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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTTGTATAAGAAAGAGCGACAGCAGTACTCTGAAGAGGTTAAAGGCGATGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTGgtatgtgcagttcttgattacatgagatatccaccaatgaatgattattcagtaaagtaaggaaacaattaggaacaaggtttattgtctgttcaaaagt...

Basic information

species Oryza sativa
transcript LOC_Os11g34300.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g34300.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G484880_T03 (Zea mays), 5'ss of exon 9
CTTTTGTATAAGAAAGAGCGACAGCAGTACTCTGAAGAGGTTAAAGGCGATGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTGgtatgtgcagttcttgattacatgagatatccaccaatgaatgattattcagtaaagtaaggaaacaattaggaa-caaggtttattgtctgttcaaaagt
||||| ||||||||||||||| | |||||  ||||||| |||||||| ||||| || || |||||| |||||||||||||||||||| ||||||||||||||| || || || |  | || ||| | | || |    |    | |||||| |     | |          | |||   ||    ||| | |       | |
CTTTTATATAAGAAAGAGCGAGATCAGTATGCTGAAGAAGTTAAAGGTGATGTCTCACCATCAACTGTATATGGAGCTGAGCATCTATTGCGCCTTTTTGgtacgtccaattgtccactaaatgtgttctc-atatgtattggtttattctgcttgttgaaatgctttggaagaagtcagaacaattatgttccttgtatt

upper sequence: LOC_Os11g34300.2 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv18s0001g09710.t01 (Vitis vinifera), 5'ss of exon 8
CTTTTGTATAAGAAAGAGCGACAGCAGTACTCTGAAGAGGTTAAAGGCGATGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTGgtatgtgcagttcttgattacatgagatatccaccaatgaat--gattattcagtaaagtaaggaaacaattaggaacaaggtttattgtctgttcaaaagt
||| ||||| | |  ||||| || |||||    ||||   ||  |    |||| || || |||||||||||||| ||||| |||||| | ||||| |||||||||         | |||  |    |||   |  | |   |  ||| | |   ||  |     ||   || ||  |  |   || ||  || |||| |   
CTTCTGTATGAAAGGGAGCGTCAACAGTATCAAGAAGCAATTGCAAATAATGTCTCTCCTTCAACTATATATGGTGCTGAACATCTATTACGCCTCTTTGgtatgatattcctctaatttgacacaataaatattatttgttttgatgaattcttattgcttcaaatggatcagttaggacacttctttcctattcacat--
















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|9865404|gb|AU101154.1|AU101154
EST:     TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTG                         TGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
genomic: TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTGgtatgtgcag ... tgctttgcagTGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
EST: gi|86844258|gb|CI337629.1|CI337629
EST:     TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCCCCTTTTTG                         TGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
genomic: TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTGgtatgtgcag ... tgctttgcagTGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
EST: gi|109712745|gb|CI105353.1|CI105353
EST:     TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTG                         TGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
genomic: TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTGgtatgtgcag ... tgctttgcagTGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
EST: gi|58679417|gb|CK068104.1|CK068104
EST:     TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTG                         TGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
genomic: TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTGgtatgtgcag ... tgctttgcagTGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
EST: gi|88491380|gb|CI428652.1|CI428652
EST:     TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTG                         TGAAATTGCCGGAGGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTC
genomic: TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTGgtatgtgcag ... tgctttgcagTGAAATTGCCGGA-GCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTC
EST: gi|86539094|gb|CI179300.1|CI179300
EST:     TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTG                         TGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
genomic: TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTGgtatgtgcag ... tgctttgcagTGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
EST: gi|66914665|gb|CX101513.1|CX101513
EST:     TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTG                         TGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
genomic: TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTGgtatgtgcag ... tgctttgcagTGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
EST: gi|88983252|gb|CI020816.1|CI020816
EST:     TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTG                         TGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
genomic: TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTGgtatgtgcag ... tgctttgcagTGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
EST: gi|86844406|gb|CI337712.1|CI337712
EST:     TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTG                         TGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
genomic: TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTGgtatgtgcag ... tgctttgcagTGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
EST: gi|88288783|gb|CI517914.1|CI517914
EST:     TGTTTCGCCCTCAACTATATATGGAGCTGAGCATTTACTGCGCCTTTTTG                         TGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
genomic: TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTGgtatgtgcag ... tgctttgcagTGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
EST: gi|86870999|gb|CI326818.1|CI326818
EST:     TGTTTCGCCCTCAAC--TATATGGAGCTGAGCATCTACTGCGCCTTTTTG                         TGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
genomic: TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTGgtatgtgcag ... tgctttgcagTGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
EST: gi|15858178|gb|BI810990.1|BI810990
EST:     TGCGCCTTTTTG                         TGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
genomic: TGCGCCTTTTTGgtatgtgcag ... tgctttgcagTGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
EST: gi|89173985|gb|CI041878.1|CI041878
EST:     TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTG                         TGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
genomic: TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTGgtatgtgcag ... tgctttgcagTGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
EST: gi|86867570|gb|CI337935.1|CI337935
EST:     TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTG                         TGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
genomic: TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTGgtatgtgcag ... tgctttgcagTGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
EST: gi|13165184|gb|AU173981.1|AU173981
EST:     TGTTTCGCCCTCAACTATATATGGAGCTGAGCATNTACTGCGCCTTTTTG                         TGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCNCTCA
genomic: TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTGgtatgtgcag ... tgctttgcagTGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
EST: gi|29639417|gb|CB644426.1|CB644426
EST:     TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTG                         TGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
genomic: TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTGgtatgtgcag ... tgctttgcagTGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
EST: gi|88476535|gb|CI413806.1|CI413806
EST:     TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTG                         TGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
genomic: TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTGgtatgtgcag ... tgctttgcagTGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
EST: gi|29665212|gb|CB661487.1|CB661487
EST:     TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTG                         TGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
genomic: TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTGgtatgtgcag ... tgctttgcagTGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
EST: gi|88830125|gb|CI074797.1|CI074797
EST:     TGTTTCGCCCTGAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTG                         TGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA
genomic: TGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTGgtatgtgcag ... tgctttgcagTGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCA

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: 14 (upstream exon), 54 (downstream exon)
Score: 15

CTTTTGTATAAGAAAGAGCGACAGCAGTACTCTGAAGAGGTTAAAGGCGATGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTGgtatgtgcag ... tgctttgcagTGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTTTGTATAAGAAAGAGCGACAGCAGTACTCTGAAGAGGTTAAAGGCGATGTTTCGCCCTCAACTATATATGGAGCTGAGCATCTACTGCGCCTTTTTGgtatgtgcagttcttgattacatgagatatccaccaatgaatgattattcagtaaagtaaggaaacaattaggaacaaggtttattgtctgttcaaaagt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA