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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGCCTCGCAATGAGACACCAATTAGTGAGAATGAGATCAGGATCACTGCACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAGgtgaccctactactattactttcctttggctatgttgttatttgaggtagaacatgcagcaaccttttttgtgccatgttttaacaattaacaggacgcg...

Basic information

species Oryza sativa
transcript LOC_Os11g06760.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g06760.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G146472_T02 (Zea mays), 5'ss of exon 3
GAAGCCTCGCAATGAGACACCAATTAGTGAGAATGAGATCAGGATCACTGCACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAGgtgaccctactactattactttcctttggctatgttgttatttgaggtagaa--catgcagcaaccttttttgtgccatgttttaacaattaacaggacgcg----
||||||||| ||||| || ||||| ||  ||||||||||||| |||||| | ||||||||||||||||||||||||||||||||||||||| |||||||||||||     | || | | |     | |||| |||||| |  ||   || ||   | |||   |  || | | |  || | | || | |||    ||| | |    
GAAGCCTCGGAATGACACGCCAATCAGCCAGAATGAGATCAGAATCACTACTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAGgtgacg----tgctgtgattcaatctgggctttgttgtcacctgtcataaaaactaagcattgatgttgtct-tatca-gatatatctattgttgggaagtgtttg

upper sequence: LOC_Os11g06760.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G050982_T01 (Zea mays), 5'ss of exon 2
GAAGCCTCGCAATGAGACACCAATTAGTGAGAATGAGATCAGGATCACTGCACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAGgtgaccctactactattactttcctttggctatgttgttatttgaggtaga-acatgcagcaaccttttttgtgccatgtt-ttaacaattaacaggacgcg--
||||||||| ||||| |||||||| ||  |||||||||| ||||| ||| | ||||||||||||||||||||||||||||||||||||||| |||||||||||||     | || | | |     |||||| ||||||||  ||   || | | | |||   |  || |||||   || |   || |  |   |||  |  |  
GAAGCCTCGGAATGACACACCAATCAGCCAGAATGAGATTAGGATTACTACTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAGgtgaca----tgctgtgattcaatcttggctttgttgttacctgtcataaacataagcattgatattatttgtcatatttaactatccctcctcagcgcttgcg

upper sequence: LOC_Os11g06760.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ11989 (Selaginella moellendorffii), 5'ss of exon 1
GAAGCCTCGCAATGAGACACCAATTAGTGAGAATGAGATCAGGATCACTGCACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAGgtgaccctactactattactttcc----tttggctatgttgttatttgaggtagaacat-gcagcaaccttttttgtgccatgttttaacaattaacaggacgcg
|||||| ||||||||||| ||||| ||||||||||||||| |||| ||  | |||||||  ||| | ||||| || | ||||| |||     || |  ||||||    |  |  |  | ||  |    |||   | ||||  | ||     | || ||| ||||                                         
GAAGCCACGCAATGAGACCCCAATCAGTGAGAATGAGATCCGGATTACCACGCAGGGGAAAATGCGCAACTACATTACCTATGCGATTAGCCTGATACAGgtgaaaagaagaagaaaaattcgcggattttcattttgtttctcttgtcttttgagcattgcag-----------------------------------------

upper sequence: LOC_Os11g06760.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ21285 (Selaginella moellendorffii), 5'ss of exon 1
GAAGCCTCGCAATGAGACACCAATTAGTGAGAATGAGATCAGGATCACTGCACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAGgtgaccctact--actattactt-tcctttggctatgttgttatttgaggta-gaacat-gcagcaaccttttttgtgccatgttttaacaattaacaggacgcg
|||||| ||||||||||| ||||| ||||||||||||||| |||| ||  | |||||||  ||| | ||||| || | ||||| |||     || |  ||||||    |    |  ||  ||  |  |||    || || |   |||   |  || ||| ||||                                         
GAAGCCACGCAATGAGACCCCAATCAGTGAGAATGAGATCCGGATTACCACGCAGGGGAAAATGCGCAACTACATTACCTATGCGATTAGCCTGATACAGgtgaaaagaaggaagaatcgctggttttttcaaaattttttcccttgtcttttgagcattgcag-----------------------------------------

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|4878454|gb|AU062753.1|AU062753
EST:     CACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAG                         GAAAATGGGCATGATGAGATTNTCATCAAAGCTATGGGAAGAGCCATCAAT
genomic: CACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAGgtgaccctac ... tctttttcagGAAAATGGGCATGATGAGATTGTCATCAAAGCTATGGGAAGAGCCATCAAT
EST: gi|88339206|gb|CI633777.1|CI633777
EST:     CACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTCGCTTGAG                         GAAAATGGGCATGATGAGATTGTCATCACAGCTATGGGAAGAGCCATCAAT
genomic: CACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAGgtgaccctac ... tctttttcagGAAAATGGGCATGATGAGATTGTCATCAAAGCTATGGGAAGAGCCATCAAT
EST: gi|88571169|gb|CI662542.1|CI662542
EST:     CACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAG                         GAAAATGGGCATGATGAGATTGTCATCAAAGCTATGGGAAGAGCCATCAAT
genomic: CACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAGgtgaccctac ... tctttttcagGAAAATGGGCATGATGAGATTGTCATCAAAGCTATGGGAAGAGCCATCAAT
EST: gi|218484821|gb|FG946766.1|FG946766
EST:     CACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAG                         GAAAATGGGCATGATGAGATTGTCATCAAAGCTATGGGAAGAGCCATCAAT
genomic: CACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAGgtgaccctac ... tctttttcagGAAAATGGGCATGATGAGATTGTCATCAAAGCTATGGGAAGAGCCATCAAT
EST: gi|56157893|gb|C27653.2|C27653
EST:     CACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAG                         GAAAATGGGCATGATGAGATTGTCATCAAAGCTATGGGAAGAGCCATCAAT
genomic: CACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAGgtgaccctac ... tctttttcagGAAAATGGGCATGATGAGATTGTCATCAAAGCTATGGGAAGAGCCATCAAT
EST: gi|25799906|gb|CA755867.1|CA755867
EST:     CACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAG                         GAAAATGGGCATGATGAGATTGTCATCAAAGCTATGGGAAGAGCCATCAAT
genomic: CACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAGgtgaccctac ... tctttttcagGAAAATGGGCATGATGAGATTGTCATCAAAGCTATGGGAAGAGCCATCAAT
EST: gi|88305212|gb|CI652932.1|CI652932
EST:     CACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAG                         GAAAATGGGCATGATGAGATTGTCATCAAAGCTATGGGAAGAGCCATCAAT
genomic: CACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAGgtgaccctac ... tctttttcagGAAAATGGGCATGATGAGATTGTCATCAAAGCTATGGGAAGAGCCATCAAT
EST: gi|88339833|gb|CI649090.1|CI649090
EST:     CACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAG                         GAAAATGGGCATGATGAGATTGTCATCAAAGCTATGGGAAGAGCCATCAAT
genomic: CACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAGgtgaccctac ... tctttttcagGAAAATGGGCATGATGAGATTGTCATCAAAGCTATGGGAAGAGCCATCAAT
EST: gi|13818900|gb|AB060279.1|AB060279
EST:     CACACGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAG                         GAAAATGGGCATGATGAGATTGTCATCAAAGCTATGGGAAGAGCCATCAAT
genomic: CACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAGgtgaccctac ... tctttttcagGAAAATGGGCATGATGAGATTGTCATCAAAGCTATGGGAAGAGCCATCAAT
EST: gi|88309325|gb|CI655333.1|CI655333
EST:     CACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAG                         GAAAATGGGCATGATGAGATTGTCATCAAAGCTATGGGAAGAGCCATCAAT
genomic: CACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAGgtgaccctac ... tctttttcagGAAAATGGGCATGATGAGATTGTCATCAAAGCTATGGGAAGAGCCATCAAT
EST: gi|29677609|gb|CB673884.1|CB673884
EST:     CACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAG                         GAAAATGGGCATGATGAGATTGTCATCAAAGCTATGGGAAGAGCCATCAAT
genomic: CACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAGgtgaccctac ... tctttttcagGAAAATGGGCATGATGAGATTGTCATCAAAGCTATGGGAAGAGCCATCAAT
EST: gi|86897912|gb|CI289086.1|CI289086
EST:     CTATATCAGCTATGGGATGTCGTTGCTTGAG                         GAAAATGGGCATGATGAGATTGTCATCAAAGCTATGGGAAGAGCCATCAAT
genomic: CTATATCAGCTATGGGATGTCGTTGCTTGAGgtgaccctac ... tctttttcagGAAAATGGGCATGATGAGATTGTCATCAAAGCTATGGGAAGAGCCATCAAT
EST: gi|88338693|gb|CI644150.1|CI644150
EST:     CACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAG                         GAAAATGGGCATGATGAGATTGTCATCAAAGCTATGGGAAGAGCCATCAAT
genomic: CACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAGgtgaccctac ... tctttttcagGAAAATGGGCATGATGAGATTGTCATCAAAGCTATGGGAAGAGCCATCAAT

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: 74 (upstream exon), 75 (downstream exon)
Score: 54

GAAGCCTCGCAATGAGACACCAATTAGTGAGAATGAGATCAGGATCACTGCACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAGgtgaccctac ... tctttttcagGAAAATGGGCATGATGAGATTGTCATCAAAGCTATGGGAAGAGCCATCAATAAGACAGTCATGGTTGTTGAATTGATCAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGCCTCGCAATGAGACACCAATTAGTGAGAATGAGATCAGGATCACTGCACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAGgtgaccctactactattactttcctttggctatgttgttatttgaggtagaacatgcagcaaccttttttgtgccatgttttaacaattaacaggacgcg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT