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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactccaataagtaaatgaacatgtttgtttttgcttaatagtaaatcggtaatgcatctgacataccgtgcatgatctaaaatacagttatcttaacagATCAGAAGCCATGCACAGAAGTACTTTTTGAAGGTTCAAAAGAATGGAACAGGCGAGCATTTGCCCCCTCCTAGGCCAAAACGGAAGGCAGCACATCCAT

Basic information

species Oryza sativa
transcript LOC_Os06g01670.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g01670.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G135052_T01 (Zea mays), 3'ss of exon 2
--tactccaataagtaaatgaacatgtttgtttttgcttaatagtaaatcggtaatgcatctgacataccgtgcatgatctaaaatacagttatcttaacagATCAGAAGCCATGCACAGAAGTACTTTTTGAAGGTTCAAAAGAATGGAACAGGCGAGCATTTGCCCCCTCCTAGGCCAAAACGGAAGGCAGCACATCCAT
     ||   |   ||    || | ||   ||  | | | ||  |   | | ||     ||| ||  || ||||||||||||||  |||| | | ||||||||| || || || ||||||||||||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||| || ||||| || |||||||
cactgtcgtcttgctattccaagacgtaaattggttcctgattttc--ttgttatgttgtctaacgaactgtgcatgatctaaacaacagctcttttaacagATTAGGAGTCACGCACAGAAGTACTTTTTGAAGGTTCAAAAGAATGGAACAGGTGAGCATTTGCCCCCACCTAGGCCAAAGCGAAAGGCTGCCCATCCAT

upper sequence: LOC_Os06g01670.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv16s0050g01180.t01 (Vitis vinifera), 3'ss of exon 2
tactccaataagtaaatgaacatgtttgtttttgcttaatagtaaatcggtaatgcatctgacataccgtgcatgatctaaaatacagttatcttaacagATCAGAAGCCATGCACAGAAGTACTTTTTGAAGGTTCAAAAGAATGGAACAGGCGAGCATTTGCCCCCTCCTAGGCCAAAACGGAAGGCAGCACATCCAT
           ||||       ||| |  || | |||  |  || |    ||  |||  |  |  |    | |  ||  ||  ||  | |   ||  |||||  | || |||||||||||||||||| |||||||||| |||||||||| |   || ||| | || || ||  |||||||| | || |||||||||||||
-----------gtaatcaggattgtataattatcctt--ttatagac---tatggcacataccccaagaagaaaaata-aacttaatgatgcttttgcagATACGTAGTCATGCACAGAAGTACTTTCTGAAGGTTCAGAAGAATGGAATAAATGAACATCTACCTCCCCCCCGGCCAAAAAGAAAAGCAGCACATCCAT

upper sequence: LOC_Os06g01670.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ36434 (Selaginella moellendorffii), 3'ss of exon 2
tactccaataagtaaatgaacatgtttgtttttgcttaatagtaaatcggtaatgcatctgacataccgtgcatgatctaaaatacagttatcttaacagATCAGAAGCCATGCACAGAAGTACTTTTTGAAGGTTCAAAAGAATGGAACAGGCGAGCATTTGCCCCCTCCTAGGCCAAAACGGAAGGCAGCACATCCAT
                          ||   || |||     ||     ||  | |  | |  ||   || | |    ||   |      || |   ||||| ||||| ||||| |||||||| |||||||| || || ||||||||||| || || ||  | || |||||  |||| || || ||  | || || ||||
-------------------------gtgaaattcctttgctttattcatgttcttcg-cggggatttagttcgt----tagtgtgtgacaatttc--cagATTAGAAGTCATGCCCAGAAGTATTTTTTGAAAGTCCAGAAGAATGGAACTGGAGAACACGTTCCTCCTCCACGGCCGAAGCGTAAATCTGCTCAACCAT

upper sequence: LOC_Os06g01670.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ04991 (Selaginella moellendorffii), 3'ss of exon 2
tactccaataagtaaatgaacatgtttgtttttgcttaatagtaaatcggtaatgcatctgacataccgtgcatgatctaaaatacagttatcttaacagATCAGAAGCCATGCACAGAAGTACTTTTTGAAGGTTCAAAAGAATGGAACAGGCGAGCATTTGCCCCCTCCTAGGCCAAAACGGAAGGCAGCACATCCAT
                          ||   || |||     ||     ||  | |  | |  ||   || | |    ||   |      || |   ||||| ||||| ||||| |||||||| |||||||| || || ||||||||||| || || ||  | || |||||  |||| ||||| ||  | || || ||||
-------------------------gtgaaattcctttgctttattcatgttcttcg-cggggatttagttcgt----tagtgtgtgacaatttc--cagATTAGAAGTCATGCCCAGAAGTATTTTTTGAAAGTCCAGAAGAATGGAACTGGAGAACACGTTCCTCCTCCACGGCCGAAACGTAAATCTGCTCAACCAT

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|88365508|gb|CI680149.1|CI680149
EST:     GTGATTGGAAAAAGATTGAAGCATATGTTGGCTCTAAGACTGTAATACAG                         ATCAGAAGCCATGCACAGAAGTACTTTTTGAAGGTTCAAAAGAATGGAACA
genomic: GTGATTGGAAAAAGATTGAAGCATATGTTGGCTCTAAGACTGTAATACAGgtatagttta ... atcttaacagATCAGAAGCCATGCACAGAAGTACTTTTTGAAGGTTCAAAAGAATGGAACA
EST: gi|88409782|gb|CI571039.1|CI571039
EST:     GTGATTGGAAAAAGATTGAAGCATATGTTGGCTCTAAGACTGTAATACAG                         ATCAGAAGCCATGCACAGAA
genomic: GTGATTGGAAAAAGATTGAAGCATATGTTGGCTCTAAGACTGTAATACAGgtatagttta ... atcttaacagATCAGAAGCCATGCACAGAA
EST: gi|33686829|gb|CF315068.1|CF315068
EST:     GTGATTGGAAAAAGATTGAAGCATATGTTGGCTCTAAGACTGTAATACAG                         ATCAGAAGCCATGCACAGAAGTACTTTTTGAAGGTTCAAAAGAATGGAACA
genomic: GTGATTGGAAAAAGATTGAAGCATATGTTGGCTCTAAGACTGTAATACAGgtatagttta ... atcttaacagATCAGAAGCCATGCACAGAAGTACTTTTTGAAGGTTCAAAAGAATGGAACA
EST: gi|29664971|gb|CB661246.1|CB661246
EST:     GATTGAAGCATATGTTGGCTCTAAGACTGTAATACAG                         ATCAGAAGCCATGCACAGAAGTACTTTTTGAAGGTTCAAAAGAATGGAACA
genomic: GATTGAAGCATATGTTGGCTCTAAGACTGTAATACAGgtatagttta ... atcttaacagATCAGAAGCCATGCACAGAAGTACTTTTTGAAGGTTCAAAAGAATGGAACA
EST: gi|88591086|gb|CI707994.1|CI707994
EST:     GTGATTGGAAAAAGATTGAAGCATATGTTGGCTCTAAGACTGTAATACAG                         ATCAGAAGCCATGCACAGAAGTACTTTTTGAAGGTTCAAAAGAATGGAACA
genomic: GTGATTGGAAAAAGATTGAAGCATATGTTGGCTCTAAGACTGTAATACAGgtatagttta ... atcttaacagATCAGAAGCCATGCACAGAAGTACTTTTTGAAGGTTCAAAAGAATGGAACA
EST: gi|88725670|gb|CI748929.1|CI748929
EST:     GTGATTGGAAAAAGATTGAAGCATATGTTGGCTCTAAGACTGTAATACAG                         ATCAGAAGCCATGCACAGAAGTACTTTTTGAAGGTTCAAAAGAATGGAACA
genomic: GTGATTGGAAAAAGATTGAAGCATATGTTGGCTCTAAGACTGTAATACAGgtatagttta ... atcttaacagATCAGAAGCCATGCACAGAAGTACTTTTTGAAGGTTCAAAAGAATGGAACA
EST: gi|29665005|gb|CB661280.1|CB661280
EST:     GATTGAAGCATATGCCTT-GCTCTAAGACTGTAATACAG                         ATCAGAAGCCATGCACAGAAGTACTTTTTGAAGGTTCAAAAGAATGGAACA
genomic: GATTGAAGCATATG--TTGGCTCTAAGACTGTAATACAGgtatagttta ... atcttaacagATCAGAAGCCATGCACAGAAGTACTTTTTGAAGGTTCAAAAGAATGGAACA
EST: gi|33674838|gb|CF303077.1|CF303077
EST:     GTGATTGGAAAAAGATTGAAGCATATGTTGGCTCTAAGACTGTAATACAG                         ATCAGAAGCCATGCACAGAAGTACTTTTTGAAGGTTCAAAAGAATGGAACA
genomic: GTGATTGGAAAAAGATTGAAGCATATGTTGGCTCTAAGACTGTAATACAGgtatagttta ... atcttaacagATCAGAAGCCATGCACAGAAGTACTTTTTGAAGGTTCAAAAGAATGGAACA
EST: gi|117235846|gb|CT847813.1|CT847813
EST:     GTGATTGGAAAAAGATTGAAGCATATGTTGGCTCTAAGACTGTAATACAGTTATCTTAACAG              
genomic: GTGATTGGAAAAAGATTGAAGCATATGTTGGCTCTAAGACTG---T--A---A---T-ACAGgtatagttta ...
EST: gi|88742890|gb|CI766398.1|CI766398
EST:     GTGATTGGAAAAAGATTGAAGCATATGTTGGCTCTAAGACTGTAATACAG                         ATCAGAAGCCATGCACAGAAGTACTTTTTGAAGGTTCAAAAGAAT
genomic: GTGATTGGAAAAAGATTGAAGCATATGTTGGCTCTAAGACTGTAATACAGgtatagttta ... atcttaacagATCAGAAGCCATGCACAGAAGTACTTTTTGAAGGTTCAAAAGAAT
EST: gi|29625024|gb|CB630035.1|CB630035
EST:     GTGATTGGAAAAAGATTGAAGCATATGTTGGCTCTAAGACTGTAATACAG                         ATCAGAAGCCATGCACAGAAGTACTTTTTGAAGGTTCAAAAGAATGGAACA
genomic: GTGATTGGAAAAAGATTGAAGCATATGTTGGCTCTAAGACTGTAATACAGgtatagttta ... atcttaacagATCAGAAGCCATGCACAGAAGTACTTTTTGAAGGTTCAAAAGAATGGAACA

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: 69 (upstream exon), 60 (downstream exon)
Score: 33

GTTTGATCGTGATTGGAAAAAGATTGAAGCATATGTTGGCTCTAAGACTGTAATACAGgtatagttta ... atcttaacagATCAGAAGCCATGCACAGAAGTACTTTTTGAAGGTTCAAAAGAATGGAACAGGCGAGCATTTGCCCCCTCCTAGGCCAAAACGGAAGGCAGCACATCCAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcggtaatgcatctgacataccgtgcatgatctaaaatacagttatcttaacagATCAGAAGCCATGCACAGAAGTACTTTTTGAAGGTTCAAAAGAATGGAACAGGCGAGCATTTGCCCCCTCCTAGGCCAAAACGGAAGGCAGCACATCCAT
                              atctaaa  putative branch site (score: 33)
                                           ttatctt  putative PPT
                                 taaaatacagttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactccaataagtaaatgaacatgtttgtttttgcttaatagtaaatcggtaatgcatctgacataccgtgcatgatctaaaatacagttatcttaacagATCAGAAGCCATGCACAGAAGTACTTTTTGAAGGTTCAAAAGAATGGAACAGGCGAGCATTTGCCCCCTCCTAGGCCAAAACGGAAGGCAGCACATCCAT

- - - - - - - - - aacatgt
- - - - - - - - - - - - - - - - tgcttaa
- - - - - - - - - - - - - - - - - - - - - - - - - - atgcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cataccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataca