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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGTATCAGAGTACTCCCATGCTAGTGTGACCAGTACTTGTCAATTGGCCAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAGgtaagcatgcatcaatttattctgttctgaccttttgttttctgtgatgactattcattgttgttactacatattcatacttgttaatcttgtggatgtt...

Basic information

species Oryza sativa
transcript LOC_Os02g35130.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g35130.2 (Oryza sativa), 5'ss of exon 2
lower sequence: AC217665.3_FGT005 (Zea mays), 5'ss of exon 1
TTTGTATCAGAGTACTCCCATGCTAGTGTGACCAGTACTTGTCAATTGGCCAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAGgtaagcatgcatcaatttattctgttctgaccttttgttt--tctgtgatgactattcattgttgttactacatattcatacttgttaatcttgtggatgtt----
||||||||||| || || ||||| ||||| || | ||||||||| ||||  |||||  | || ||||| ||||| ||| |||||||||||||||| |||||||||    | ||||||| |  ||||    |  | ||||   || |||  | || ||   |||| | | |  ||    | | ||   |  ||   | ||| |    
TTTGTATCAGAATATTCACATGCCAGTGTTACTAATACTTGTCAGTTGGGAAGCACTACCCTGAAGGACGGCCGCACCATCAATGTTATTGATACACCAGgtaag---acttcaatttttaatgttacttctatctgttcaatccgtgg-gtctttttggtgttataattttatgagtagatttaaaagacta--gaatgcttaga
















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|88742174|gb|CI765682.1|CI765682
EST:     CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAG                         GATTATTTGAAATGACCATTACATCTGAGGATGCCGGTAAAGAAATTGTTA
genomic: CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAGgtaagcatgc ... tctctaatagGATTATTTGAAATGACCATTACATCTGAGGATGCCGGTAAAGAAATTGTTA
EST: gi|33380835|gb|CF196178.1|CF196178
EST:     CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAG                         GATTATTTGAAATGACCATTACATCTGAGGATGCCGGTAAAGAAATTGTTA
genomic: CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAGgtaagcatgc ... tctctaatagGATTATTTGAAATGACCATTACATCTGAGGATGCCGGTAAAGAAATTGTTA
EST: gi|88333408|gb|CI642445.1|CI642445
EST:     CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAG                         GATTATTTGAAATGACCATTACATCT
genomic: CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAGgtaagcatgc ... tctctaatagGATTATTTGAAATGACCATTACATCT
EST: gi|88592598|gb|CI710710.1|CI710710
EST:     CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAG                         GATTATTTGAAATGACCATTACATCTGA
genomic: CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAGgtaagcatgc ... tctctaatagGATTATTTGAAATGACCATTACATCTGA
EST: gi|88424310|gb|CI581865.1|CI581865
EST:     CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAG                         GATTATTTGAAATGACCATTACATCTGAGGA
genomic: CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAGgtaagcatgc ... tctctaatagGATTATTTGAAATGACCATTACATCTGAGGA
EST: gi|88381562|gb|CI682222.1|CI682222
EST:     CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAG                         GATTATTTGAAATGACCATTACATCTGAGGATGCCGGTAAAGAAATTGTTA
genomic: CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAGgtaagcatgc ... tctctaatagGATTATTTGAAATGACCATTACATCTGAGGATGCCGGTAAAGAAATTGTTA
EST: gi|88761356|gb|CI770912.1|CI770912
EST:     CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAG                         GATTATTTGAAATGACCATTACATCTGAGGATGCC
genomic: CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAGgtaagcatgc ... tctctaatagGATTATTTGAAATGACCATTACATCTGAGGATGCC
EST: gi|88329563|gb|CI648627.1|CI648627
EST:     CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAG                         GATTATTTGAAATGACCATTACATCTGAGGATGCCGGTAAAGAAATTGTTA
genomic: CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAGgtaagcatgc ... tctctaatagGATTATTTGAAATGACCATTACATCTGAGGATGCCGGTAAAGAAATTGTTA
EST: gi|88348617|gb|CI634212.1|CI634212
EST:     CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAG                         GATTATTTGAAATGACCATTACATCTGAGGATGCCGGTAAAGAAATTGTTA
genomic: CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAGgtaagcatgc ... tctctaatagGATTATTTGAAATGACCATTACATCTGAGGATGCCGGTAAAGAAATTGTTA
EST: gi|88336951|gb|CI627031.1|CI627031
EST:     CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAG                         GATTATTTGAAATGACCATTACATCTGAGGATGCCGGTAAAGAAATTGTTA
genomic: CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAGgtaagcatgc ... tctctaatagGATTATTTGAAATGACCATTACATCTGAGGATGCCGGTAAAGAAATTGTTA
EST: gi|88342052|gb|CI644389.1|CI644389
EST:     CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAG                         GATTATTTGAAATGACCATTACATCTGAGGATGCCGGTAAAGAAATTGTTA
genomic: CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAGgtaagcatgc ... tctctaatagGATTATTTGAAATGACCATTACATCTGAGGATGCCGGTAAAGAAATTGTTA
EST: gi|29678306|gb|CB674581.1|CB674581
EST:     CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAG                         GATTATTTGAAATGACCATTACATCTGAGGATGCCGGTAAAGAAATTGTTA
genomic: CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAGgtaagcatgc ... tctctaatagGATTATTTGAAATGACCATTACATCTGAGGATGCCGGTAAAGAAATTGTTA
EST: gi|88327626|gb|CI646819.1|CI646819
EST:     CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAG                         GATTATTTGAAATGACCATTACATCTGAGGATG
genomic: CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAGgtaagcatgc ... tctctaatagGATTATTTGAAATGACCATTACATCTGAGGATG
EST: gi|88744424|gb|CI767784.1|CI767784
EST:     CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAG                         GATTATTTGAAATGACCATTACATCTGA
genomic: CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAGgtaagcatgc ... tctctaatagGATTATTTGAAATGACCATTACATCTGA
EST: gi|88329955|gb|CI652342.1|CI652342
EST:     CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAG                         GATTATTTGAAATGACCATTACATCTGAGGATGCCGGTAAAGAAATTGTTA
genomic: CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAGgtaagcatgc ... tctctaatagGATTATTTGAAATGACCATTACATCTGAGGATGCCGGTAAAGAAATTGTTA
EST: gi|88761455|gb|CI771011.1|CI771011
EST:     CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAG                         GATTATTTGAAATGACCATTA
genomic: CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAGgtaagcatgc ... tctctaatagGATTATTTGAAATGACCATTA
EST: gi|88733176|gb|CI756353.1|CI756353
EST:     CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAG                         GATTATTTGAAATGACC
genomic: CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAGgtaagcatgc ... tctctaatagGATTATTTGAAATGACC
EST: gi|88344317|gb|CI655711.1|CI655711
EST:     CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAG                         GATTATTTGAAATGACCATTACATCTGAGGATGCCGGTAAAGAAATTGTTA
genomic: CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAGgtaagcatgc ... tctctaatagGATTATTTGAAATGACCATTACATCTGAGGATGCCGGTAAAGAAATTGTTA
EST: gi|88735635|gb|CI759143.1|CI759143
EST:     CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAG                         GATTATTTGAAATGACCATTACATCTGAGGATGCCGGTAAAG
genomic: CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAGgtaagcatgc ... tctctaatagGATTATTTGAAATGACCATTACATCTGAGGATGCCGGTAAAG
EST: gi|33675112|gb|CF303351.1|CF303351
EST:     CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAG                         GATTATTTGAAATGACCATTACATCTGAGGATGCCGGTAAAGAAATTGTTA
genomic: CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAGgtaagcatgc ... tctctaatagGATTATTTGAAATGACCATTACATCTGAGGATGCCGGTAAAGAAATTGTTA
EST: gi|33684157|gb|CF312396.1|CF312396
EST:     CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAG                         GATTATTTGAAATGACCATTACATCTGAGGATGCCGGTAAAGAAATTGTTA
genomic: CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAGgtaagcatgc ... tctctaatagGATTATTTGAAATGACCATTACATCTGAGGATGCCGGTAAAGAAATTGTTA
EST: gi|88340780|gb|CI636940.1|CI636940
EST:     CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAG                         GATTATTTGAAATGACCATTACATCTGAGGATGCCGGT
genomic: CAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAGgtaagcatgc ... tctctaatagGATTATTTGAAATGACCATTACATCTGAGGATGCCGGT

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), 72 (downstream exon)
Score: 34

TTTGTATCAGAGTACTCCCATGCTAGTGTGACCAGTACTTGTCAATTGGCCAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAGgtaagcatgc ... tctctaatagGATTATTTGAAATGACCATTACATCTGAGGATGCCGGTAAAGAAATTGTTAAGTGTATGAGTATGGCCAAGGATGGGATACATGCAGTGCTGATGGTTTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGTATCAGAGTACTCCCATGCTAGTGTGACCAGTACTTGTCAATTGGCCAGCACCGCGCTAAAGGATGGCCGTACCCTCAATGTTATTGATACGCCAGgtaagcatgcatcaatttattctgttctgaccttttgttttctgtgatgactattcattgttgttactacatattcatacttgttaatcttgtggatgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG