Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGAAATTATGGAAATGCAGAAAAATTTCTTCCCAGAAATGCAGAAAAATCAGgtaaatgttttggtcaaacttatgtttgtgttttgtaatattctaatgagtaaactgtgtctacaatacataaatttggtaggtgtgtgcgatctagtgc...

Basic information

species Oryza sativa
transcript LOC_Os08g36790.1
intron # 3
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|88341024|gb|CI638580.1|CI638580
EST:     AAATTATGGAAATGCAGAAAAATTTCTTCCCAGAAATGCAGAAAAATCAG                         GTATTAGAGGCGGTCAACAATCCTTACGGACAAAAGAAGCGTTGCCTAAGA
genomic: AAATTATGGAAATGCAGAAAAATTTCTTCCCAGAAATGCAGAAAAATCAGgtaaatgttt ... tggcaagcagGTATTAGAGGCGGTCAACAATCCTTACGGACAAAAGAAGCGTTGCCTAAGA
EST: gi|88977434|gb|CI025170.1|CI025170
EST:     ATGG-AATGCAG-AAAATTTCTTCCCGGAAATGCAGAAAAATCAG                         GTATTAGAGGCGGTCAACAATCCTTACGGACAAAAGAAGCGTTGCCTAAGA
genomic: ATGGAAATGCAGAAAAATTTCTTCCCAGAAATGCAGAAAAATCAGgtaaatgttt ... tggcaagcagGTATTAGAGGCGGTCAACAATCCTTACGGACAAAAGAAGCGTTGCCTAAGA
EST: gi|56157703|gb|C25467.2|C25467
EST:     AAATTATGGAAATGCAGAAAAATTTCTTCCCAGAAATGCAGAAAAATCAG                         GTATTAGAGGCGGTCAACAATCCTTACGGACAAAAGAAGCGTTGCCTAAGA
genomic: AAATTATGGAAATGCAGAAAAATTTCTTCCCAGAAATGCAGAAAAATCAGgtaaatgttt ... tggcaagcagGTATTAGAGGCGGTCAACAATCCTTACGGACAAAAGAAGCGTTGCCTAAGA
EST: gi|109712388|gb|CI104996.1|CI104996
EST:     AAATTATGGAAATGCAGAAAAATTTCTTCCCAGAAATGCAGAAAAATCAG                         GTATTAGAGGCGGTCAACAATCCTTACGGACAAAAGAAGCGTTGCCTAAGA
genomic: AAATTATGGAAATGCAGAAAAATTTCTTCCCAGAAATGCAGAAAAATCAGgtaaatgttt ... tggcaagcagGTATTAGAGGCGGTCAACAATCCTTACGGACAAAAGAAGCGTTGCCTAAGA
EST: gi|86906441|gb|CI294564.1|CI294564
EST:     ATGGAAATGCAGAAAAATTTCTTCCCGAGAAATGCAGAAAAATCAG                         GTATTAGAGGCGGTCAACAATCCTTACGGACAAAAGAAGCGTTGCCTAAGA
genomic: ATGGAAATGCAGAAAAATTTCTTCCC-AGAAATGCAGAAAAATCAGgtaaatgttt ... tggcaagcagGTATTAGAGGCGGTCAACAATCCTTACGGACAAAAGAAGCGTTGCCTAAGA
EST: gi|86502655|gb|CI145288.1|CI145288
EST:     AAATTATGGAAATGCAGAAAAATTTCTTCCCAGAAATGCAGAAAAATCAG                         GTATTAGAGGCGGTCAACAATCCTTACGGACAAAAGAAGCGTTGCCTAAGA
genomic: AAATTATGGAAATGCAGAAAAATTTCTTCCCAGAAATGCAGAAAAATCAGgtaaatgttt ... tggcaagcagGTATTAGAGGCGGTCAACAATCCTTACGGACAAAAGAAGCGTTGCCTAAGA
EST: gi|88957374|gb|CI095315.1|CI095315
EST:     TTCTTCCCAGAAATGCAGAAAAATCAG                         GTATTAGAGGCGGTCAACAATCCTTACGGACAAAAGAAGCGTTGCCTAAGA
genomic: TTCTTCCCAGAAATGCAGAAAAATCAGgtaaatgttt ... tggcaagcagGTATTAGAGGCGGTCAACAATCCTTACGGACAAAAGAAGCGTTGCCTAAGA
EST: gi|88353911|gb|CI634702.1|CI634702
EST:     AAATTATGGAAATGCAGAAAAATTTCTTCCCAGAAATGCAGAAAAATCAG                         GTATTAGAGGCGGTCAACAATCCTTACGGACAAAAGAAGCGTTGCCTAAGA
genomic: AAATTATGGAAATGCAGAAAAATTTCTTCCCAGAAATGCAGAAAAATCAGgtaaatgttt ... tggcaagcagGTATTAGAGGCGGTCAACAATCCTTACGGACAAAAGAAGCGTTGCCTAAGA

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: 50 (upstream exon), 68 (downstream exon)
Score: 29

GAGGAAATTATGGAAATGCAGAAAAATTTCTTCCCAGAAATGCAGAAAAATCAGgtaaatgttt ... tggcaagcagGTATTAGAGGCGGTCAACAATCCTTACGGACAAAAGAAGCGTTGCCTAAGAAGAACATTGACAGGTCCCTGGTAAAATTTGAGTTATTGATAACCGGAGC




<











<


<