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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTTGAACCCCTCAGGAACCGCCTTTCGGAGAATACTGAGATACAGAGTGCCAAATTGgtaggccagcttactgtattaatttccatttcaatgatctcaaatataaattggtgtataatattttaatttaggaataagatgagatgaatctagagac...

Basic information

species Oryza sativa
transcript LOC_Os04g23890.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g23890.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G032351_T01 (Zea mays), 5'ss of exon 8
GCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTTGAACCCCTCAGGAACCGCCTTTCGGAGAATACTGAGATACAGAGTGCCAAATTGgtaggccagcttactgt-attaatttccatttcaatgatctcaaatata-----aattggtgtataatattttaatttaggaat--aagatgagatgaatctagagac
|||||||||||||||||| || ||| | |||||||| || |||||||||||||| ||||| || || || ||||| |||||  |||| ||||| ||||||||||  ||   || | | | |||||| |||||  ||| | | || || |     ||| |||| | ||||    || ||   |||  || |  | ||||          
GCTTCAATACTTCATTGGAGTTCAATTGGATGGAAGCGACCATGTTGAACCCCTTAGGAATCGTCTCTCTGAGAACACTGAACTACAAAGTGCTAAATTGgtagctcaatctattctcagtaattttcattttgatggtttaaactagatctataataggtgcacaataagccaactttaaaatgtaaaacaaaatgagg--------

upper sequence: LOC_Os04g23890.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA16G19560.1 (Glycine max), 5'ss of exon 11
GCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTTGAACCCCTCAGGAACCGCCTTTCGGAGAATACTGAGATACAGAGTGCCAAATTGgtaggc-cagcttact--gtattaatttccatttcaatgatctcaaatataaattggtgtataatattttaatttaggaataagatgagatgaatctagagac
 |||||||||||||||||||| ||||| ||||||||||||||||| |||||| | |  |||||||| || ||||  ||||||  ||| ||||| || |||||  |    |  | ||  || |||  ||     | | || |    || |||  ||| ||  |  | |||  ||||     |  ||| |    || |||   | 
ACTTCAATACTTCATTGGTGTTCAACTAGATGGAAGTGATCATGTAGAACCCTTAAAAAACCGCCTGTCTGAGACAACTGAGCAACAAAGTGCTAAGTTGgtgagtattgtcttctcagtcttagctttgtacttactggttc--aagatactttgatgctttgtttttatatttcactttgggat-atgcaaaactaagaat

upper sequence: LOC_Os04g23890.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA08G33560.1 (Glycine max), 5'ss of exon 9
GCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTTGAACCCCTCAGGAACCGCCTTTCGGAGAATACTGAGATACAGAGTGCCAAATTGgtaggc-cagcttact--gtattaatttccatttcaatgatctcaaatataaattggtgtataatattttaatttaggaataagatgagatgaatctagagac
 |||||||||||||||||||| ||||| ||||||||||||||||| |||||| | |  |||||||| || ||||  ||||||  ||| ||||| || |||||  |    |  | ||  || |||  ||     | | || | |||| | ||  ||| ||  |  | |||  ||||     |  ||| |    || |||   | 
ACTTCAATACTTCATTGGTGTTCAACTAGATGGAAGTGATCATGTAGAACCCTTAAAAAACCGCCTGTCTGAGACAACTGAGCAACAAAGTGCTAAGTTGgtgagtattgtcttctcagtcttagctttgtacttactggt-tcaagt-tactttgatgctttgtttttatatttcactttgtgat-atgcaaaactaagaat

upper sequence: LOC_Os04g23890.2 (Oryza sativa), 5'ss of exon 9
lower sequence: AT5G58140.4 (Arabidopsis thaliana), 5'ss of exon 10
GCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTTGAACCCCTCAGGAACCGCCTTTCGGAGAATACTGAGATACAGAGTGCCAAATTGgtaggccagcttactgtattaatttccatttcaatgatctcaaatataaattggtgtataatattttaatttaggaataagatgagatgaatctagagac
||||||||||||||| |||||||| |||||||||||||||||||| || ||||||   || ||  | || ||||  || ||||| |||||| | ||||||||| |   | ||  | |  || |     |||  |  |||||   |    ||    | | | |||   |  || |  | ||  | ||              
GCTTCAATACTTCATCGGTGTGCAGCTTGATGGAAGTGATCATGTAGAGCCCCTCCAAAATCGTTTGTCTGAGAGAACAGAGATGCAGAGTTCGAAATTGgtatgt--ggttcatatcctactgagttttttgaacatctc--tttcctatcaaaggagactatgaca--ttggtcacaattttag--------------

upper sequence: LOC_Os04g23890.2 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv03s0038g04210.t01 (Vitis vinifera), 5'ss of exon 9
GCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTTGAACCCCTCAGGAACCGCCTTTCGGAGAATACTGAGATACAGAGTGCCAAATTGgtaggccagcttactgtattaatttccatt-tcaatgatctcaaatataaattggtgtataatattttaatttaggaataagatgagatgaatctagagac--
 |||||||||||||||||||| ||| | ||||||||||||||| | ||||||||| | |||||||| || ||| | ||||||  ||| ||||| ||  |||||       ||  |       |||  ||| |  ||||    || |   | |  ||||     |     |||    |  ||  ||| |   ||||||| |   
ACTTCAATACTTCATTGGTGTCCAATTAGATGGAAGTGATCATCTGGAACCCCTCCGAAACCGCCTGTCAGAGCAAACTGAGCAACAAAGTGCTAAGCTGgtatatatattttttcaccatctttgaattgtttatgagtggaagttggactgagtgtgggggaa---gattctaaacaaaactgatacagatctagaaatga

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|29612810|gb|CB617823.1|CB617823
EST:     CCCTCAGGAACCGCCTTTCAGAGAATACTGAGATACAGAGTGCCAAATTG                         GTCAAAGCTACAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGAT
genomic: CCCTCAGGAACCGCCTTTCGGAGAATACTGAGATACAGAGTGCCAAATTGgtaggccagc ... gtccaattagGTCAAAGCTACAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGAT
EST: gi|14571435|gb|BI118803.1|BI118803
EST:     CCCTCAGGAACCGCCTTTCAGAGAATACTGAGATACAGAGTGCCAAATTG                         GTCAAAGCCACAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGAT
genomic: CCCTCAGGAACCGCCTTTCGGAGAATACTGAGATACAGAGTGCCAAATTGgtaggccagc ... gtccaattagGTCAAAGCTACAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGAT
EST: gi|29666947|gb|CB663222.1|CB663222
EST:     CCCTCAGGAACCGCCTTTCGGAGAATACTGAGATACAGAGTGCCAAATTG                         GTCAAAGCTACAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGAT
genomic: CCCTCAGGAACCGCCTTTCGGAGAATACTGAGATACAGAGTGCCAAATTGgtaggccagc ... gtccaattagGTCAAAGCTACAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGAT
EST: gi|58587914|gb|CF986222.1|CF986222
EST:     CCCTCAGGAACCGCCTTTCAGAGAATACTGAGATACAGAGTGCCAAATTG                         GTCAAAGCTACAGCGGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGAT
genomic: CCCTCAGGAACCGCCTTTCGGAGAATACTGAGATACAGAGTGCCAAATTGgtaggccagc ... gtccaattagGTCAAAGCTACAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGAT
EST: gi|29615865|gb|CB620877.1|CB620877
EST:     CCCTCAGGAACCGCCTTTCAGAGAATACTGAGATACAGAGTGCCAAATTG                         GTCAAAGCTACAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGAT
genomic: CCCTCAGGAACCGCCTTTCGGAGAATACTGAGATACAGAGTGCCAAATTGgtaggccagc ... gtccaattagGTCAAAGCTACAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGAT
EST: gi|29686409|gb|CB682684.1|CB682684
EST:     CCCTCAGGAACCGCCTTTCGGAGAATACTGAGATACAGAGTGCCAAATTG                         GTCAAAGCTACAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGAT
genomic: CCCTCAGGAACCGCCTTTCGGAGAATACTGAGATACAGAGTGCCAAATTGgtaggccagc ... gtccaattagGTCAAAGCTACAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGAT
EST: gi|29680789|gb|CB677064.1|CB677064
EST:     CCCTCAGGAACCGCCTTTCGGAGAATACTGAGATACAGAGTGCCAAATTG                         GTCAAAGCTACAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGAT
genomic: CCCTCAGGAACCGCCTTTCGGAGAATACTGAGATACAGAGTGCCAAATTGgtaggccagc ... gtccaattagGTCAAAGCTACAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGAT
EST: gi|29613843|gb|CB618856.1|CB618856
EST:     CCCTCAGGAACCGCCTTTCAGAGAATACTGAGATACAGAGTGCCAAATTG                         GTCAAAGCTACAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGAT
genomic: CCCTCAGGAACCGCCTTTCGGAGAATACTGAGATACAGAGTGCCAAATTGgtaggccagc ... gtccaattagGTCAAAGCTACAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGAT
EST: gi|29646469|gb|CB651476.1|CB651476
EST:     CCCTCAGGAACCGCCTTTCGGAGAATACTGAGATACAGAGTGCCAAATTG                         GTCAAAGCTACAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGAT
genomic: CCCTCAGGAACCGCCTTTCGGAGAATACTGAGATACAGAGTGCCAAATTGgtaggccagc ... gtccaattagGTCAAAGCTACAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGAT

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: 71 (upstream exon), 75 (downstream exon)
Score: 43

GCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTTGAACCCCTCAGGAACCGCCTTTCGGAGAATACTGAGATACAGAGTGCCAAATTGgtaggccagc ... gtccaattagGTCAAAGCTACAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGATGCCAACTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTTGAACCCCTCAGGAACCGCCTTTCGGAGAATACTGAGATACAGAGTGCCAAATTGgtaggccagcttactgtattaatttccatttcaatgatctcaaatataaattggtgtataatattttaatttaggaataagatgagatgaatctagagac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA