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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCCGGCCCCGTGCTTCTTCGACCTGGGCACCCGCACTGGTGCGGGATTGGACTCACAGATTCTAGGGTTTCGCCCCTCGCGGCGATTCCACCACCCAAGgtacgttattatacctccaattccccccaccccctcaccatcttcttctttcttgtaccaaattgcaattgccacgccctgcagattccctctcctcctt...

Basic information

species Oryza sativa
transcript LOC_Os01g73970.1
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|88342077|gb|CI644414.1|CI644414
EST:     GACTCACAGATTCTAGGGTTTCGCCCCTCGCGGCGATTCCACCACCCAAG                         GTTTGCGTTCCTTCTGTTGGTGCATACACGACTCCACCTATCACCGTTATG
genomic: GACTCACAGATTCTAGGGTTTCGCCCCTCGCGGCGATTCCACCACCCAAGgtacgttatt ... tgtccttcagGTTTGCGTTCCTTCTGTTGGTGCATACACGACTCCACCTATCACCGTTATG
EST: gi|88347448|gb|CI637388.1|CI637388
EST:     GACTCACAGATTCTAGGGTTTCGCCCCTCGCGGCGATTCCACCACCCAAG                         GTTTGCGTTCCTTCTGTTGGTGCATACACGACTCCACCTATCACCGTTATG
genomic: GACTCACAGATTCTAGGGTTTCGCCCCTCGCGGCGATTCCACCACCCAAGgtacgttatt ... tgtccttcagGTTTGCGTTCCTTCTGTTGGTGCATACACGACTCCACCTATCACCGTTATG
EST: gi|88321718|gb|CI672859.1|CI672859
EST:     GACTCACAGATTCTAGGGTTTCGCCCCTCGCGGCGATTCCACCACCCAAG                         GTTTGCGTTCCTTCTGTTGGTGCATACACGACTCCACCTATCACCGTTATG
genomic: GACTCACAGATTCTAGGGTTTCGCCCCTCGCGGCGATTCCACCACCCAAGgtacgttatt ... tgtccttcagGTTTGCGTTCCTTCTGTTGGTGCATACACGACTCCACCTATCACCGTTATG
EST: gi|29659847|gb|CB656122.1|CB656122
EST:     GACTCACAGATTCTAGGGTTTCGCCCCTCGCGGCGATTCCACCACCCAAG                         GTTTGCGTTCCTTCTGTTGGTGCATACACGACTCCACCTATCACCGTTATG
genomic: GACTCACAGATTCTAGGGTTTCGCCCCTCGCGGCGATTCCACCACCCAAGgtacgttatt ... tgtccttcagGTTTGCGTTCCTTCTGTTGGTGCATACACGACTCCACCTATCACCGTTATG
EST: gi|88576799|gb|CI673325.1|CI673325
EST:     GACTCACAGATTCTAGGGTTTCGCCCCTCGCGGCGATTCCACCACCCAAG                         GTTTGCGTTCCTTCTGTTGGTGCATACACGACTCCACCTATCACCGTTATG
genomic: GACTCACAGATTCTAGGGTTTCGCCCCTCGCGGCGATTCCACCACCCAAGgtacgttatt ... tgtccttcagGTTTGCGTTCCTTCTGTTGGTGCATACACGACTCCACCTATCACCGTTATG
EST: gi|88340221|gb|CI652570.1|CI652570
EST:     GACTCACAGATTCTAGGGTTTCGCCCCTCGCGGCGATTCCACCACCCAAG                         GTTTGCGTTCCTTCTGTTGGTGCATACACGACTCCACCTATCACCGTTATG
genomic: GACTCACAGATTCTAGGGTTTCGCCCCTCGCGGCGATTCCACCACCCAAGgtacgttatt ... tgtccttcagGTTTGCGTTCCTTCTGTTGGTGCATACACGACTCCACCTATCACCGTTATG
EST: gi|88739320|gb|CI762828.1|CI762828
EST:     GACTCACAGATTCTAGGGTTTCGCCCCTCGCGGCGATTCCACCACCCAAG                         GTTTGCGTTCCTTCTGTTGGTGCATACACAACTCCACCTATCACCGTTATG
genomic: GACTCACAGATTCTAGGGTTTCGCCCCTCGCGGCGATTCCACCACCCAAGgtacgttatt ... tgtccttcagGTTTGCGTTCCTTCTGTTGGTGCATACACGACTCCACCTATCACCGTTATG
EST: gi|88664581|gb|CI699791.1|CI699791
EST:     GACTCACAGATTCTAGGGTTTCGCCCCTCGCGGCGATTCCACCACCCAAG                         GTTTGCGTTCCTTCTGTTGGTGCATACACGACTCCACCTATCACCGTTATG
genomic: GACTCACAGATTCTAGGGTTTCGCCCCTCGCGGCGATTCCACCACCCAAGgtacgttatt ... tgtccttcagGTTTGCGTTCCTTCTGTTGGTGCATACACGACTCCACCTATCACCGTTATG
EST: gi|29663567|gb|CB659842.1|CB659842
EST:     GACTCACAGATTCTAGGGTTTCGCCCCTCGCGGCGATTCCACCACCCAGG                         GTTTGCGTTCCTTCTGTTGGTGCATACACGACTCCACCTATCACCGTTATG
genomic: GACTCACAGATTCTAGGGTTTCGCCCCTCGCGGCGATTCCACCACCCAAGgtacgttatt ... tgtccttcagGTTTGCGTTCCTTCTGTTGGTGCATACACGACTCCACCTATCACCGTTATG
EST: gi|29656275|gb|CB652550.1|CB652550
EST:     GACTCACAGATTCTAGGGTTTCGCCCCTCGCGGCGATTCCACCACCCAAG                         GTTTGCGTTCCTTCTGTTGGTGCATACACGACTCCACCTATCACCGTTATG
genomic: GACTCACAGATTCTAGGGTTTCGCCCCTCGCGGCGATTCCACCACCCAAGgtacgttatt ... tgtccttcagGTTTGCGTTCCTTCTGTTGGTGCATACACGACTCCACCTATCACCGTTATG

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), 36 (downstream exon)
Score: 26

CCCCGGCCCCGTGCTTCTTCGACCTGGGCACCCGCACTGGTGCGGGATTGGACTCACAGATTCTAGGGTTTCGCCCCTCGCGGCGATTCCACCACCCAAGgtacgttatt ... tgtccttcagGTTTGCGTTCCTTCTGTTGGTGCATACACGACTCCACCTATCACCGTTATGTTCTCGCTGCGCAATGCATAGAAGCTGCACTCACGAGGCTCCATCTCCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCCGGCCCCGTGCTTCTTCGACCTGGGCACCCGCACTGGTGCGGGATTGGACTCACAGATTCTAGGGTTTCGCCCCTCGCGGCGATTCCACCACCCAAGgtacgttattatacctccaattccccccaccccctcaccatcttcttctttcttgtaccaaattgcaattgccacgccctgcagattccctctcctcctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccacgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctctc