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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcacagtcaattaagttgtcagcactgaccagttgggaagttcttttgtctcctttcatatttacatcgatactgacccatcgattccaatttctttagGAGTCGCTGGCCTCAAGAAAAACAGCAAGAGAGCGTTGGATTCGAGTAATGCACAGACCAGCTCTGGATTAACTGCTTTTAACCCGGTAGATAAC

Basic information

species Oryza sativa
transcript LOC_Os01g64900.1
intron # 30
splice site 3'
intron type U2

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|86480040|gb|CI122673.1|CI122673
EST:     TGATATTGACGACAATTTTGTGAAGCAGCCTTTTTCAAATAACAGAACAG                         GAGTCGCTGGCCTCAAGAAAAACAGCAAGAGAGCGTTGGATTCGAGTAATG
genomic: TGATATTGACGACAATTTTGTGAAGCAGCCTTTTTCAAATAACAGAACAGgtaaatgagt ... atttctttagGAGTCGCTGGCCTCAAGAAAAACAGCAAGAGAGCGTTGGATTCGAGTAATG
EST: gi|88490440|gb|CI427712.1|CI427712
EST:     TGATATTGACGACAATTTTGTGAAGCAGCCTTTTTCAAATAACAGAACAG                         GAGTCGCTGGCCTCAAGAAAAACAGCAAGAGAGCGTTGGATTCGAGTAATG
genomic: TGATATTGACGACAATTTTGTGAAGCAGCCTTTTTCAAATAACAGAACAGgtaaatgagt ... atttctttagGAGTCGCTGGCCTCAAGAAAAACAGCAAGAGAGCGTTGGATTCGAGTAATG
EST: gi|88485866|gb|CI423137.1|CI423137
EST:     TGATATTGACGACAATTTTGTGAAGCAGCCTTTTTCAAATAACAGAACA-                         GAGGTCGCTGGCCTCAAGGAAAACAGCAAGAGAGCGTTGGATTCGAGTAAT
genomic: TGATATTGACGACAATTTTGTGAAGCAGCCTTTTTCAAATAACAGAACAGgtaaatgagt ... atttctttagGA-GTCGCTGGCCTCAAGAAAAACAGCAAGAGAGCGTTGGATTCGAGTAAT
EST: gi|88477928|gb|CI415199.1|CI415199
EST:     TGATATTGACGACAATTTTGTGAAGCAGCCTTTTTCAAATAACAGAACAG                         GAGTCGCTGGCCTCAAGAAAAACAGCAAGAGAGCGTTGGATTCGAGTAATG
genomic: TGATATTGACGACAATTTTGTGAAGCAGCCTTTTTCAAATAACAGAACAGgtaaatgagt ... atttctttagGAGTCGCTGGCCTCAAGAAAAACAGCAAGAGAGCGTTGGATTCGAGTAATG
EST: gi|88844808|gb|CI021383.1|CI021383
EST:     TGATATTGACGACAATTTTGTGAAGCAGCCTTTTTCAAATAACAGAACAG                         GAGTCGCTGGCCTCAAGAAAAACAGCAAGAGAGCGTTGGATTCGAGTAATG
genomic: TGATATTGACGACAATTTTGTGAAGCAGCCTTTTTCAAATAACAGAACAGgtaaatgagt ... atttctttagGAGTCGCTGGCCTCAAGAAAAACAGCAAGAGAGCGTTGGATTCGAGTAATG
EST: gi|88487985|gb|CI425256.1|CI425256
EST:     TGATATTGACGACAATTTTGTGAANCAGCCTTTTTCAAATAACAGAACAG                         GAGTCGCTGGCCTCAAGAAAAACACCAAGAGANCGTTGGATTCGAGTAATG
genomic: TGATATTGACGACAATTTTGTGAAGCAGCCTTTTTCAAATAACAGAACAGgtaaatgagt ... atttctttagGAGTCGCTGGCCTCAAGAAAAACAGCAAGAGAGCGTTGGATTCGAGTAATG
EST: gi|88473882|gb|CI411153.1|CI411153
EST:     TGATATTGACGACAATTTTGTGAAGCAGCCTTTTTCAAATAACAGAACAG                         GAGTCGCTGGCCTCAAGAAAAACANCAAGAGAGCGTTGGATTCGAGTAATG
genomic: TGATATTGACGACAATTTTGTGAAGCAGCCTTTTTCAAATAACAGAACAGgtaaatgagt ... atttctttagGAGTCGCTGGCCTCAAGAAAAACAGCAAGAGAGCGTTGGATTCGAGTAATG

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: 19 (upstream exon), 60 (downstream exon)
Score: 2

TGATCCTGATGAAGATGGTGATATTGACGACAATTTTGTGAAGCAGCCTTTTTCAAATAACAGAACAGgtaaatgagt ... atttctttagGAGTCGCTGGCCTCAAGAAAAACAGCAAGAGAGCGTTGGATTCGAGTAATGCACAGACCAGCTCTGGATTAACTGCTTTTAACCCGGTAGATAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtctcctttcatatttacatcgatactgacccatcgattccaatttctttagGAGTCGCTGGCCTCAAGAAAAACAGCAAGAGAGCGTTGGATTCGAGTAATGCACAGACCAGCTCTGGATTAACTGCTTTTAACCCGGTAGATAAC
                          tactgac  putative branch site (score: 2)
                                              tttcttt  putative PPT
         tttcatatttacat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcacagtcaattaagttgtcagcactgaccagttgggaagttcttttgtctcctttcatatttacatcgatactgacccatcgattccaatttctttagGAGTCGCTGGCCTCAAGAAAAACAGCAAGAGAGCGTTGGATTCGAGTAATGCACAGACCAGCTCTGGATTAACTGCTTTTAACCCGGTAGATAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
tgcacag
- - - - - - - - - - - gcactga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatactg