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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcacagcagcctgcaaagtcaaatgcttcaacagtttaacttacacaaaagaaatccaattcaacatcagattaaagaaaataaaactgttttttatttttcttatcttacagGCTTTGGGGTGCATTATCAAAGGTCGGAGTATAGCCTCCATGCTTGATTCAGTACTAGAGTCACACAAAGAAAATGAGCTAGATGTGATCTGTCAGATAA

Basic information

species Oryza sativa
transcript LOC_Os05g48660.2
intron # 6
splice site 3'
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|86260928|gb|CI066603.1|CI066603
EST:     TCTCAGGGAAACCCCCTTACTCTGAAAACGAGGGCTCCCTGGCGAATCTG                         GCTTTGGGGTGCATTATCAAAGGTCGGAGTATAGCCTCCATGCTTGATTCA
genomic: TCTCAGGGAAACCCCCTTACTCTGAAAACGAGGGCTCCCTGGCGAATCTGgtaatcacag ... tatcttacagGCTTTGGGGTGCATTATCAAAGGTCGGAGTATAGCCTCCATGCTTGATTCA
EST: gi|86879065|gb|CI315448.1|CI315448
EST:     TCTCA-GGAAACCCCCTTACTCTGAAAACGAGGGCTCCCTGGCGAATCTGG                         GCTTTGGGGTGCATTATCAAAGGTCGGAGTATAGCCTCCATGCTTGATTC
genomic: TCTCAGGGAAACCCCCTTACTCTGAAAACGAGGGCTCCCTGGCGAATCT-Ggtaatcacag ... tatcttacagGCTTTGGGGTGCATTATCAAAGGTCGGAGTATAGCCTCCATGCTTGATTC
EST: gi|89190179|gb|CI392229.1|CI392229
EST:     CTCCCTGGCGAATCTG                         GCTTTGGGGTGCATTATCAAAGGTCGGAGTATAGCCTCCATGCTTGATTCA
genomic: CTCCCTGGCGAATCTGgtaatcacag ... tatcttacagGCTTTGGGGTGCATTATCAAAGGTCGGAGTATAGCCTCCATGCTTGATTCA
EST: gi|86834313|gb|CI344073.1|CI344073
EST:     CTGGCGAATCTG                         GCTTTGGGGTGCATTATCAAAGGTCGGAGTATAGCCTCCATGCTTGATTCA
genomic: CTGGCGAATCTGgtaatcacag ... tatcttacagGCTTTGGGGTGCATTATCAAAGGTCGGAGTATAGCCTCCATGCTTGATTCA
EST: gi|88997719|gb|CI390308.1|CI390308
EST:     GGCTCCCTGGCGAATCTG                         GCTTTGGGGTGCATTATCAAAGCTCGGAGTATAGCCTCCATGCTTGATTCA
genomic: GGCTCCCTGGCGAATCTGgtaatcacag ... tatcttacagGCTTTGGGGTGCATTATCAAAGGTCGGAGTATAGCCTCCATGCTTGATTCA
EST: gi|88842124|gb|CI081380.1|CI081380
EST:     TCTCAGGGAAACCCCCTTACTCTGAAAACGAGGGCTCCCTGGCGAATCTG                         GCTTTGGGGTGCATTATCAAAGGTCGGAGTATAGCCTCCATGCTTGATTCA
genomic: TCTCAGGGAAACCCCCTTACTCTGAAAACGAGGGCTCCCTGGCGAATCTGgtaatcacag ... tatcttacagGCTTTGGGGTGCATTATCAAAGGTCGGAGTATAGCCTCCATGCTTGATTCA
EST: gi|88975635|gb|CI021717.1|CI021717
EST:     TCTCAGGGAAACCCCCTTACTCTGAAAACGAGGGCTCCCTGGCGAATCTG                         GCTTTGGGGTGCATTATCAAAGGTCGGAGTATAGCCTCCACGCTTGATTCA
genomic: TCTCAGGGAAACCCCCTTACTCTGAAAACGAGGGCTCCCTGGCGAATCTGgtaatcacag ... tatcttacagGCTTTGGGGTGCATTATCAAAGGTCGGAGTATAGCCTCCATGCTTGATTCA
EST: gi|88994080|gb|CI116044.1|CI116044
EST:     TCTCAGGGAAACCCCCTTACTCTGAAAACGAGGGCTCCCTGGCGAATCTG                         GCTTTGGGGTGCATTATCAAAGGTCGGAGTATAGCCTCCATGCTTGATTCA
genomic: TCTCAGGGAAACCCCCTTACTCTGAAAACGAGGGCTCCCTGGCGAATCTGgtaatcacag ... tatcttacagGCTTTGGGGTGCATTATCAAAGGTCGGAGTATAGCCTCCATGCTTGATTCA
EST: gi|86495926|gb|CI138559.1|CI138559
EST:     TCTCAGGGAAACCCCCTTACTCTGAAAACGAGGGCTCCCTGGCGAATCTG                         GCTTTGGGGTGCATTATCAAAGGTCGGAGTATAGCCTCCATGCTTGATTCA
genomic: TCTCAGGGAAACCCCCTTACTCTGAAAACGAGGGCTCCCTGGCGAATCTGgtaatcacag ... tatcttacagGCTTTGGGGTGCATTATCAAAGGTCGGAGTATAGCCTCCATGCTTGATTCA
EST: gi|88257508|gb|CI359896.1|CI359896
EST:     AGGGCTCCCTGGCGAATCTG                         GCTTTGGGGTGCATTATCAAAGGTCGGAGTATAGCCTCCATGCTTGATTCA
genomic: AGGGCTCCCTGGCGAATCTGgtaatcacag ... tatcttacagGCTTTGGGGTGCATTATCAAAGGTCGGAGTATAGCCTCCATGCTTGATTCA
EST: gi|88836361|gb|CI078258.1|CI078258
EST:     TCTCAGGGAAACCCCCTTACTCTGAAAACGAGGGCTCCCTGGCGAATCTG                         GCTTTGGGGTGCATTATCAAAGGTCGGAGTATAGCCTCCATGCTTGATTCA
genomic: TCTCAGGGAAACCCCCTTACTCTGAAAACGAGGGCTCCCTGGCGAATCTGgtaatcacag ... tatcttacagGCTTTGGGGTGCATTATCAAAGGTCGGAGTATAGCCTCCATGCTTGATTCA
EST: gi|88835694|gb|CI370799.1|CI370799
EST:     CAGGGAAACCCCCTTACTCTGAAAACGAGGGCTCCCTGGCGAATCTG                         GCTTTGGGGTGCATTATCAAAGGTCGGAGTATAGCCTCCATGCTTGATTCA
genomic: CAGGGAAACCCCCTTACTCTGAAAACGAGGGCTCCCTGGCGAATCTGgtaatcacag ... tatcttacagGCTTTGGGGTGCATTATCAAAGGTCGGAGTATAGCCTCCATGCTTGATTCA

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), 26 (downstream exon)
Score: 1

TAGACTGGCAGGGAACGTTTACAGTTTTGGCATACTGCTTCTTGAAATCATCTCAGGGAAACCCCCTTACTCTGAAAACGAGGGCTCCCTGGCGAATCTGgtaatcacag ... tatcttacagGCTTTGGGGTGCATTATCAAAGGTCGGAGTATAGCCTCCATGCTTGATTCAGTACTAGAGTCACACAAAGAAAATGAGCTAGATGTGATCTGTCAGATAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcaacatcagattaaagaaaataaaactgttttttatttttcttatcttacagGCTTTGGGGTGCATTATCAAAGGTCGGAGTATAGCCTCCATGCTTGATTCAGTACTAGAGTCACACAAAGAAAATGAGCTAGATGTGATCTGTCAGATAA
                            ctgttttttatttttc  CT-rich tract
            attaaagaaaataaaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcacagcagcctgcaaagtcaaatgcttcaacagtttaacttacacaaaagaaatccaattcaacatcagattaaagaaaataaaactgttttttatttttcttatcttacagGCTTTGGGGTGCATTATCAAAGGTCGGAGTATAGCCTCCATGCTTGATTCAGTACTAGAGTCACACAAAGAAAATGAGCTAGATGTGATCTGTCAGATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA