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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCCGCCATGGTGGCCCTGTAGGATCGCGTGCTGGGCCGGCGTTTCTGAATCTGCGTGCTCCCGCACTTCGTCATGACAGTAAAAAGCATCCTTTGAGAGgtactgattttcttgcatatgtgtaattttgcattggatgacaatataagctcgttactgcccatacactaacaagtggagaaaaactgaaaattgttat...

Basic information

species Oryza sativa
transcript LOC_Os02g40080.1
intron # 2
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|58661520|gb|CK050200.1|CK050200
EST:     TCTGCGTGCTCCCGCACTTCGTCATGACAGTAAAAAGCATCCTTTGAGAG                         TTGGTGCTGCCTCTTCATTTTTCACAAAGTATGATCCTATCAAAGGCATCA
genomic: TCTGCGTGCTCCCGCACTTCGTCATGACAGTAAAAAGCATCCTTTGAGAGgtactgattt ... tttgtttcagTTGGTGCTGCCTCTTCATTATTCACAAAGTATGATCCTATCAAAGGCATCA
EST: gi|86884211|gb|CI311658.1|CI311658
EST:     TCTGCGTGCTCCCGCACTTCGTCATGACAGTAAAAAGCATCCTTTGAGAG                         TTGGTGCTGCCTCTTCATTATTCACAAAGTATGATCCTATCAAAGGCATCA
genomic: TCTGCGTGCTCCCGCACTTCGTCATGACAGTAAAAAGCATCCTTTGAGAGgtactgattt ... tttgtttcagTTGGTGCTGCCTCTTCATTATTCACAAAGTATGATCCTATCAAAGGCATCA
EST: gi|33687462|gb|CF315701.1|CF315701
EST:     TCTGCGTGCTCCCGCACTTCGTCATGACAGTAAAAAGCATCCTTTGAGAG                         TTGGTGCTGCCTCTTCATTATTCACAAAGTATGATCCTATCAAAGGCATCA
genomic: TCTGCGTGCTCCCGCACTTCGTCATGACAGTAAAAAGCATCCTTTGAGAGgtactgattt ... tttgtttcagTTGGTGCTGCCTCTTCATTATTCACAAAGTATGATCCTATCAAAGGCATCA
EST: gi|33381477|gb|CF196820.1|CF196820
EST:     TCTGCGTGCTCCCGCACTTCGTCATGACAGTAAAAAGCATCCTTTGAGAG                         TTGGTGCTGCCTCTTCATTATTCACAAAGTATGATCCTATCAAAGGCATCA
genomic: TCTGCGTGCTCCCGCACTTCGTCATGACAGTAAAAAGCATCCTTTGAGAGgtactgattt ... tttgtttcagTTGGTGCTGCCTCTTCATTATTCACAAAGTATGATCCTATCAAAGGCATCA
EST: gi|88441636|gb|CI599541.1|CI599541
EST:     TCTGCGTGCTCCCGCACTTCGTCATGACAGTAAAAAGCATACTTTGAGAG                         TTGGTGCTGCCTCTTCATTATTCAAAAAGTATGATCCTATCAAAGGCATCA
genomic: TCTGCGTGCTCCCGCACTTCGTCATGACAGTAAAAAGCATCCTTTGAGAGgtactgattt ... tttgtttcagTTGGTGCTGCCTCTTCATTATTCACAAAGTATGATCCTATCAAAGGCATCA
EST: gi|58676344|gb|CK065031.1|CK065031
EST:     TCTGCGTGCTCCCGCACTTCGTGGTGACAGTAAAAAGCATCCTTTGAGAG                         TTGGTGCTGCCTCTTCATTTTTCACAAAGTATGATCCTATCAAATGCATCA
genomic: TCTGCGTGCTCCCGCACTTCGTCATGACAGTAAAAAGCATCCTTTGAGAGgtactgattt ... tttgtttcagTTGGTGCTGCCTCTTCATTATTCACAAAGTATGATCCTATCAAAGGCATCA
EST: gi|33682487|gb|CF310726.1|CF310726
EST:     TCTGCGTGCTCCCGCACTTCGTCATGACAGTAAAAAGCATCCTTTGAGAG                         TTGGTGCTGCCTCTTCATTATTCACAAAGTATGATCCTATCAAAGGCATCA
genomic: TCTGCGTGCTCCCGCACTTCGTCATGACAGTAAAAAGCATCCTTTGAGAGgtactgattt ... tttgtttcagTTGGTGCTGCCTCTTCATTATTCACAAAGTATGATCCTATCAAAGGCATCA
EST: gi|56157496|gb|D28302.3|D28302
EST:     TCTGCGTGCTCCCGCACTTCGTCATGACAGTAAAAAGCATCCTTTGAGAG                         TTGGTGCTGCCTCTTCATTATTCACAAAGTATGATCCTATCAAAGGCATCA
genomic: TCTGCGTGCTCCCGCACTTCGTCATGACAGTAAAAAGCATCCTTTGAGAGgtactgattt ... tttgtttcagTTGGTGCTGCCTCTTCATTATTCACAAAGTATGATCCTATCAAAGGCATCA

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), 74 (downstream exon)
Score: 23

AGCCGCCATGGTGGCCCTGTAGGATCGCGTGCTGGGCCGGCGTTTCTGAATCTGCGTGCTCCCGCACTTCGTCATGACAGTAAAAAGCATCCTTTGAGAGgtactgattt ... tttgtttcagTTGGTGCTGCCTCTTCATTATTCACAAAGTATGATCCTATCAAAGGCATCAAACCATTGCTGTCAATTGACAAGTTACGTCCTAGAACTCAAGTTGGCTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCCGCCATGGTGGCCCTGTAGGATCGCGTGCTGGGCCGGCGTTTCTGAATCTGCGTGCTCCCGCACTTCGTCATGACAGTAAAAAGCATCCTTTGAGAGgtactgattttcttgcatatgtgtaattttgcattggatgacaatataagctcgttactgcccatacactaacaagtggagaaaaactgaaaattgttat

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