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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggctgctgggattcgagcctaggtctccacggccacaacgtggaattctcaccaattctcaccactaaactacgtggaattcctattttcttcttacagAGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAG

Basic information

species Oryza sativa
transcript LOC_Os04g45070.1
intron # 1
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|58592200|gb|CF990508.1|CF990508
EST:     GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGA                         AGGTTGCAGATGAACCTCCTGC
genomic: GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGAgtgagtggct ... cttcttacagAGGTTGCAGATGAACCTCCTGC
EST: gi|86884366|gb|CI310950.1|CI310950
EST:     GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGA                         AGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
genomic: GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGAgtgagtggct ... cttcttacagAGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
EST: gi|87004303|gb|CI298835.1|CI298835
EST:     GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGA                         AGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
genomic: GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGAgtgagtggct ... cttcttacagAGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
EST: gi|88311646|gb|CI574863.1|CI574863
EST:     GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGA                         AGGTTGCAGATGAAACTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
genomic: GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGAgtgagtggct ... cttcttacagAGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
EST: gi|88975844|gb|CI024095.1|CI024095
EST:     GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGA                         AGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
genomic: GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGAgtgagtggct ... cttcttacagAGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
EST: gi|50878545|gb|AF527706.1|AF527706
EST:     GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGA                         AGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
genomic: GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGAgtgagtggct ... cttcttacagAGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
EST: gi|88827642|gb|CI778207.1|CI778207
EST:     GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGA                         AGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTA
genomic: GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGAgtgagtggct ... cttcttacagAGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTA
EST: gi|58693172|gb|CK081859.1|CK081859
EST:     GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGA                         AGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
genomic: GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGAgtgagtggct ... cttcttacagAGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
EST: gi|29670320|gb|CB666595.1|CB666595
EST:     GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGA                         AGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
genomic: GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGAgtgagtggct ... cttcttacagAGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
EST: gi|38470437|gb|CF954568.1|CF954568
EST:     GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGA                         AGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
genomic: GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGAgtgagtggct ... cttcttacagAGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
EST: gi|88404224|gb|CI575712.1|CI575712
EST:     GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGA                         AGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
genomic: GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGAgtgagtggct ... cttcttacagAGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
EST: gi|88741665|gb|CI765173.1|CI765173
EST:     GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGA                         AGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
genomic: GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGAgtgagtggct ... cttcttacagAGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
EST: gi|38471661|gb|CF955792.1|CF955792
EST:     GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGA                         AGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
genomic: GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGAgtgagtggct ... cttcttacagAGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
EST: gi|88445327|gb|CI587221.1|CI587221
EST:     GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGA                         AGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
genomic: GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGAgtgagtggct ... cttcttacagAGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
EST: gi|87005481|gb|CI285703.1|CI285703
EST:     GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGA                         AGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
genomic: GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGAgtgagtggct ... cttcttacagAGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
EST: gi|29670321|gb|CB666596.1|CB666596
EST:     GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGA                         AGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
genomic: GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGAgtgagtggct ... cttcttacagAGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
EST: gi|88406228|gb|CI594008.1|CI594008
EST:     GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGA                         AGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
genomic: GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGAgtgagtggct ... cttcttacagAGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
EST: gi|89165064|gb|CI255121.1|CI255121
EST:     GCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGA                         AGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
genomic: GCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGAgtgagtggct ... cttcttacagAGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
EST: gi|88367239|gb|CI564003.1|CI564003
EST:     GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGA                         AGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
genomic: GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGAgtgagtggct ... cttcttacagAGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
EST: gi|58601478|gb|CK012006.1|CK012006
EST:     GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGA                         AGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
genomic: GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGAgtgagtggct ... cttcttacagAGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
EST: gi|88406404|gb|CI596531.1|CI596531
EST:     GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGA                         AGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
genomic: GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGAgtgagtggct ... cttcttacagAGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
EST: gi|88405645|gb|CI598925.1|CI598925
EST:     GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGA                         AGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG
genomic: GGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGAgtgagtggct ... cttcttacagAGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATG

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: 73 (upstream exon), 75 (downstream exon)
Score: 413

GACGTCGCCGAGGAGAAGGCCGTCATCCCCGCCCCCGCGCCGCCGGCCGAGGAGGAGAAGCCTCCCGTCGACGACTCCAAGGCGCTGGCCATCGTCGAGAgtgagtggct ... cttcttacagAGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctcaccaattctcaccactaaactacgtggaattcctattttcttcttacagAGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAG
                  cactaaa  putative branch site (score: 413)
                                   ttcctattttcttctt  putative PPT
                                       tattttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggctgctgggattcgagcctaggtctccacggccacaacgtggaattctcaccaattctcaccactaaactacgtggaattcctattttcttcttacagAGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAG

- gctgctg
- - - - - - - - - - - - -ctccacg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cactaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctacgtg