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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtacaatattatcctatatatattgtgactgttcatgcttgtacattgttcaattaatactgtcacacttatatgcatctctgtttgtgttcctcattagGCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTAAAGCCTATAAGTACAAAGCAGAACTACTTGTTAAGGACTACCTGCTAGC

Basic information

species Oryza sativa
transcript LOC_Os05g43540.1
intron # 1
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|14192049|gb|AU184260.1|AU184260
EST:     ACCCGCNCCGCNCAG                         GCTGTNGAGTTATNACGTATTTGATTATGGATCTGCCATTGATGGCTGNTA
genomic: ACCCGCGCCGCGCAGgtgaggcctc ... tcctcattagGCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
EST: gi|33691826|gb|CF320065.1|CF320065
EST:     TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAG                         GCTGTTGAGTTATCACATATTTGATTATGGATCTGCCATTGATGGCTGCTA
genomic: TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAGgtgaggcctc ... tcctcattagGCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
EST: gi|87017390|gb|CI287930.1|CI287930
EST:     TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAG                         GCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
genomic: TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAGgtgaggcctc ... tcctcattagGCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
EST: gi|88396750|gb|CI620083.1|CI620083
EST:     TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAG                         GCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
genomic: TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAGgtgaggcctc ... tcctcattagGCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
EST: gi|88744411|gb|CI767771.1|CI767771
EST:     TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAG                         GCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCCA
genomic: TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAGgtgaggcctc ... tcctcattagGCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
EST: gi|88738580|gb|CI762088.1|CI762088
EST:     TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAG                         GCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
genomic: TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAGgtgaggcctc ... tcctcattagGCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
EST: gi|88732544|gb|CI755721.1|CI755721
EST:     TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAG                         GCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
genomic: TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAGgtgaggcctc ... tcctcattagGCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
EST: gi|88299491|gb|CI574604.1|CI574604
EST:     TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAG                         GCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
genomic: TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAGgtgaggcctc ... tcctcattagGCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
EST: gi|88733324|gb|CI756501.1|CI756501
EST:     TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAG                         GCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
genomic: TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAGgtgaggcctc ... tcctcattagGCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
EST: gi|88324944|gb|CI644955.1|CI644955
EST:     TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAG                         GCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
genomic: TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAGgtgaggcctc ... tcctcattagGCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
EST: gi|88731489|gb|CI755102.1|CI755102
EST:     TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAG                         GCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
genomic: TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAGgtgaggcctc ... tcctcattagGCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
EST: gi|88317525|gb|CI672101.1|CI672101
EST:     TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAG                         GCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
genomic: TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAGgtgaggcctc ... tcctcattagGCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
EST: gi|88362871|gb|CI614227.1|CI614227
EST:     TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAG                         GCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
genomic: TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAGgtgaggcctc ... tcctcattagGCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
EST: gi|29666719|gb|CB662994.1|CB662994
EST:     TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAG                         GCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
genomic: TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAGgtgaggcctc ... tcctcattagGCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
EST: gi|88724208|gb|CI747467.1|CI747467
EST:     TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAG                         GCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
genomic: TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAGgtgaggcctc ... tcctcattagGCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
EST: gi|88407568|gb|CI586409.1|CI586409
EST:     TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAG                         GCTGTTGAGTTATCACGTATTTGGTTATGGATCTGCCATTGATGGCTGCTA
genomic: TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAGgtgaggcctc ... tcctcattagGCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
EST: gi|88732137|gb|CI757314.1|CI757314
EST:     TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAG                         GCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
genomic: TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAGgtgaggcctc ... tcctcattagGCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
EST: gi|88386133|gb|CI570768.1|CI570768
EST:     TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAG                         GCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
genomic: TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAGgtgaggcctc ... tcctcattagGCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
EST: gi|88377308|gb|CI600463.1|CI600463
EST:     TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAG                         GCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
genomic: TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAGgtgaggcctc ... tcctcattagGCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
EST: gi|88592808|gb|CI710936.1|CI710936
EST:     TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAG                         GCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
genomic: TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAGgtgaggcctc ... tcctcattagGCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
EST: gi|88402501|gb|CI598728.1|CI598728
EST:     TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAG                         GCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
genomic: TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAGgtgaggcctc ... tcctcattagGCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
EST: gi|88406052|gb|CI593832.1|CI593832
EST:     TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAG                         GCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
genomic: TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAGgtgaggcctc ... tcctcattagGCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
EST: gi|66920779|gb|CX107627.1|CX107627
EST:     TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAG                         GCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
genomic: TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAGgtgaggcctc ... tcctcattagGCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
EST: gi|88311212|gb|CI570286.1|CI570286
EST:     TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAG                         GCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA
genomic: TCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAGgtgaggcctc ... tcctcattagGCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTA

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: 41 (upstream exon), 74 (downstream exon)
Score: 5

TTCCGCCGTGGGGAAGGGAGCAATCGGCAAGCCAATCCAATCCGGTTGCTTCTCCTCCAATCCAACCTCGTCGGCGGCGGCGGCGACCCGCGCCGCGCAGgtgaggcctc ... tcctcattagGCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTAAAGCCTATAAGTACAAAGCAGAACTACTTGTTAAGGACTACCTGCTAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttcaattaatactgtcacacttatatgcatctctgtttgtgttcctcattagGCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTAAAGCCTATAAGTACAAAGCAGAACTACTTGTTAAGGACTACCTGCTAGC
      aattaat  putative branch site (score: 5)
 ttcctcatt  putative PPT
 aattaatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaatattatcctatatatattgtgactgttcatgcttgtacattgttcaattaatactgtcacacttatatgcatctctgtttgtgttcctcattagGCTGTTGAGTTATCACGTATTTGATTATGGATCTGCCATTGATGGCTGCTAAAGCCTATAAGTACAAAGCAGAACTACTTGTTAAGGACTACCTGCTAGC

- - - - - - - - - - - - gtgactg
- - - - - - - - - - - - - - - -ttcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgtcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atatgca