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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCACTCGCCGCCTTCTCTCCTCTCGCGCCGTTTCGCTCCCTGACCCTCCGCCGCCGCCGCCGCCGATCATCATGAGgtgattcccgccgcccaatctctacttcccttcttacggttaacgaatctcttctattgcttagtttctgtcgctatggccttctgtgattctgcgcgct...

Basic information

species Oryza sativa
transcript LOC_Os08g44450.1
intron # 1
splice site 5'
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|58596330|gb|CK006858.1|CK006858
EST:     GCCGTTTCGCTCCCTGACCCT---CCGCCGCCGCCGCCGATCATCGTGAG                         TAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGA
genomic: GCCGTTTCGCTCCCTGACCCTCCGCCGCCGCCGCCGCCGATCATCATGAGgtgattcccg ... tcaattgcagTAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGA
EST: gi|218501569|gb|FG968626.1|FG968626
EST:     GCCGTTTCGCTCCCTGACCCT---CCGCCGCCGCCGCCGATCATCATGAG                         TAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGA
genomic: GCCGTTTCGCTCCCTGACCCTCCGCCGCCGCCGCCGCCGATCATCATGAGgtgattcccg ... tcaattgcagTAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGA
EST: gi|29637359|gb|CB642368.1|CB642368
EST:     ATCATCATGAG                         TAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGA
genomic: ATCATCATGAGgtgattcccg ... tcaattgcagTAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGA
EST: gi|58604026|gb|CK014554.1|CK014554
EST:     GCCGTTTCGCTCCCTGACCCT---CCGCCGCCGCCGCCGATCATCATGAG                         TAAG-TGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGA
genomic: GCCGTTTCGCTCCCTGACCCTCCGCCGCCGCCGCCGCCGATCATCATGAGgtgattcccg ... tcaattgcagTAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGA
EST: gi|58679944|gb|CK068631.1|CK068631
EST:     GCCGTTTCGCTCCCTGA-CCT---CCGCCG-CGCCGCCGATCATCATGAG                         TAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGA
genomic: GCCGTTTCGCTCCCTGACCCTCCGCCGCCGCCGCCGCCGATCATCATGAGgtgattcccg ... tcaattgcagTAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGA
EST: gi|27554288|gb|CA998188.1|CA998188
EST:     ATCATCATGAG                         TAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGA
genomic: ATCATCATGAGgtgattcccg ... tcaattgcagTAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGA
EST: gi|38474392|gb|CF958524.1|CF958524
EST:     GCCGTTTCGCTCCCTGACCCT---CCGCCGCCGCCGCCGATCATCATGAG                         TAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGA
genomic: GCCGTTTCGCTCCCTGACCCTCCGCCGCCGCCGCCGCCGATCATCATGAGgtgattcccg ... tcaattgcagTAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGA
EST: gi|218502837|gb|FG950277.1|FG950277
EST:     TTCGCTCCCTGACCCT---CCGCCGCCGCCGCCGATCATCATGAG                         TAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGA
genomic: TTCGCTCCCTGACCCTCCGCCGCCGCCGCCGCCGATCATCATGAGgtgattcccg ... tcaattgcagTAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGA
EST: gi|38483017|gb|CF966819.1|CF966819
EST:     GCCGTTTCGCTCCCTGACCCT---CCGCCGCCGCCGCCGATCATCATGAG                         TAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGA
genomic: GCCGTTTCGCTCCCTGACCCTCCGCCGCCGCCGCCGCCGATCATCATGAGgtgattcccg ... tcaattgcagTAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGA
EST: gi|33811047|gb|CF331414.1|CF331414
EST:     ATCATCATGAG                         TAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGA
genomic: ATCATCATGAGgtgattcccg ... tcaattgcagTAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGA
EST: gi|29687000|gb|CB683275.1|CB683275
EST:     ATCATCATGAG                         TAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGA
genomic: ATCATCATGAGgtgattcccg ... tcaattgcagTAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGA
EST: gi|58588784|gb|CF987092.1|CF987092
EST:     CCGCCGCCGCCGCCGATCATCATGAG                         TAAGTTGCAGAGCGAGGTTCTCAGGGGAAGCCATCTCCCAGGTTGTTGGGG
genomic: CCGCCGCCGCCGCCGATCATCATGAGgtgattcccg ... tcaattgcagTAAGTTGCAGAGCGAGGTTCTCA-AGGAAGCCATCTCCCAGGTTGTTGGGG
EST: gi|218497208|gb|FG946438.1|FG946438
EST:     GCCGTTTCGCTCCCTGACCCT---CCGCCGCCGCCGCCGATCATCATGAG                         TAAGTTGCAGAGCGAGGTTCTC-AGGAAGCCATCTCCCAGGTTGTTGGGGA
genomic: GCCGTTTCGCTCCCTGACCCTCCGCCGCCGCCGCCGCCGATCATCATGAGgtgattcccg ... tcaattgcagTAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGA
EST: gi|33823303|gb|CF337452.1|CF337452
EST:     GCCGCCGCCGATCATCATGAG                         TAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGA
genomic: GCCGCCGCCGATCATCATGAGgtgattcccg ... tcaattgcagTAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGA
EST: gi|27577252|gb|CA999946.1|CA999946
EST:     ATCATCATGAG                         C
genomic: ATCATCATGAGgtgattcccg ... tcaattgcag-
EST: gi|27577252|gb|CA999946.1|CA999946
EST:     ATCATCATGAG                         C
genomic: ATCATCATGAGgtgattcccg ... tcaattgcag-
EST: gi|58595844|gb|CK006372.1|CK006372
EST:     GCTCCCTGACCCT---CCGCCGCCGCCGCCGATCATCATGAG                         TAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGA
genomic: GCTCCCTGACCCTCCGCCGCCGCCGCCGCCGATCATCATGAGgtgattcccg ... tcaattgcagTAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGA
EST: gi|27554610|gb|CA998510.1|CA998510
EST:     ATCATCATGAG                         TAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGA
genomic: ATCATCATGAGgtgattcccg ... tcaattgcagTAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGA
EST: gi|58694951|gb|CK083638.1|CK083638
EST:     GCCGTTTCGCTCCCTGACCCT---CCGCCG-CGCCGCCGATCATCATGAG                         TAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGA
genomic: GCCGTTTCGCTCCCTGACCCTCCGCCGCCGCCGCCGCCGATCATCATGAGgtgattcccg ... tcaattgcagTAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGA

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: 67 (upstream exon), 75 (downstream exon)
Score: 41

TCACTCGCCGCCTTCTCTCCTCTCGCGCCGTTTCGCTCCCTGACCCTCCGCCGCCGCCGCCGCCGATCATCATGAGgtgattcccg ... tcaattgcagTAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGAATCCAAGGAGAAGGGCAGGAAGTTCACCGAGACCGTTGAGCTTCAGATT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCACTCGCCGCCTTCTCTCCTCTCGCGCCGTTTCGCTCCCTGACCCTCCGCCGCCGCCGCCGCCGATCATCATGAGgtgattcccgccgcccaatctctacttcccttcttacggttaacgaatctcttctattgcttagtttctgtcgctatggccttctgtgattctgcgcgct

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