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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACGACAGTATGTTGGGGCTTGAGAGATCGTTGGCTGAACTATGATGGAGTTGAAGATTTTTGTGGCAGTGCAAATTACAAAATTTTAGAACTGCCAATGgtttgttgtctttaccccacccccaccctcctcttgtcctcaccaggggaaaaaatattcaaaattaccctgttccatgaaaaaagagagtaaaataaaa...

Basic information

species Oryza sativa
transcript LOC_Os01g69060.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g69060.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G025659_T02 (Zea mays), 5'ss of exon 9
AACGACAGTATGTTGGGGCTTGAGAGATCGTTGGCTGAACTATGATGGAGTTGAAGATTTTTGTGGCAGTGCAAATTACAAAATTTTAGAACTGCCAATGgtttgttgtctttaccc---cacccccaccctcctcttgtcctcacca------ggggaaaaaatattcaaaattaccctgt-tccatgaaaaaagagagtaaaataaaa------------------------------------------------------------------------------------------
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GACAACAGTATGCTGGGGCATGAGAGATCGTTGGCTAAGCTATGATGGGGTGGAAGAATTTTTTGGAGGCCTAAACCAGAAGATTGTAGAACTGCCAATGgtttgtcatgaaaacccagctattttcaactttaactcattttcatgactatttatgcatggggtggtgtggtttgtgttgcatgcataaggacatgtggttgtatgcgtgaacgaagaacacattttctggatttatttcttccttttccttcatttgatattatattgtcatatcattttgtgcaatgacttgtgcag
















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|88995955|gb|CI037246.1|CI037246
EST:     AAAATTTTAGAACTGCCAATG                         GCAGGGCACCATGTGCAGGAGGACCGTGGTGAAGAGCTAGGCAAGCTAGTC
genomic: AAAATTTTAGAACTGCCAATGgtttgttgtc ... tatcatgcagGCAGGGCACCATGTGCAGGAGGACCGTGGTGAAGAGCTAGGCAAGCTAGTC
EST: gi|29639813|gb|CB644822.1|CB644822
EST:     TTGAAGATTTTTGTGGCAGTGCAAATTACAAAATTTTAGAACTGCCAATG                         GCAGGGCACCATGTGCAGGAGGACCGTGGTGAAGAGCTAGGCAAGCTAGTC
genomic: TTGAAGATTTTTGTGGCAGTGCAAATTACAAAATTTTAGAACTGCCAATGgtttgttgtc ... tatcatgcagGCAGGGCACCATGTGCAGGAGGACCGTGGTGAAGAGCTAGGCAAGCTAGTC
EST: gi|88848470|gb|CI086992.1|CI086992
EST:     CAGTGCAAATTACAAAATTTTAGAACTGCCAATG                         GCAGGGCACCATGTGCAGGAGGACCGTGGTGAAGAGCTAGGCAAGCTAGTC
genomic: CAGTGCAAATTACAAAATTTTAGAACTGCCAATGgtttgttgtc ... tatcatgcagGCAGGGCACCATGTGCAGGAGGACCGTGGTGAAGAGCTAGGCAAGCTAGTC
EST: gi|66923779|gb|CX110627.1|CX110627
EST:     TTGAAGATTTTTGTGGCAGTGAAAATTACAAAATTTTAGAACTGCCAATG                         GCAGGGCACCATGTGCAAGAGGACCGTGGTGAAGAGCTAGGCAAGCTAGTC
genomic: TTGAAGATTTTTGTGGCAGTGCAAATTACAAAATTTTAGAACTGCCAATGgtttgttgtc ... tatcatgcagGCAGGGCACCATGTGCAGGAGGACCGTGGTGAAGAGCTAGGCAAGCTAGTC
EST: gi|86849508|gb|CI299701.1|CI299701
EST:     TTGAAGATTTTTGTGGCAGTGCAAATTACAAAATTTTAGAACTGCCAATG                         GCAGGGCACCATGTGCAGGAGGACCGTGGTGAAGAGCTAGGCAAGCTAGTC
genomic: TTGAAGATTTTTGTGGCAGTGCAAATTACAAAATTTTAGAACTGCCAATGgtttgttgtc ... tatcatgcagGCAGGGCACCATGTGCAGGAGGACCGTGGTGAAGAGCTAGGCAAGCTAGTC
EST: gi|86523000|gb|CI163206.1|CI163206
EST:     TTGAAGATTTTTGTGGCAGTGCAAATTACAAAATTTTAGAACTGCCAATG                         GCAGGGCACCATGTGCAGGAGGACCGTGGTGAAGAGCTAGGCAAGCTAGTC
genomic: TTGAAGATTTTTGTGGCAGTGCAAATTACAAAATTTTAGAACTGCCAATGgtttgttgtc ... tatcatgcagGCAGGGCACCATGTGCAGGAGGACCGTGGTGAAGAGCTAGGCAAGCTAGTC

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: 59 (upstream exon), 46 (downstream exon)
Score: 4

AACGACAGTATGTTGGGGCTTGAGAGATCGTTGGCTGAACTATGATGGAGTTGAAGATTTTTGTGGCAGTGCAAATTACAAAATTTTAGAACTGCCAATGgtttgttgtc ... tatcatgcagGCAGGGCACCATGTGCAGGAGGACCGTGGTGAAGAGCTAGGCAAGCTAGTCAAACGTATTCTAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACGACAGTATGTTGGGGCTTGAGAGATCGTTGGCTGAACTATGATGGAGTTGAAGATTTTTGTGGCAGTGCAAATTACAAAATTTTAGAACTGCCAATGgtttgttgtctttaccccacccccaccctcctcttgtcctcaccaggggaaaaaatattcaaaattaccctgttccatgaaaaaagagagtaaaataaaa

- - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctcacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa