACCGTGTTGCGGACATCTCGACAGTTCTGCAACCAGGAGATACGCTCAAG                         GTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACT
genomic: ACCGTGTTGCGGACATCTCGACAGTTCTGCAACCAGGAGATACGCTCAAGgtattttttg ... atgctattagGTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACT
EST: gi|29645770|gb|CB650777.1|CB650777
EST:     ACCGTGTTGCGGACATCTCGACAGTTCTGCAACCAGGAGATACGCTCAAG                         GTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACT
genomic: ACCGTGTTGCGGACATCTCGACAGTTCTGCAACCAGGAGATACGCTCAAGgtattttttg ... atgctattagGTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACT
EST: gi|87010736|gb|CI312428.1|CI312428
EST:     ACCGTGTTGCGGACATCTCGACAGTTCTGCAACCAGGAGATACGCTCAAG                         GTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACT
genomic: ACCGTGTTGCGGACATCTCGACAGTTCTGCAACCAGGAGATACGCTCAAGgtattttttg ... atgctattagGTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACT
EST: gi|29660751|gb|CB657026.1|CB657026
EST:     ACCGTGTTGCGGACATCTCGACAGTTCTGCAACCAGGAGATACGCTCAAG                         GTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACT
genomic: ACCGTGTTGCGGACATCTCGACAGTTCTGCAACCAGGAGATACGCTCAAGgtattttttg ... atgctattagGTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACT
EST: gi|29638932|gb|CB643941.1|CB643941
EST:     ACCGTGTTGCGGACATCTCGACAGTTCTGCAACCAGGAGATACGCTCAAG                         GTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACT
genomic: ACCGTGTTGCGGACATCTCGACAGTTCTGCAACCAGGAGATACGCTCAAGgtattttttg ... atgctattagGTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACT
EST: gi|218480258|gb|FG945869.1|FG945869
EST:     ACCGTGTTGCGGACATCTCGACAGTTCTGCAACCAGGAGATACGCTCAAG                         GTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACT
genomic: ACCGTGTTGCGGACATCTCGACAGTTCTGCAACCAGGAGATACGCTCAAGgtattttttg ... atgctattagGTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACT

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: 74 (upstream exon), 74 (downstream exon)
Score: 115

CGACATTGGTGGAATCAATGGCCTTCTCCATGTCAGCCAGATTAGTCATGACCGTGTTGCGGACATCTCGACAGTTCTGCAACCAGGAGATACGCTCAAGgtattttttg ... atgctattagGTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACTAAAAAGCTTGAGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactatctaaagtttatagagctaaggccagagtattttttttaaatgctattagGTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACTAAAAAGCTTGAGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTG
    atctaaa  putative branch site (score: 115)
                               agtattttttttaaat  TA-rich tract