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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGAGAGATCGGCATCGGCACTCCACCACAGAACTTCACTGTGATATTCGACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCGgtaggttcatcacctaacagacttatgaaactattgtgcacgtatacagtagaaaatgactgtatttttgtaaggaagaatgtttgatgttttgatgtctatgctttccag

Basic information

species Oryza sativa
transcript LOC_Os01g18630.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g18630.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G077233_T04 (Zea mays), 5'ss of exon 2
TGGAGAGATCGGCATCGGCACTCCACCACAGAACTTCACTGTGATATTCGACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCGgtaggttcatcacctaacagacttatgaaactattgtgcacgtatacagtagaaaatgactgtatttttgtaaggaagaatgtttgatgttttgatgtctatgctttccag
|||| ||||| |||||||||| ||||||||||||||||| |||||||||||||||||||||||||||||||||||||| |||   || || || ||||||||| |||| | |||| | ||  |||||| || ||  ||||  |||   |  | |||| |  |||| ||  |            ||| | |||  ||| | |||  || |||
TGGACAGATCAGCATCGGCACGCCACCACAGAACTTCACAGTGATATTCGACACTGGAAGCTCCAACTTGTGGGTTCCCTCATCCAAGTGCTACTTTTCGgtatgttctttacctgataggtttatgagacaatcttgca--tattttgatgcaaataag-gtatgttaat------------ttggtatttctatggccatgtattacag
















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|88420647|gb|CI564483.1|CI564483
EST:     ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCG                         ATAGCCATGCTACTTACACCACAGGTACAAGTCAAAAGGG
genomic: ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCGgtaggttcat ... tgctttccagATAGC-ATGCTACTTACACCACAGGTACAAGTCAAAAGGG
EST: gi|88401360|gb|CI585916.1|CI585916
EST:     CACTGGAAGCTCCAACTTGTGGGTTCCATCAGCTGAAATGTTATTTTTCG                         ATAGCATGCTACTTACACCACAGG
genomic: CACTGGAAGCTCCAACTTGTGGGTTCCATCAG-TGAAATGTTATTTTTCGgtaggttcat ... tgctttccagATAGCATGCTACTTACACCACAGG
EST: gi|38477201|gb|CF961334.1|CF961334
EST:     ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCG                         ATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
genomic: ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCGgtaggttcat ... tgctttccagATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
EST: gi|29645987|gb|CB650994.1|CB650994
EST:     ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCG                         ATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
genomic: ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCGgtaggttcat ... tgctttccagATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
EST: gi|300216028|gb|HO088654.1|HO088654
EST:     ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCG                         ATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
genomic: ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCGgtaggttcat ... tgctttccagATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
EST: gi|117226899|gb|CT848683.1|CT848683
EST:     ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCG                         ATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
genomic: ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCGgtaggttcat ... tgctttccagATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
EST: gi|29631102|gb|CB636111.1|CB636111
EST:     ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCG                         ATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
genomic: ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCGgtaggttcat ... tgctttccagATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
EST: gi|29639114|gb|CB644123.1|CB644123
EST:     ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCG                         ATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
genomic: ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCGgtaggttcat ... tgctttccagATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
EST: gi|33655849|gb|CF278463.1|CF278463
EST:     ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCG                         ATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
genomic: ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCGgtaggttcat ... tgctttccagATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
EST: gi|88395139|gb|CI609455.1|CI609455
EST:     ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCG                         ATAGCATGCTACTTACACCACAGGT
genomic: ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCGgtaggttcat ... tgctttccagATAGCATGCTACTTACACCACAGGT
EST: gi|29643123|gb|CB648130.1|CB648130
EST:     ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCG                         ATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
genomic: ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCGgtaggttcat ... tgctttccagATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
EST: gi|88453344|gb|CI565786.1|CI565786
EST:     ACACTGGAAGCTCCAACTTGTGGGTTC-ATCAGTGAAATGTTATTTTTCG                         ATAGCATGCTACTTA-ACCACAGGTA-AAGTGAAA-GGGT
genomic: ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCGgtaggttcat ... tgctttccagATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGT
EST: gi|88390396|gb|CI607432.1|CI607432
EST:     ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCG                         ATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGT
genomic: ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCGgtaggttcat ... tgctttccagATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGT
EST: gi|2428018|gb|C72481.1|C72481
EST:     CTGGGAAGCTCCAACTTGTGGGGTTCCATCAGTGAAATGTTATTTTTCCG                         ATAGCATGCTACTTACACCACAGGTACAAGTCNAAAGGGTCGA
genomic: CTGG-AAGCTCCAACTTGTGGG-TTCCATCAGTGAAATGTTATTTTTC-Ggtaggttcat ... tgctttccagATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGA
EST: gi|29662753|gb|CB659028.1|CB659028
EST:     ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCG                         ATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
genomic: ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCGgtaggttcat ... tgctttccagATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
EST: gi|88416903|gb|CI573618.1|CI573618
EST:     ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCG                         ATAGCATGCTACTTACACCAC
genomic: ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCGgtaggttcat ... tgctttccagATAGCATGCTACTTACACCAC
EST: gi|29665539|gb|CB661814.1|CB661814
EST:     ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCG                         ATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
genomic: ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCGgtaggttcat ... tgctttccagATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
EST: gi|33664969|gb|CF295936.1|CF295936
EST:     ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCG                         ATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
genomic: ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCGgtaggttcat ... tgctttccagATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
EST: gi|300215808|gb|HO088434.1|HO088434
EST:     ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCG                         ATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
genomic: ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCGgtaggttcat ... tgctttccagATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
EST: gi|88304198|gb|CI599886.1|CI599886
EST:     ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCG                         ATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
genomic: ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCGgtaggttcat ... tgctttccagATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
EST: gi|218504625|gb|FG968741.1|FG968741
EST:     ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCG                         ATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
genomic: ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCGgtaggttcat ... tgctttccagATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
EST: gi|88395886|gb|CI593088.1|CI593088
EST:     ACACTGGAAGCTCCAACTTGTGGGT-CCATCAGTGAAATGTTATTTTTCG                         ATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCG
genomic: ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCGgtaggttcat ... tgctttccagATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCG
EST: gi|88399126|gb|CI603793.1|CI603793
EST:     ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCG                         ATAGCATGCTACTTACACCACAGGTACA
genomic: ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCGgtaggttcat ... tgctttccagATAGCATGCTACTTACACCACAGGTACA
EST: gi|88401348|gb|CI585904.1|CI585904
EST:     ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCG                         ATACCATGCTACTTACACCACAGG
genomic: ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCGgtaggttcat ... tgctttccagATAGCATGCTACTTACACCACAGG
EST: gi|38471583|gb|CF955714.1|CF955714
EST:     ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCG                         ATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
genomic: ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCGgtaggttcat ... tgctttccagATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
EST: gi|33654015|gb|CF276629.1|CF276629
EST:     ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCG                         ATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
genomic: ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCGgtaggttcat ... tgctttccagATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
EST: gi|29635435|gb|CB640444.1|CB640444
EST:     ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCG                         ATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC
genomic: ACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCGgtaggttcat ... tgctttccagATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTAC

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), 75 (downstream exon)
Score: 107

TGGAGAGATCGGCATCGGCACTCCACCACAGAACTTCACTGTGATATTCGACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCGgtaggttcat ... tgctttccagATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGAGAGATCGGCATCGGCACTCCACCACAGAACTTCACTGTGATATTCGACACTGGAAGCTCCAACTTGTGGGTTCCATCAGTGAAATGTTATTTTTCGgtaggttcatcacctaacagacttatgaaactattgtgcacgtatacagtagaaaatgactgtatttttgtaaggaagaatgtttgatgttttgatgtctatgctttccag

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