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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggatccaactgttactcttgttactccaattataaaaaggagaaagttgcatctgatttgtgtcatctctgaaatattaacgcactctttgtttttgcagCCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCACTGTTTATGGAATGGAGAAGTCAAGCCA

Basic information

species Oryza sativa
transcript LOC_Os02g02530.2
intron # 10
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|86436738|gb|CI118460.1|CI118460
EST:     TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAG                         CCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAGgtgagtcatg ... gtttttgcagCCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|88246627|gb|CI246476.1|CI246476
EST:     ACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAG                         CCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: ACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAGgtgagtcatg ... gtttttgcagCCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|86536960|gb|CI177166.1|CI177166
EST:     TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAG                         CCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAGgtgagtcatg ... gtttttgcagCCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|3768652|gb|AU032679.1|AU032679
EST:     TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAG                         CCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAGgtgagtcatg ... gtttttgcagCCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|89190059|gb|CI013626.1|CI013626
EST:     TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAG                         CCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAGgtgagtcatg ... gtttttgcagCCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|88263333|gb|CI367107.1|CI367107
EST:     CAAGCCGCACAG                         CCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: CAAGCCGCACAGgtgagtcatg ... gtttttgcagCCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|3764135|gb|AU030635.1|AU030635
EST:     TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAG                         CCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAGgtgagtcatg ... gtttttgcagCCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|86505531|gb|CI148164.1|CI148164
EST:     TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAG                         CCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAGgtgagtcatg ... gtttttgcagCCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|29629872|gb|CB634881.1|CB634881
EST:     TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCTGCACAG                         CCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAGgtgagtcatg ... gtttttgcagCCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|89180263|gb|CI044542.1|CI044542
EST:     TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAG                         CCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAGgtgagtcatg ... gtttttgcagCCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|88841193|gb|CI080647.1|CI080647
EST:     AACTGGTTTCAAGCCGCACAG                         CCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: AACTGGTTTCAAGCCGCACAGgtgagtcatg ... gtttttgcagCCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|86431949|gb|CI085560.1|CI085560
EST:     TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAG                         CCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAGgtgagtcatg ... gtttttgcagCCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|8858846|gb|AU096164.1|AU096164
EST:     TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAG                         CCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAGgtgagtcatg ... gtttttgcagCCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|88974741|gb|CI023037.1|CI023037
EST:     TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAG                         CCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAGgtgagtcatg ... gtttttgcagCCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|88268306|gb|CI378241.1|CI378241
EST:     ATAATTGTGATGAACTGGTTTCAAGCCGCACAAG                         CCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCA
genomic: ATAATTGTGATGAACTGGTTTCAAGCCGCAC-AGgtgagtcatg ... gtttttgcagCCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCA
EST: gi|88227079|gb|CI228559.1|CI228559
EST:     TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAG                         CCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAGgtgagtcatg ... gtttttgcagCCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|88201253|gb|CI201608.1|CI201608
EST:     TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAG                         CCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAGgtgagtcatg ... gtttttgcagCCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|86251700|gb|CI018892.1|CI018892
EST:     ATTGTGATGAACTGGTTTCAAGCCGCACAG                         CCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: ATTGTGATGAACTGGTTTCAAGCCGCACAGgtgagtcatg ... gtttttgcagCCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|87031167|gb|CI259747.1|CI259747
EST:     TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAG                         CCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAGgtgagtcatg ... gtttttgcagCCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|88836000|gb|CI371105.1|CI371105
EST:     ATTGTGATGAACT-GTTTCAAGCCGCACAG                         CCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: ATTGTGATGAACTGGTTTCAAGCCGCACAGgtgagtcatg ... gtttttgcagCCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|89168583|gb|CI038937.1|CI038937
EST:     TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAG                         CCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAGgtgagtcatg ... gtttttgcagCCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|86428283|gb|CI074964.1|CI074964
EST:     TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAG                         CCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAGgtgagtcatg ... gtttttgcagCCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|29660567|gb|CB656842.1|CB656842
EST:     TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAG                         CCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAGgtgagtcatg ... gtttttgcagCCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|29631479|gb|CB636488.1|CB636488
EST:     TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAG                         CCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: TGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAGgtgagtcatg ... gtttttgcagCCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC

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: 64 (upstream exon), 75 (downstream exon)
Score: 8

AAGAGGAATTAAGAACCGCTACTTCAATAGTGCATTTTTGGGTTATACGGTGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAGgtgagtcatg ... gtttttgcagCCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCACTGTTTATGGAATGGAGAAGTCAAGCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgcatctgatttgtgtcatctctgaaatattaacgcactctttgtttttgcagCCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCACTGTTTATGGAATGGAGAAGTCAAGCCA
                             tattaac  putative branch site (score: 8)
                                     cactctttgttttt  CT-rich tract
                        tgaaatattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggatccaactgttactcttgttactccaattataaaaaggagaaagttgcatctgatttgtgtcatctctgaaatattaacgcactctttgtttttgcagCCTGCCCTCTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCACTGTTTATGGAATGGAGAAGTCAAGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT