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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtcatagctcgcaaacttgtttatctttttgtgctttccagaaaacataagcaatagactgatttttgcatgaacatattttccaacccatctttcaattgcaatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATCGTGCTATAAAGAAAAAGATGGAGATCGGAAAACTTGGATAATTCCATAT

Basic information

species Oryza sativa
transcript LOC_Os03g20520.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g20520.1 (Oryza sativa), 3'ss of exon 12
lower sequence: EFJ21748 (Selaginella moellendorffii), 3'ss of exon 12
gtctgtcatagctcgcaaacttgtttatctttttgtgctttccagaaaacataagcaatagactgatttttgcatgaacatattttccaacccatctttcaattgcaatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATCGTGCTATAAAGAAAAAGATGGAGATCGGAAAACTTGGATAATTCCATAT
                                                   ||||  ||   ||  ||  |||||      |   || ||   |   |     ||   | | |||||| ||||||||||  |||||||||| || || ||  |||||||||| ||||| || |||||||||||||||||||| || |||  |  || |    |   
--------------------------------------------------gtaagtcatcccctcgttgctgcat---tccaagatctaattgag--tgtggctggggttg-acagGGGTTTTCACTGTCTCTGGCATCATCGACTCGTTCATCTACCATGGACATCGGGCAATAAAGAAAAAGATGGAGATTGGCAAATATATATGAGAAAAACA

upper sequence: LOC_Os03g20520.1 (Oryza sativa), 3'ss of exon 12
lower sequence: EFJ06790 (Selaginella moellendorffii), 3'ss of exon 12
gtctgtcatagctcgcaaacttgtttatctttttgtgctttccagaaaacataagcaatagactgatttttgcatgaacatattttccaacccatctttcaattgcaatcgt--acagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATCGTGCTATAAAGAAAAAGATGGAGATCGGAAAACTTGGATAATTCCATAT
                                                          ||     |    | | |      |||    || | |  |     | || |  |   |||||| ||||||||||  |||||||||| || || ||  |||||||||| ||||| || |||||||||||||||||||| || |||  |  || |    |   
---------------------------------------------------------gtaagtcaacccct-cgttgctgcattccaaaatctaattgagtgtggctacggatgacagGGGTTTTCACTGTCTCTGGCATCATCGACTCGTTCATCTACCATGGACATCGGGCAATAAAGAAAAAGATGGAGATTGGCAAATATATATGAGAAAAACA
















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|88221975|gb|CI221931.1|CI221931
EST:     AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAG                         GGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
genomic: AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAGgtctgtcata ... aatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
EST: gi|88465562|gb|CI522313.1|CI522313
EST:     AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTTTTGGAG                         GGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
genomic: AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAGgtctgtcata ... aatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
EST: gi|86851807|gb|CI316376.1|CI316376
EST:     AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAG                         GGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
genomic: AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAGgtctgtcata ... aatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
EST: gi|88846777|gb|CI373545.1|CI373545
EST:     AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAG                         GGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
genomic: AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAGgtctgtcata ... aatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
EST: gi|88413220|gb|CI523781.1|CI523781
EST:     GCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAG                         GGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
genomic: GCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAGgtctgtcata ... aatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
EST: gi|88484721|gb|CI421992.1|CI421992
EST:     TCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAG                         GGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
genomic: TCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAGgtctgtcata ... aatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
EST: gi|218482003|gb|FG956575.1|FG956575
EST:     AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAG                         GGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
genomic: AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAGgtctgtcata ... aatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
EST: gi|88304507|gb|CI518163.1|CI518163
EST:     CGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAG                         GGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
genomic: CGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAGgtctgtcata ... aatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
EST: gi|88266278|gb|CI377180.1|CI377180
EST:     AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAG                         GGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
genomic: AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAGgtctgtcata ... aatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
EST: gi|5002852|gb|AU067961.1|AU067961
EST:     AAATCCATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGNG                         GGATTTTCACTGTTNCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
genomic: AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAGgtctgtcata ... aatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
EST: gi|218492797|gb|FG953626.1|FG953626
EST:     AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAG                         GGATTTTCACTTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCAT
genomic: AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAGgtctgtcata ... aatcgtacagGGATTTTCACT-GTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCAT
EST: gi|218505492|gb|FG958279.1|FG958279
EST:     AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAG                         GGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
genomic: AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAGgtctgtcata ... aatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
EST: gi|25803052|gb|CA759013.1|CA759013
EST:     AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAG                         GGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
genomic: AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAGgtctgtcata ... aatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
EST: gi|88847669|gb|CI018360.1|CI018360
EST:     AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAG                         GGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
genomic: AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAGgtctgtcata ... aatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
EST: gi|88989740|gb|CI107427.1|CI107427
EST:     AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAG                         GGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
genomic: AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAGgtctgtcata ... aatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
EST: gi|88256781|gb|CI359169.1|CI359169
EST:     AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAG                         GGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
genomic: AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAGgtctgtcata ... aatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
EST: gi|89193410|gb|CI050708.1|CI050708
EST:     AAATACATCGCTTCTTCACTTCCTGACCAACATATGTGCTATTGTTGGAG                         GGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
genomic: AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAGgtctgtcata ... aatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
EST: gi|8859147|gb|AU096465.1|AU096465
EST:     AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAG                         GGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
genomic: AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAGgtctgtcata ... aatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
EST: gi|701663|gb|D47954.1|D47954
EST:     AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAG                         GGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
genomic: AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAGgtctgtcata ... aatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
EST: gi|89181360|gb|CI112866.1|CI112866
EST:     AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAG                         GGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
genomic: AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAGgtctgtcata ... aatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
EST: gi|89189327|gb|CI048866.1|CI048866
EST:     AAATACATCGCTTCTTCACTTCCTGACCAACATATGTGCTATTGTTGGAG                         GGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
genomic: AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAGgtctgtcata ... aatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
EST: gi|58675353|gb|CK064040.1|CK064040
EST:     AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAG                         GGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
genomic: AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAGgtctgtcata ... aatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
EST: gi|86873742|gb|CI341175.1|CI341175
EST:     AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAG                         GGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
genomic: AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAGgtctgtcata ... aatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
EST: gi|86490016|gb|CI132649.1|CI132649
EST:     AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAG                         GGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
genomic: AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAGgtctgtcata ... aatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
EST: gi|86429502|gb|CI076183.1|CI076183
EST:     AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAG                         GGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
genomic: AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAGgtctgtcata ... aatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
EST: gi|29657637|gb|CB653912.1|CB653912
EST:     AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAG                         GGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
genomic: AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAGgtctgtcata ... aatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
EST: gi|58690521|gb|CK079208.1|CK079208
EST:     AAATACATCGCTTCTTCACTTCCTGACGAACATATGTGCTATTGTTGGAG                         GGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
genomic: AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAGgtctgtcata ... aatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
EST: gi|88844531|gb|CI020378.1|CI020378
EST:     AAATACATCGCTTCTTCACTTCCTGACCAACATATGTGCTATTGTTGGAG                         GGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC
genomic: AAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAGgtctgtcata ... aatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATC

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: 61 (upstream exon), 75 (downstream exon)
Score: 9

GTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAGgtctgtcata ... aatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATCGTGCTATAAAGAAAAAGATGGAGATCGGAAAACTTGGATAATTCCATAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgatttttgcatgaacatattttccaacccatctttcaattgcaatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATCGTGCTATAAAGAAAAAGATGGAGATCGGAAAACTTGGATAATTCCATAT
 gactgat  putative branch site (score: 9)
               aacatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtcatagctcgcaaacttgtttatctttttgtgctttccagaaaacataagcaatagactgatttttgcatgaacatattttccaacccatctttcaattgcaatcgtacagGGATTTTCACTGTTGCTGGCATCATAGATTCTTTTGTCTACCATGGTCATCGTGCTATAAAGAAAAAGATGGAGATCGGAAAACTTGGATAATTCCATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC