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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgatcgattccactctttcctgacttcatctttagttagaggcagaaactgataatatgttatttttcagCTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTCATTGCTAAGCTTCAAGAGGTTGAGGATTGGTTGTACGAAGATGGTGAGG

Basic information

species Oryza sativa
transcript LOC_Os01g08560.1
intron # 6
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|58677519|gb|CK066206.1|CK066206
EST:     AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAG                         CTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTC
genomic: AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAGgtttgatcga ... tatttttcagCTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTC
EST: gi|218481790|gb|FG945721.1|FG945721
EST:     AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAG                         CTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTC
genomic: AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAGgtttgatcga ... tatttttcagCTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTC
EST: gi|58597595|gb|CK008123.1|CK008123
EST:     AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACGAG                         CTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACCAGGAAGCATTC
genomic: AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAGgtttgatcga ... tatttttcagCTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTC
EST: gi|2310021|gb|C26176.1|C26176
EST:     AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAG                         CTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTC
genomic: AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAGgtttgatcga ... tatttttcagCTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTC
EST: gi|29636673|gb|CB641682.1|CB641682
EST:     AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAG                         CTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTC
genomic: AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAGgtttgatcga ... tatttttcagCTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTC
EST: gi|27553959|gb|CA997859.1|CA997859
EST:     AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAG                         CTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTC
genomic: AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAGgtttgatcga ... tatttttcagCTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTC
EST: gi|86831930|gb|CI303370.1|CI303370
EST:     AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAG                         CTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTC
genomic: AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAGgtttgatcga ... tatttttcagCTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTC
EST: gi|29619080|gb|CB624092.1|CB624092
EST:     AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAG                         CTGTATGACAAGTACAATGATTTTGTGACTGCT
genomic: AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAGgtttgatcga ... tatttttcagCTGTATGACAAGTACAATGATTTTGTGACTGCT
EST: gi|86829544|gb|CI286738.1|CI286738
EST:     AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACGAG                         CTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTC
genomic: AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAGgtttgatcga ... tatttttcagCTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTC

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: 75 (upstream exon), 72 (downstream exon)
Score: 93

GGAAAAAGAGTATGAAATGGCTCTTCAGGACAGGGTGATGGAAGAGACAAAAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAGgtttgatcga ... tatttttcagCTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTCATTGCTAAGCTTCAAGAGGTTGAGGATTGGTTGTACGAAGATGGTGAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcctgacttcatctttagttagaggcagaaactgataatatgttatttttcagCTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTCATTGCTAAGCTTCAAGAGGTTGAGGATTGGTTGTACGAAGATGGTGAGG
                                            ttatttttc  CT-rich tract
                              aaactgataatatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgatcgattccactctttcctgacttcatctttagttagaggcagaaactgataatatgttatttttcagCTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTCATTGCTAAGCTTCAAGAGGTTGAGGATTGGTTGTACGAAGATGGTGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG