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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actattcttcattgtctattttaactgttgagttacatagttttgtactctcactcttatacctaacttttccctggaatgaaaccttttctgtatacagGGCAGAATCACAGTCCCTGCATCACTGGTCTGCCAAATATTGTCCTCTTTTGCCACCCCCCAGGTCTACTATCGCAGCTGCATTCAGCCCAGATGGGAAA

Basic information

species Oryza sativa
transcript LOC_Os02g18820.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g18820.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G353548_T04 (Zea mays), 3'ss of exon 2
------------------------------actattcttcattgtctattttaactgttgagttacatagttttgtactctcactcttatacctaacttttccctggaatgaaaccttttctgtatacagGGCAGAATCACAGTCCCTGCATCACTGGTCTGCCAAATATTGTCCTCTTTTGCCACCCCCCAGGTCTACTATCGCAGCTGCATTCAGCCCAGATGGGAAA
                              |  |   | ||     ||||   |||  |||||  |||     | |  || ||   ||||   ||     |   | |  | ||  | |  |||| |||||||||||||||| ||||||||||| |||||||||||| ||||| |||||||||||||| || ||||| ||||| |||||||| ||||| |||||||| |||
gtaaggatttttttgtctcaatgatattcaagaacagtccacaacatattc--actactgagtcgcatgtgagtctgttcgcatctttatttttattggctgattcgtttaaa--cctcactgtgtacagGGCAGAATCACTGTCCCTGCATCGCTGGTCTGCCAAGTATTGCCCTCTTTTGCCACCTCCTAGGTCAACTATTGCAGCTGCTTTCAGTCCAGATGGAAAA

upper sequence: LOC_Os02g18820.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G007229_T01 (Zea mays), 3'ss of exon 2
--------------------actattcttcatt-gtc-----tattttaactgttgagttacatagttttgtactctcactcttatacctaacttttccctggaatgaaaccttttctgtatacagGGCAGAATCACAGTCCCTGCATCACTGGTCTGCCAAATATTGTCCTCTTTTGCCACCCCCCAGGTCTACTATCGCAGCTGCATTCAGCCCAGATGGGAAA
                      ||||    |   |||     ||| |  |||  ||||| ||||     | |  || ||   || |   |     ||  || |  | ||  | |  |||   ||||||||||||||||||||||||||  |||||||||||| ||||| |||||||||||||| || ||||| ||||| |||||||| ||||| |||||||| |||
gtaaggaaagccttttttgagatatttaagaccagtccataatatatcgactactgagtcacatgtgagtctgttcacatctttcttttttttggttggctcgtttaaa--cctcactgggaacagGGCAGAATCACAGTCCCTGCATAGCTGGTCTGCCAAGTATTGCCCTCTTTTGCCACCTCCTAGGTCAACTATTGCAGCTGCTTTCAGTCCAGATGGAAAA

upper sequence: LOC_Os02g18820.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA03G32620.2 (Glycine max), 3'ss of exon 2
---------actattc--ttcattgtctattttaactgttgag------ttacatagttttgtactctcactcttat--acctaacttttccctggaatgaaaccttttctgta-----ta-cagGGCAGAATCACAGTCCCTGCATCACTGGTCTGCCAAATATTGTCCTCTTTTGCCACCCCCCAGGTCTACTATCGCAGCTGCATTCAGCCCAGATGGGAAA
           ||||   | ||     ||| |  |      ||      ||       |||| | | |  || |  |  |   || |      | |     ||| | |     |     || |||||  ||  |  ||||  |||  || | |||||| || ||||||||| | ||||| || || ||||||||||| ||||| ||||| |||||||||||||||
gtactttcacttatttagtccacaagttatatcgaggaaaaagcatgccttttgagaatttgaaattttgctttcttcaagaaaagtcaattttagggactaacttctctgacaatgattatcagGGTTGAGGCTGAGTCATTGCGGCATTTGTCTGCTAAGTATTGTCCTTTGTTGCCTCCTCCAAGGTCTACTATTGCAGCAGCATTTAGCCCAGATGGGAAA

upper sequence: LOC_Os02g18820.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA19G35370.3 (Glycine max), 3'ss of exon 2
-----------actattcttcattgtctattttaactgttgagt-----tacatagttttgtactctcactcttatacctaa----cttttccctggaatgaaaccttttctg----tatacagGGCAGAATCACAGTCCCTGCATCACTGGTCTGCCAAATATTGTCCTCTTTTGCCACCCCCCAGGTCTACTATCGCAGCTGCATTCAGCCCAGATGGGAAA
           | | |  | |||    ||| || |      ||      |       |||| | | |   | |  |    ||    |  ||    ||| | |   || |        | | |||||  ||  |  ||||  |||  || | |||||| || ||||||||| |  |||| || || ||||||||||| ||||| ||||| |||||||||||||||
gtacttacactaatttagtccataagttatattgaggaaaaagcatgcctttgagaatttgaaattttgttttcttcaagaagagtcaattttggggactaatgtctctgacaatgattttcagGGTTGAGGCTGAGTCATTGCGGCATTTGTCTGCTAAGTATTGTCCTTTGGTGCCTCCTCCAAGGTCTACTATTGCAGCAGCATTTAGCCCAGATGGGAAA

upper sequence: LOC_Os02g18820.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 2
----actattcttcattgtctattttaactgttgagttacatagttttgtactctcactcttatacctaacttttccctggaatgaaaccttttctgtatacagGGCAGAATCACAGTCCCTGCATCACTGGTCTGCCAAATATTGTCCTCTTTTGCCACCCCCCAGGTCTACTATCGCAGCTGCATTCAGCCCAGATGGGAAA
    || |   ||     ||| |||| |      ||||   |  || |||  |||  || || || ||  ||||         |    |||||||||| |  |||| |||  || | ||  |||| || |  || ||||  |||||||||||  |||| || || ||||||||||| ||||| |||||||| |||||||| |||
tcgtacaaggtttttgcttctgttttcata--caagttttttgcttctgttttctttctttt-tatctttctttctttcttttttgttccttttctgt-tctagGGTAGAGGCAGATTCATTGCAGCATTTATCAGCCAGGTATTGTCCTCTGATGCCTCCTCCGAGGTCTACTATTGCAGCAGCATTCAGTCCAGATGGAAAA

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|58671891|gb|CK060577.1|CK060577
EST:     AATGAACTAAGATATGCAGCTACAGATGCTAAACATGATATATATTCATG                         GGCAGAATCACAGTCCCTGCATCACTGGTCTGCCAAATATTGTCCTCTTTT
genomic: AATGAACTAAGATATGCAGCTACAGATGCTAAACATGATATATATTCATGgtacggggtc ... ctgtatacagGGCAGAATCACAGTCCCTGCATCACTGGTCTGCCAAATATTGTCCTCTTTT
EST: gi|88435271|gb|CI581991.1|CI581991
EST:     AATGAACTAAGATATGCAGCTACAGATGCTAAACATGATATATATTCATG                         GGCAGAATCACAGTCCCTGCATCACTGGTCTGCCAAATATTGTCCTCTTTT
genomic: AATGAACTAAGATATGCAGCTACAGATGCTAAACATGATATATATTCATGgtacggggtc ... ctgtatacagGGCAGAATCACAGTCCCTGCATCACTGGTCTGCCAAATATTGTCCTCTTTT
EST: gi|29674170|gb|CB670445.1|CB670445
EST:     AATGAACTAAGATATGCAGCTACAGATGCTAAACATGATATATATTCATG                         GGCAGAATCACAGTCCCTGCATCACTGGTCTGCCAAATATTGTCCTCTTTT
genomic: AATGAACTAAGATATGCAGCTACAGATGCTAAACATGATATATATTCATGgtacggggtc ... ctgtatacagGGCAGAATCACAGTCCCTGCATCACTGGTCTGCCAAATATTGTCCTCTTTT
EST: gi|58671698|gb|CK060384.1|CK060384
EST:     AATGAACTAAGATATGCAGCTACAGATGCTAAACATGATATATATTCATG                         GGCAGAATCACAGTCCCTGCATCACTGGTCTGCCAAATATTGTCCTCTTTT
genomic: AATGAACTAAGATATGCAGCTACAGATGCTAAACATGATATATATTCATGgtacggggtc ... ctgtatacagGGCAGAATCACAGTCCCTGCATCACTGGTCTGCCAAATATTGTCCTCTTTT
EST: gi|87014230|gb|CI305008.1|CI305008
EST:     AATGAACTAAGATATGCAGCTACAGATGCTAAACATGATATATATTCATG                         GGCAGAATCACAGTCCCTGCATCACTGGTCTGCCAAATATTGTCCTCTTTT
genomic: AATGAACTAAGATATGCAGCTACAGATGCTAAACATGATATATATTCATGgtacggggtc ... ctgtatacagGGCAGAATCACAGTCCCTGCATCACTGGTCTGCCAAATATTGTCCTCTTTT

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: 75 (upstream exon), 75 (downstream exon)
Score: 42

ACCAAGCTAAAAAACTTTGGAGCAAATCTCCAGGAAATGATGCTGATTCCAATGAACTAAGATATGCAGCTACAGATGCTAAACATGATATATATTCATGgtacggggtc ... ctgtatacagGGCAGAATCACAGTCCCTGCATCACTGGTCTGCCAAATATTGTCCTCTTTTGCCACCCCCCAGGTCTACTATCGCAGCTGCATTCAGCCCAGATGGGAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactctcactcttatacctaacttttccctggaatgaaaccttttctgtatacagGGCAGAATCACAGTCCCTGCATCACTGGTCTGCCAAATATTGTCCTCTTTTGCCACCCCCCAGGTCTACTATCGCAGCTGCATTCAGCCCAGATGGGAAA
               acctaac  putative branch site (score: 42)
                                       ccttttctgt  putative PPT
                  taactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actattcttcattgtctattttaactgttgagttacatagttttgtactctcactcttatacctaacttttccctggaatgaaaccttttctgtatacagGGCAGAATCACAGTCCCTGCATCACTGGTCTGCCAAATATTGTCCTCTTTTGCCACCCCCCAGGTCTACTATCGCAGCTGCATTCAGCCCAGATGGGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - ctgttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaatgaaa