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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgaattcgaatgcacttctcttttttttgtatttatttgatcacaccaagagaacaagatggtactcttttgggttttgagcattcatgtgtgctgtttggtcatcagagtaccatctcatcgtagtgactgagtttattctggtcatttatgttcttggggtactgtacttccagAGGCCCAGCTTAGCAGTGATCTGGAAGAGCTGAAAGCTGCACACCTGAACTTGACGCGGCAGTGCGATTCGTTGGAGGAAAGCTTCAACAAGGAGAAGGC

Basic information

species Oryza sativa
transcript LOC_Os04g53760.2
intron # 3
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|88386555|gb|CI575333.1|CI575333
EST:     AAGCTCCGTAGCTACGATGGATGCAGAGAATGCC-AGCACGCCAAGTTGG                         AGGCCCAGCTTACCAGTGATCTGG
genomic: AAGCTCCGTAG-TACGATGGATGCAGAGAATGCCCAGCACGCCAAGTTGGgtaatgaatt ... gtacttccagAGGCCCAGCTTAGCAGTGATCTGG
EST: gi|29623653|gb|CB628664.1|CB628664
EST:     GAAGCTCCGTAGTACGATGGATGCAGAGAATGCCCAGCACGCCAAGTTGG                         AGGCCCAGCTTAGCAGTGATCTGGAAGAGCTGAAAGCTGCACACCTGAACT
genomic: GAAGCTCCGTAGTACGATGGATGCAGAGAATGCCCAGCACGCCAAGTTGGgtaatgaatt ... gtacttccagAGGCCCAGCTTAGCAGTGATCTGGAAGAGCTGAAAGCTGCACACCTGAACT
EST: gi|29635281|gb|CB640290.1|CB640290
EST:     GAAGCTCCGTAGTACGATGGATGCAGAGAATGCCCAGCACGCCAAGTTGG                         AGGCCCAGCTTANCAGTGATCTGGAAGAGCTGAAAGCTGCACACCTGAACT
genomic: GAAGCTCCGTAGTACGATGGATGCAGAGAATGCCCAGCACGCCAAGTTGGgtaatgaatt ... gtacttccagAGGCCCAGCTTAGCAGTGATCTGGAAGAGCTGAAAGCTGCACACCTGAACT
EST: gi|29637659|gb|CB642668.1|CB642668
EST:     GAAGCTCCGTAGTACGATGGATGCAGAGAATGCCCAGCACGCCAAGTTGG                         AGGCCCAGCTTAGCAGTGATCTGGAAGAGCTGAAAGCTGCACACCTGAACT
genomic: GAAGCTCCGTAGTACGATGGATGCAGAGAATGCCCAGCACGCCAAGTTGGgtaatgaatt ... gtacttccagAGGCCCAGCTTAGCAGTGATCTGGAAGAGCTGAAAGCTGCACACCTGAACT
EST: gi|88386498|gb|CI575276.1|CI575276
EST:     GAAGCTCCGTAGTACGATGGATGCAGAGAATGCC-AGCACGCCAAGTTGG                         AGGCGCAGCTTAGCAGTGATCTGGAAGA
genomic: GAAGCTCCGTAGTACGATGGATGCAGAGAATGCCCAGCACGCCAAGTTGGgtaatgaatt ... gtacttccagAGGCCCAGCTTAGCAGTGATCTGGAAGA
EST: gi|88385811|gb|CI568479.1|CI568479
EST:     GAAGCTCCGTAGTACGATGGATGCAGAGAATGCCCAGCACGCCAAGTTGG                         AGGCCCAGCTTAGCAGTGATCTGGAAGAGCTGAAAGCTGCACACCTGAACT
genomic: GAAGCTCCGTAGTACGATGGATGCAGAGAATGCCCAGCACGCCAAGTTGGgtaatgaatt ... gtacttccagAGGCCCAGCTTAGCAGTGATCTGGAAGAGCTGAAAGCTGCACACCTGAACT
EST: gi|88427363|gb|CI569401.1|CI569401
EST:     GAAGCTCCGTAGTACGATGGATGCAGAGAATGCCCAGCACGCCAAGTTGG                         AGGCCCAGCTTAGCAGTGATCTGGAAGAGCTGATAGCTGCACACCTGAACT
genomic: GAAGCTCCGTAGTACGATGGATGCAGAGAATGCCCAGCACGCCAAGTTGGgtaatgaatt ... gtacttccagAGGCCCAGCTTAGCAGTGATCTGGAAGAGCTGAAAGCTGCACACCTGAACT
EST: gi|88454426|gb|CI569998.1|CI569998
EST:     GAAGCTCCGTAGTACGATGGATGCAGAGAATGCACAGCACGCCAAGTTGG                         AGGCCCAGCTTAGCAGTGATCTGGAAGAGCTGAA
genomic: GAAGCTCCGTAGTACGATGGATGCAGAGAATGCCCAGCACGCCAAGTTGGgtaatgaatt ... gtacttccagAGGCCCAGCTTAGCAGTGATCTGGAAGAGCTGAA

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: 74 (upstream exon), 30 (downstream exon)
Score: 5

TGCATCCGCTGGTACATTGAGTTGGAGGACGGCTACTTGGTCGAGCAGGAGAAGCTCCGTAGTACGATGGATGCAGAGAATGCCCAGCACGCCAAGTTGGgtaatgaatt ... gtacttccagAGGCCCAGCTTAGCAGTGATCTGGAAGAGCTGAAAGCTGCACACCTGAACTTGACGCGGCAGTGCGATTCGTTGGAGGAAAGCTTCAACAAGGAGAAGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtagtgactgagtttattctggtcatttatgttcttggggtactgtacttccagAGGCCCAGCTTAGCAGTGATCTGGAAGAGCTGAAAGCTGCACACCTGAACTTGACGCGGCAGTGCGATTCGTTGGAGGAAAGCTTCAACAAGGAGAAGGC
                                              tacttcc  CT-rich tract
                         atttatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgaattcgaatgcacttctcttttttttgtatttatttgatcacaccaagagaacaagatggtactcttttgggttttgagcattcatgtgtgctgtttggtcatcagagtaccatctcatcgtagtgactgagtttattctggtcatttatgttcttggggtactgtacttccagAGGCCCAGCTTAGCAGTGATCTGGAAGAGCTGAAAGCTGCACACCTGAACTTGACGCGGCAGTGCGATTCGTTGGAGGAAAGCTTCAACAAGGAGAAGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA