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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGCGCTCATGGAGAAGAACCAGAAGTACGTCGCCGACCCGCCCACCATCGAGAGGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtcggtccaccctcacgatctccctccaccttctccacgatctcttagtcctccacatctgaattatctctattgtttagattgcgcactccattagaac...

Basic information

species Oryza sativa
transcript LOC_Os05g45740.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g45740.2 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S130_298V6.1 (Physcomitrella patens), 5'ss of exon 1
GGGCGCTCATGGAGAAGAACCAGAAGTACGTCGCCGACCCGCCCACCATCGAGAGGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtcggtc-caccctcacgatctccc-tccaccttctccacgatctcttagtcctccacatctgaatt-atctctattgtttagattgcgcactccattagaac-
 |  | |||||||  ||||| || |  | |||| | | ||  ||||  |||||| ||| ||||||||||| ||||| ||||||||||| |||||||| ||||| |   ||||||  |  | | |  | || ||||     ||| |||     ||   | ||    || |||  | | ||| | |||  |    |   | |    
AGCAGGTCATGGAAGAGAACAAGCAACATGTCGTCCATCCAGCCACAGTCGAGAAGTGTCAGGAGCTCTCTAAGCAACTCTTCTACACTCGCCTCGCTAGgtctgcgacaccctttctcttttctgtacagcttc----ggatttctcttctctgatcttccttgttgatccttgtcgttcatattttgttgcctccttgcctt

upper sequence: LOC_Os05g45740.2 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ11912 (Selaginella moellendorffii), 5'ss of exon 1
GGGCGCTCATGGAGAAGAACCAGAAGTACGTCGCCGACCCGCCCACCATCGAGAGGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtcggtccaccctcacgatctccctccaccttctccacgatctcttagtcctccacatctgaattatctctattgtttagattgcgcactccattagaac
 | ||||  | |||  |||| || | ||| |||  ||   ||| ||  | |||| |||  | |||||||||||||||||| ||||||| ||||| |||||||  |         | |   |||||     ||   | ||   ||     ||| | |    | |                                     
AGACGCTGCTCGAGCGGAACAAGCATTACATCGTGGAAGAGCCGACGGTGGAGAAGTGTAACGAGCTCTCCAAGCAGCTCCTCTACACGCGCCTGGCCAGgtatgg--------atggaatcccttgga-ttgatcgcggaatcgcgacccttctctctcgcag------------------------------------
















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|87019657|gb|CI284343.1|CI284343
EST:     GAGAGGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAG                         CCTTCCTGGTCGCTATGAGGCATTCTGGAAGGAAGCGGATCAAGTGAAGAA
genomic: GAGAGGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtcggtccac ... tttcttgcagCCTTCCTGGTCGCTATGAGGCATTCTGGAAGGAAGCGGATCAAGTGAAGAA
EST: gi|88341490|gb|CI635688.1|CI635688
EST:     GAGAGGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAG                         CCTTCCTGGTCGCTATGAGGCATTCTGGAAGGAAGCGGATCAAGTGAAGAA
genomic: GAGAGGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtcggtccac ... tttcttgcagCCTTCCTGGTCGCTATGAGGCATTCTGGAAGGAAGCGGATCAAGTGAAGAA
EST: gi|88210854|gb|CI209130.1|CI209130
EST:     GAGAGGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAG                         CCTTCCTGGTCGCTATGAGGCATTCTGGAAGGAAGCGGATCAAGTGAAGAA
genomic: GAGAGGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtcggtccac ... tttcttgcagCCTTCCTGGTCGCTATGAGGCATTCTGGAAGGAAGCGGATCAAGTGAAGAA
EST: gi|55439000|gb|CV732801.1|CV732801
EST:     GAGAGGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAG                         CCTTCCTGGTCGCTATGAGGCATTCTGGAAGGAAGCGGATCAAGTGAAGAA
genomic: GAGAGGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtcggtccac ... tttcttgcagCCTTCCTGGTCGCTATGAGGCATTCTGGAAGGAAGCGGATCAAGTGAAGAA
EST: gi|55414848|gb|CV727224.1|CV727224
EST:     GAGAGGTGCCAGGAGCTCTCCAAGCAGCTTTTTTACACCCGCCTCGCCAG                         CCTTCCTGGTCGCTATGAGGCATTCTGGAAGGAAGCGGATCAAGTGAAGAA
genomic: GAGAGGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtcggtccac ... tttcttgcagCCTTCCTGGTCGCTATGAGGCATTCTGGAAGGAAGCGGATCAAGTGAAGAA
EST: gi|88237696|gb|CI237545.1|CI237545
EST:     GAGAGGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAG                         CCTTCCTGGTCGCTATGAGGCATTCTGGAAGGAAGCGGATCAAGTGAAGAA
genomic: GAGAGGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtcggtccac ... tttcttgcagCCTTCCTGGTCGCTATGAGGCATTCTGGAAGGAAGCGGATCAAGTGAAGAA
EST: gi|88518342|gb|CI445996.1|CI445996
EST:     GGAGCTCTCCAAGCAGCTCTTNTACACCCCCCTCGCCAG                         CCTTCCTGGTCGCTATGAGGCATTCTGGAAGGAAGCGGATCAAGTGAAGAA
genomic: GGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtcggtccac ... tttcttgcagCCTTCCTGGTCGCTATGAGGCATTCTGGAAGGAAGCGGATCAAGTGAAGAA
EST: gi|88284628|gb|CI406074.1|CI406074
EST:     GAGAGGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAG                         CCTTCCTGGTCGCTATGAGGCATTCTGGAAGGAAGCGGATCAAGTGAAGAA
genomic: GAGAGGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtcggtccac ... tttcttgcagCCTTCCTGGTCGCTATGAGGCATTCTGGAAGGAAGCGGATCAAGTGAAGAA
EST: gi|88243741|gb|CI242863.1|CI242863
EST:     GAGAGGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAG                         CCTTCCTGGTCGCTATGAGGCATTCTGGAAGGAAGCGGATCAAGTGAAGAA
genomic: GAGAGGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtcggtccac ... tttcttgcagCCTTCCTGGTCGCTATGAGGCATTCTGGAAGGAAGCGGATCAAGTGAAGAA
EST: gi|88213071|gb|CI212735.1|CI212735
EST:     GAGAGGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAG                         CCTTCCTGGTCGCTATGAGGCATTCTGGAAGGAAGCGGATCAAGTGAAGAA
genomic: GAGAGGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtcggtccac ... tttcttgcagCCTTCCTGGTCGCTATGAGGCATTCTGGAAGGAAGCGGATCAAGTGAAGAA
EST: gi|88961487|gb|CI096780.1|CI096780
EST:     CCCGCCTCGCCAG                         CCTTCCTGGTCGCTATGAGGCATTCTGGAAGGAAGCGGATCAAGTGAAGAA
genomic: CCCGCCTCGCCAGgtcggtccac ... tttcttgcagCCTTCCTGGTCGCTATGAGGCATTCTGGAAGGAAGCGGATCAAGTGAAGAA

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: 58 (upstream exon), 75 (downstream exon)
Score: 7

GGGCGCTCATGGAGAAGAACCAGAAGTACGTCGCCGACCCGCCCACCATCGAGAGGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtcggtccac ... tttcttgcagCCTTCCTGGTCGCTATGAGGCATTCTGGAAGGAAGCGGATCAAGTGAAGAACTTGTGGAGAAACAGAAAGGATCTGAACGTTGAGCATGCTGGCGTTGCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGCGCTCATGGAGAAGAACCAGAAGTACGTCGCCGACCCGCCCACCATCGAGAGGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtcggtccaccctcacgatctccctccaccttctccacgatctcttagtcctccacatctgaattatctctattgtttagattgcgcactccattagaac

- - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caccctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgcactcc