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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATTTAAAGTCTGGAGGAGCAACCTTGAAGCTCTGAATGTAGACCTGCAAGACTTCTTTGTGCAGCTTTTTAACCTCATTCTGGAGTATCGGCCTGACAGgtttgaattctatttattttggtgctggtgatggggaagaaatatatatactcttgtcctttctaaaacacagattcatggataggtagcatcatagcaa...

Basic information

species Oryza sativa
transcript LOC_Os06g30320.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g30320.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G104983_T01 (Zea mays), 5'ss of exon 10
CATTTAAAGTCTGGAGGAGCAACCTTGAAGCTCTGAATGTAGACCTGCAAGACTTCTTTGTGCAGCTTTTTAACCTCATTCTGGAGTATCGGCCTGACAGgtttgaattctatttattttggtgctggtgatggggaagaaatatatatactc-ttgtcctttctaaaacacagattcatggataggtagcatcatagcaa-
  |||||||||||||||||||||||||| || |||||||| || ||||| || |||||||||||||| | ||||||||| ||||||||||||||||||||||||   |||  ||  | ||| || | || ||  ||||||| ||  |||| |  |  |   ||  | ||  ||   | |    |   | | || ||      
TGTTTAAAGTCTGGAGGAGCAACCTTGAGGCACTGAATGTGGATCTGCAGGATTTCTTTGTGCAGCTCTATAACCTCATACTGGAGTATCGGCCTGACAGgttttgtttcc-ttactcttgatgatagttataaggaagaactacctatagttatcatttgttgaacaatccaagataacctgttaat-gtattattctttt

upper sequence: LOC_Os06g30320.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT1G79150.1 (Arabidopsis thaliana), 5'ss of exon 10
CATTTAAAGTCTGGAGGAGCAACCTTGAAGCTCTGAATGTAGACCTGCAAGACTTCTTTGTGCAGCTTTTTAACCTCATTCTGGAGTATCGGCCTGACAGgtttgaattctatttattttggtgctggtgatggggaagaaatatatatactcttgtcctttctaaaacacagattcatggataggtagcatcatagcaa
| || ||||||  |||||||||| |  | ||  ||||||| ||| |||||||||||||||| || ||||  ||||||||||| ||||| || ||||  |||||||  || ||  | |||      |  | |     | || |||  |  | ||| ||    ||||||||||   ||  ||    | ||            
CCTTCAAAGTCATGAGGAGCAACTTAAATGCCTTGAATGTTGACTTGCAAGACTTCTTTGTCCAACTTTACAACCTCATTCTCGAGTACCGCCCTGGAAGgtttg--ttataactttttcctcttttttaacc---acgacataagttaaatctagtttagtctaaaacac---tttgtgatgtgatacag---------
















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|66918195|gb|CX105043.1|CX105043
EST:     GACTTCTTTGTGCAGCTTTTTAACCTCATTCTGGAGTATCGGCCTGACAG                         AGATCGTGGTGAGGTATTAGCTGATGCTCTGAAGACACTTCTCTGGGAAGG
genomic: GACTTCTTTGTGCAGCTTTTTAACCTCATTCTGGAGTATCGGCCTGACAGgtttgaattc ... ctctatccagAGATCGTGGTGAGGTATTAGCTGATGCTCTGAAGACACTTCTCTGGGAAGG
EST: gi|218488760|gb|FG952855.1|FG952855
EST:     GACTTCTTTGTGCAGCTTTTTAACCTCATTCTGGAGTATCGGCCTGACAG                         AGATCGTGGTGAGGTATTGGCTGATGCTCTGAAGACACTTCTCTGGGAAGG
genomic: GACTTCTTTGTGCAGCTTTTTAACCTCATTCTGGAGTATCGGCCTGACAGgtttgaattc ... ctctatccagAGATCGTGGTGAGGTATTAGCTGATGCTCTGAAGACACTTCTCTGGGAAGG
EST: gi|27546861|gb|CA764891.2|CA764891
EST:     GACTTCTTTGTGCAGCTTTTTAACCTCATTCTGGAGTATCGGCCTGACAG                         AGATCGTGGTGAGGTATT-GACTGATGCTCTGAAGACACTTCTCTGGGAAG
genomic: GACTTCTTTGTGCAGCTTTTTAACCTCATTCTGGAGTATCGGCCTGACAGgtttgaattc ... ctctatccagAGATCGTGGTGAGGTATTAG-CTGATGCTCTGAAGACACTTCTCTGGGAAG
EST: gi|58684363|gb|CK073050.1|CK073050
EST:     GACTTCTTTGTGCAGCTTTTTAACCTCATTCTGGAGTATCGGCCTGACAG                         AGATCGTGGTGAGGTATTGGCTGATGCTCTGAAGACACTTCTCTGGGAAGG
genomic: GACTTCTTTGTGCAGCTTTTTAACCTCATTCTGGAGTATCGGCCTGACAGgtttgaattc ... ctctatccagAGATCGTGGTGAGGTATTAGCTGATGCTCTGAAGACACTTCTCTGGGAAGG

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: 68 (upstream exon), 74 (downstream exon)
Score: 7

CATTTAAAGTCTGGAGGAGCAACCTTGAAGCTCTGAATGTAGACCTGCAAGACTTCTTTGTGCAGCTTTTTAACCTCATTCTGGAGTATCGGCCTGACAGgtttgaattc ... ctctatccagAGATCGTGGTGAGGTATTAGCTGATGCTCTGAAGACACTTCTCTGGGAAGGCAAACAGCAGGATATGATAAGAGCAGCTGCTTTCATTAAACGCCTAGCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATTTAAAGTCTGGAGGAGCAACCTTGAAGCTCTGAATGTAGACCTGCAAGACTTCTTTGTGCAGCTTTTTAACCTCATTCTGGAGTATCGGCCTGACAGgtttgaattctatttattttggtgctggtgatggggaagaaatatatatactcttgtcctttctaaaacacagattcatggataggtagcatcatagcaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggggaag