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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgagaacatgcgtgctcgatcttaggtatttcctctggtctagcatcagcaagacaactccctgcctagtgacaaaatagtttttaccttgatgtgcagGCAATGGCCCAGGTTGGAGGTCTGGTTATGTTGCAACCTGAAGTTGGTGGATCTCGAGAGAACTTCTTTTTTGCAGGGATTGATAAAGTGAGATTTCGTA

Basic information

species Oryza sativa
transcript LOC_Os05g36000.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g36000.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G055667_T01 (Zea mays), 3'ss of exon 3
atgagaacatgcgtgctcgat--cttaggtatttcctctggtctagcatcagcaagacaactccctgcctagtgacaaaatagtttttaccttgatgtg-cagGCAATGGCCCAGGTTGGAGGTCTGGTTATGTTGCAACCTGAAGTTGGTGGATCTCGAGAGAACTTCTTTTTTGCAGGGATTGATAAAGTGAGATTTCGTA
     |   |   | |  ||   | |      | ||| | ||||      | |        |  ||     ||     |  | |||||||| |||| |  ||||||||||||||||| |||||  | || |||||||| |||||||| ||||||||||||||||||||||||||||| ||||| ||||||||||| || || |
---gcatttttttttcctgaagacattaaagctacctattgtctcaagcaaactttctggttgacttgtacgtactggacaattttttaccatgatttttcagGCAATGGCCCAGGTCGGAGGAATAGTGATGTTGCAGCCTGAAGTGGGTGGATCTCGAGAGAACTTCTTTTTTGCGGGGATCGATAAAGTGAGGTTCCGGA

upper sequence: LOC_Os05g36000.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G05800.1 (Glycine max), 3'ss of exon 3
atgagaacatgcgtgctcgatcttaggtatttcctctggtctagcatcagcaagacaactccctgcctagtgacaaaatagtttttaccttgatg--tgcagGCAATGGCCCAGGTTGGAGGTCTGGTTATGTTGCAACCTGAAGTTGGTGGATCTCGAGAGAACTTCTTTTTTGCAGGGATTGATAAAGTGAGATTTCGTA
   |   |       ||      |    |  |  ||| || |    || |    |  | ||       | ||   | ||     | |  |   |   ||||||||||||| || ||||| ||| |||| ||||||||||||||||| || || ||||| || |||||||| ||||| || || || |||||| | |||||||
--aacttctgaaagactttgagatgaacaactagtcttgtatgatttctgttgcaataatcttctttaaatgtggacatgaacatgaggtcatttgctgcagGCAATGGCACAAGTTGGTGGTTTGGTCATGTTGCAACCTGAAGTGGGAGGTTCTCGTGAAAACTTCTTCTTTGCTGGAATAGACAAAGTGCGGTTTCGTA

upper sequence: LOC_Os05g36000.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G19200.1 (Glycine max), 3'ss of exon 2
----------atgagaacatgcgtgctcgatcttaggtatttcctctggtctagca-tcagcaagacaactccctgcctagtgacaaaatagtttttaccttgatgtgcagGCAATGGCCCAGGTTGGAGGTCTGGTTATGTTGCAACCTGAAGTTGGTGGATCTCGAGAGAACTTCTTTTTTGCAGGGATTGATAAAGTGAGATTTCGTA
              |||  |  | ||  ||||||   |  || ||||| | ||  | || ||   | ||      |   |   |||| |    |||| |       ||||||||||||| || ||||| ||| |||| ||||||||||||||||| || || ||||| || |||||||| ||||| || || || |||||| | |||||||
aacctggaatgcatgaaagtaggggcgggatcttgtatgatttctctgttgtaataatctgctttaaaa----gcggacatgaacaagaggtcttttgc-------tgcagGCAATGGCACAAGTTGGTGGTTTGGTCATGTTGCAACCTGAAGTGGGAGGCTCTCGTGAAAACTTCTTCTTTGCTGGAATAGACAAAGTGCGGTTTCGTA

upper sequence: LOC_Os05g36000.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA05G24650.1 (Glycine max), 3'ss of exon 3
atgagaacatgcgtgctcgatcttaggtatttcctctggtctagcat---cagcaagacaactcc--ctgcctagtgacaaaatagtttttaccttgatgtgcagGCAATGGCCCAGGTTGGAGGTCTGGTTATGTTGCAACCTGAAGTTGGTGGATCTCGAGAGAACTTCTTTTTTGCAGGGATTGATAAAGTGAGATTTCGTA
  ||   |||  ||   | | |   |  |   | | ||   ||  ||   ||||| |    ||     |  |||  |      | |  ||  | || ||  ||||||||| || || ||||| ||  ||||||||||||| ||||||||||| || ||||| ||||| ||||| ||||| || || || |||||| ||||| | |
--gattgcataagt-tccaacccatgaaagagcttttgcgttaagattgacagcagggtgtctgtaattttctaaaggttctgttgaattatctttaat--gcagGCAATCGCACAAGTTGGTGGCTTGGTTATGTTGCAGCCTGAAGTTGGAGGTTCTCGTGAGAATTTCTTCTTTGCTGGAATAGACAAAGTGCGATTTAGGA

upper sequence: LOC_Os05g36000.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G07870.1 (Glycine max), 3'ss of exon 3
atgagaacatgcgtgctcgatctta-ggtatttcctctggtctagcatcagcaagacaactccctgcctagtgacaaaatagttt---ttaccttgatgtgcagGCAATGGCCCAGGTTGGAGGTCTGGTTATGTTGCAACCTGAAGTTGGTGGATCTCGAGAGAACTTCTTTTTTGCAGGGATTGATAAAGTGAGATTTCGTA
              | || | || | || |   | | ||   || |||   ||| |     |  |   |    | |   |   ||   ||| ||     ||||||||||||| |||||||| ||  |||||||||||||||||||| |||| || |||||  | || ||||| ||||| || || || |||||| ||||| | |
---ctgctgcttaagatccaactaatggaagagcttttgtgttaacattgacaacaggtgcctgtaattttctaaaggttctgttgaattatctctg-atgcagGCAATGGCACAGGTTGGTGGCTTGGTTATGTTGCAACCTGAAATTGGAGGTTCTCGCAATAATTTCTTCTTTGCTGGAATAGACAAAGTGCGATTTAGGA

upper sequence: LOC_Os05g36000.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT2G22230.1 (Arabidopsis thaliana), 3'ss of exon 3
atgagaacatgcgtgctcgatcttaggtatttcctc----tggtctagcatcagcaagacaactccctgcctagtgacaaaatagtttttaccttgatgtgcagGCAATGGCCCAGGTTGGAGGTCTGGTTATGTTGCAACCTGAAGTTGGTGGATCTCGAGAGAACTTCTTTTTTGCAGGGATTGATAAAGTGAGATTTCGTA
    || ||    | ||| ||   |   ||  || |    ||||  || || |        |    |     | ||| ||   ||  |||    ||   ||||||||||||| || || |||||| | || ||| |||| || ||||| || || |||| ||| |||||||| ||||| || |||||||||||||||||||| |
-gaggatcacagatcctctataaaaaagataaccgccatatggttgagtattaatgtcttgaagatcatttcactgaaaagtcagagtttg---tgtattgcagGCAATGGCGCAAGTCGGAGGTATAGTAATGCTGCAGCCGGAAGTAGGAGGCTCTCAAGATAACTTCTTCTTTGCTGGTATTGATAAAGTGAGATTTCGCA

upper sequence: LOC_Os05g36000.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv12s0055g01100.t01 (Vitis vinifera), 3'ss of exon 3
atgagaacatgcgtgctcgatcttaggtatttcctctggtctagca-tcagcaagacaactccctgcct-----agtgacaaaatagtttttaccttgatg--tgcagGCAATGGCCCAGGTTGGAGGTCTGGTTATGTTGCAACCTGAAGTTGGTGGATCTCGAGAGAACTTCTTTTTTGCAGGGATTGATAAAGTGAGATTTCGTA
            |  ||    | ||  |||    |  ||  |   | | |   |  |        | ||     ||||  ||| |  ||||    ||| ||  | ||||||||||| |||||||| ||  |||| ||| | ||||||||||| || || ||||| || || ||||| ||||| || ||||| ||||| ||||| || |
--------ggaaggccttacacataaatatactgtaaggctttatacttaaacatgctgtctttggtctgatggagtggtaaattttttttctgtttgttggatacagGCAATGGCACAGGTTGGTGGCTTGGTAATGCTACAACCTGAAGTGGGAGGCTCTCGTGAAAATTTCTTCTTTGCTGGAATTGACAAAGTAAGATTCCGGA

upper sequence: LOC_Os05g36000.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv00s0357g00070.t01 (Vitis vinifera), 3'ss of exon 3
atgagaacatgcgtgctcgatcttaggtatttcc--tctggtctagcatcagcaagacaactccctgcctagtgacaaaatagtttttaccttgatgtgcagGCAATGGCCCAGGTTGGAGGTCTGGTTATGTTGCAACCTGAAGTTGGTGGATCTCGAGAGAACTTCTTTTTTGCAGGGATTGATAAAGTGAGATTTCGTA
 ||  ||  |   |   | | | |   | | ||   | |||  | | ||     | |     | ||    | ||   |   |  |  |   | |  || ||||||||||| |||||||| ||  |||||||| | |||||||||||||| || ||||| ||||| ||||| |||||||| || || |||||||| || |  |
ttgttaaattctttttacaaccctgtttctatcaagtttggatttggatacattacatgtgcctctagtaattgctgatgaaagtggttggtgg--gtccagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGCTCTCGTGAGAATTTCTTCTTTGCAGGAATCGACAAAGTGAGGTTCCAGA

upper sequence: LOC_Os05g36000.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv00s0357g00020.t01 (Vitis vinifera), 3'ss of exon 3
atgagaacatgcgtgctcgatcttaggtatttcc--tctggtctagcatcagcaagacaactccctgcctagtgacaaaatagtttttaccttgatgtgcagGCAATGGCCCAGGTTGGAGGTCTGGTTATGTTGCAACCTGAAGTTGGTGGATCTCGAGAGAACTTCTTTTTTGCAGGGATTGATAAAGTGAGATTTCGTA
 ||  ||  |   |   | | | |   | | ||   |  |   | | ||     | |     | ||    | ||   |   |  |  |   | |  || ||||||||||| |||||||| ||  |||||||| | |||||||||||||| || ||||| ||||| ||||| |||||||| || || |||||||| || || |
ttgttaaattctttttacaaccctgtttctatcaagttcgcatttggatacattacatgtgcctctagtaattgctgatgaaagtggttggtgg--gtccagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGCTCTCGTGAGAATTTCTTCTTTGCAGGAATCGACAAAGTGAGGTTCCGGA

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|88543080|gb|CI470452.1|CI470452
EST:     ACCTATAATGCCTGGTGTTCTTATGGTGGAG                         GCAATGGCCCAGGTTGGAGTTCTGGTTATGTTGCAACCTGAAGTT-GTGGA
genomic: ACCTATAATGCCTGGTGTTCTTATGGTGGAGgtatacattg ... tgatgtgcagGCAATGGCCCAGGTTGGAGGTCTGGTTATGTTGCAACCTGAAGTTGGTGGA
EST: gi|86523011|gb|CI163217.1|CI163217
EST:     CAGGGCATTTTCCGGAGAGACCTATAATGCCTGGTGTTCTTATAGTGGAG                         GCAATGGCCCAGGTTGGAGGTCTGGTTATGTTGCAACCTGAAGTTGGTGGA
genomic: CAGGGCATTTTCCGGAGAGACCTATAATGCCTGGTGTTCTTATGGTGGAGgtatacattg ... tgatgtgcagGCAATGGCCCAGGTTGGAGGTCTGGTTATGTTGCAACCTGAAGTTGGTGGA
EST: gi|86527691|gb|CI167897.1|CI167897
EST:     CAGGGCATTTTCCGGAGAGACCTATAATGCCTGGTGTTCTTATAGTGGAG                         GCAATGGCCCAGGTTGGAGGTCTGGTTATGTTGCAACCTGAAGTTGGTGGA
genomic: CAGGGCATTTTCCGGAGAGACCTATAATGCCTGGTGTTCTTATGGTGGAGgtatacattg ... tgatgtgcagGCAATGGCCCAGGTTGGAGGTCTGGTTATGTTGCAACCTGAAGTTGGTGGA

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: 42 (upstream exon), 74 (downstream exon)
Score: 9

GGAATATGCTGTTGGGATCAAGAATGTTACAATAAATGATAACTTCTTCCCAGGGCATTTTCCGGAGAGACCTATAATGCCTGGTGTTCTTATGGTGGAGgtatacattg ... tgatgtgcagGCAATGGCCCAGGTTGGAGGTCTGGTTATGTTGCAACCTGAAGTTGGTGGATCTCGAGAGAACTTCTTTTTTGCAGGGATTGATAAAGTGAGATTTCGTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcagcaagacaactccctgcctagtgacaaaatagtttttaccttgatgtgcagGCAATGGCCCAGGTTGGAGGTCTGGTTATGTTGCAACCTGAAGTTGGTGGATCTCGAGAGAACTTCTTTTTTGCAGGGATTGATAAAGTGAGATTTCGTA
                                          ccttgat  putative branch site (score: 9)
                                    tttttacctt  CT-rich tract
                           acaaaatagttttta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgagaacatgcgtgctcgatcttaggtatttcctctggtctagcatcagcaagacaactccctgcctagtgacaaaatagtttttaccttgatgtgcagGCAATGGCCCAGGTTGGAGGTCTGGTTATGTTGCAACCTGAAGTTGGTGGATCTCGAGAGAACTTCTTTTTTGCAGGGATTGATAAAGTGAGATTTCGTA

- - - - -tgcgtgc
- - - - - - - - - - - - - - - - - - - - - - catcagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gacaaaa