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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcctcattttgtacttctaaattacctcctcgtaatttttaaaatgttcaaatgccagtttttcacttaactggctcccagGTCAACAAGATCTTTGCCGAAAATGCGTTTGATGCTGTTATGCACTTTGCTGCTGTTGCCTATGTGGGTGAGAGTACATTGGAACCCCTTAG

Basic information

species Oryza sativa
transcript LOC_Os08g03570.1
intron # 5
splice site 3'
intron type U12 (go to U12 genes for details)

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|29639521|gb|CB644530.1|CB644530
EST:     AGCCAGGAAGACTTCAGTTTATCTATGCTGATCTTGGAGATCAAAAAACT                         GTCAACAAGATCTTTGCCGANAATGCGTTTGATGCTGTTATGCACTTTGCT
genomic: AGCCAGGAAGACTTCAGTTTATCTATGCTGATCTTGGAGATCAAAAAACTgtatcctcat ... tggctcccagGTCAACAAGATCTTTGCCGAAAATGCGTTTGATGCTGTTATGCACTTTGCT
EST: gi|218499746|gb|FG949515.1|FG949515
EST:     AGCCAGGAAGACTTCAGTTTATCTATGCTGATCTTGGAGATCAAAAAACT                         GTCAACAAGATCTTTGCCGAAAATGCGTTTGATGCTGTTATGCACTTTGCT
genomic: AGCCAGGAAGACTTCAGTTTATCTATGCTGATCTTGGAGATCAAAAAACTgtatcctcat ... tggctcccagGTCAACAAGATCTTTGCCGAAAATGCGTTTGATGCTGTTATGCACTTTGCT
EST: gi|29660517|gb|CB656792.1|CB656792
EST:     GCCAGAAAGACTTCAGTTTATCTATGCTGATCTTGGAGATCNNNNNNNCT                         GTCAACAAGATCTTTGCCGAAAATGCGTTTGATGCTGTTATGCACTTTGC
genomic: GCCAGGAAGACTTCAGTTTATCTATGCTGATCTTGGAGATCAAAAAA-CTgtatcctcat ... tggctcccagGTCAACAAGATCTTTGCCGAAAATGCGTTTGATGCTGTTATGCACTTTGC
EST: gi|117233153|gb|CT848014.1|CT848014
EST:     AGCCAGGAAGACTTCAGTTTATCTATGCTGATCTTGGAGATCAAAAAACT                         GTCAACAAGATCTTTGCCGAAAATGCGTTTGATGCTGTTATGCACTTTGCT
genomic: AGCCAGGAAGACTTCAGTTTATCTATGCTGATCTTGGAGATCAAAAAACTgtatcctcat ... tggctcccagGTCAACAAGATCTTTGCCGAAAATGCGTTTGATGCTGTTATGCACTTTGCT
EST: gi|58695746|gb|CK084433.1|CK084433
EST:     AGCCAGGAAGACTTCAGTTTATCTATGCTGATCTTGGAGATCAAAAAACT                         GTCAACAAGATCTTTGCC
genomic: AGCCAGGAAGACTTCAGTTTATCTATGCTGATCTTGGAGATCAAAAAACTgtatcctcat ... tggctcccagGTCAACAAGATCTTTGCC

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: 66 (upstream exon), 74 (downstream exon)
Score: 25

TTCTAGAGGAAACATGGGAGCAGTAAAGGTTCTCCAAGAGTTGTTCCCCCAGCCAGGAAGACTTCAGTTTATCTATGCTGATCTTGGAGATCAAAAAACTgtatcctcat ... tggctcccagGTCAACAAGATCTTTGCCGAAAATGCGTTTGATGCTGTTATGCACTTTGCTGCTGTTGCCTATGTGGGTGAGAGTACATTGGAACCCCTTAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctcgtaatttttaaaatgttcaaatgccagtttttcacttaactggctcccagGTCAACAAGATCTTTGCCGAAAATGCGTTTGATGCTGTTATGCACTTTGCTGCTGTTGCCTATGTGGGTGAGAGTACATTGGAACCCCTTAG
 tcacttaac  putative branch site 
                                                ctccc  putative PPT
      taatttttaaaatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcctcattttgtacttctaaattacctcctcgtaatttttaaaatgttcaaatgccagtttttcacttaactggctcccagGTCAACAAGATCTTTGCCGAAAATGCGTTTGATGCTGTTATGCACTTTGCTGCTGTTGCCTATGTGGGTGAGAGTACATTGGAACCCCTTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT