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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatccctgcttgtttactatgttgtggtactagtattagcataaccaaatgatatcctaactttgaaacttaggtggctaacaattttctaccattttctagGGATCTTAGTGAACAGGAGAGTGAGCGCAAGGAACTAGAGGAG

Basic information

species Oryza sativa
transcript LOC_Os01g55730.1
intron # 5
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|33381195|gb|CF196538.1|CF196538
EST:     CTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAGCGCTTGTCGGAAG                         GGATCTTAGTGAACAGGAGAGTGAGCGCAAGGAACTAGAGGAG
genomic: CTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAGCGCTTGTCGGAAGgtgatccctg ... cattttctagGGATCTTAGTGAACAGGAGAGTGAGCGCAAGGAACTAGAGGAG
EST: gi|38470771|gb|CF954902.1|CF954902
EST:     CTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAGCGCTTGTCGGAAG                         GGATCTTAGTGAACAGGAGAGTGAGCGCAAGGAACTAGAGGAG
genomic: CTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAGCGCTTGTCGGAAGgtgatccctg ... cattttctagGGATCTTAGTGAACAGGAGAGTGAGCGCAAGGAACTAGAGGAG
EST: gi|3767261|gb|AU031371.1|AU031371
EST:     CTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAGCGCTTGTCGGAAG                         GGATCTTAGTGAACAGGAGAGTGAGCGCAAGGAACTAGAGGAG
genomic: CTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAGCGCTTGTCGGAAGgtgatccctg ... cattttctagGGATCTTAGTGAACAGGAGAGTGAGCGCAAGGAACTAGAGGAG
EST: gi|88518445|gb|CI446099.1|CI446099
EST:     TGCTGCACTTGTGTTAAAGCGCTTGTCGGAAG                         GGATCTTAGTGAACAGGAGAGTGAGCGCAAGGAACTAGAGGAG
genomic: TGCTGCACTTGTGTTAAAGCGCTTGTCGGAAGgtgatccctg ... cattttctagGGATCTTAGTGAACAGGAGAGTGAGCGCAAGGAACTAGAGGAG
EST: gi|88727187|gb|CI750842.1|CI750842
EST:     CTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAGCGCTTGTCGGAAG                         GGATCTTAGTGAACAGGA
genomic: CTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAGCGCTTGTCGGAAGgtgatccctg ... cattttctagGGATCTTAGTGAACAGGA
EST: gi|88420754|gb|CI564590.1|CI564590
EST:     CTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAGCGCTTGTCGGAAG                         GGATCTTAGTGAACAGGAGAGTGAGCGCAAGGAACTA
genomic: CTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAGCGCTTGTCGGAAGgtgatccctg ... cattttctagGGATCTTAGTGAACAGGAGAGTGAGCGCAAGGAACTA
EST: gi|88296284|gb|CI667674.1|CI667674
EST:     CTTGGGATCTGCGCGAAGTGCTGCACTTGTGTTAAAGCGCTCGTCGGAAG                         GGATCTTAGTGAACAGGAG
genomic: CTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAGCGCTTGTCGGAAGgtgatccctg ... cattttctagGGATCTTAGTGAACAGGAG
EST: gi|66932185|gb|CX119033.1|CX119033
EST:     CTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAGCGCTTGTCGGAAG                         GGATCTTAGTGAACAGGAGAGTGAGCGCAAGGAACTAGAGGAG
genomic: CTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAGCGCTTGTCGGAAGgtgatccctg ... cattttctagGGATCTTAGTGAACAGGAGAGTGAGCGCAAGGAACTAGAGGAG

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: 53 (upstream exon), 39 (downstream exon)
Score: 23

CTTGCTCCAAGGACCTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAGCGCTTGTCGGAAGgtgatccctg ... cattttctagGGATCTTAGTGAACAGGAGAGTGAGCGCAAGGAACTAGAGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgatatcctaactttgaaacttaggtggctaacaattttctaccattttctagGGATCTTAGTGAACAGGAGAGTGAGCGCAAGGAACTAGAGGAG
                                     ttttctaccattttct  CT-rich tract
                               taacaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatccctgcttgtttactatgttgtggtactagtattagcataaccaaatgatatcctaactttgaaacttaggtggctaacaattttctaccattttctagGGATCTTAGTGAACAGGAGAGTGAGCGCAAGGAACTAGAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG