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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctctgatatctttcaaattatcacaggaacgacttatgaatcaattcttgtttacaatcatgtcctattccagctaggtaacttagtagaata...

Basic information

species Oryza sativa
transcript LOC_Os02g09060.1
intron # 10
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|58680116|gb|CK068803.1|CK068803
EST:     GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAG                         GGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
genomic: GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
EST: gi|88838045|gb|CI372613.1|CI372613
EST:     GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAG                         GGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
genomic: GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
EST: gi|86483356|gb|CI125989.1|CI125989
EST:     GTAAAAAACATGGAGATGTGGAGGGAAAGAATTCAAAAAGTAAAAGAAAG                         GGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
genomic: GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
EST: gi|88548190|gb|CI476539.1|CI476539
EST:     GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAG                         GGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
genomic: GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
EST: gi|88554522|gb|CI484709.1|CI484709
EST:     AGGGAGAGAATTCAAAAAGTAAAAGAAAG                         GGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
genomic: AGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
EST: gi|88218548|gb|CI218397.1|CI218397
EST:     GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAG                         GGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
genomic: GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
EST: gi|86500028|gb|CI142661.1|CI142661
EST:     GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAG                         GGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
genomic: GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
EST: gi|88544584|gb|CI472696.1|CI472696
EST:     CAAAAAGTAAAAGAAAG                         GGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
genomic: CAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
EST: gi|88535090|gb|CI463864.1|CI463864
EST:     AAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAG                         GGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
genomic: AAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
EST: gi|88259444|gb|CI363737.1|CI363737
EST:     GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAG                         GGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
genomic: GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
EST: gi|29678198|gb|CB674473.1|CB674473
EST:     GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAG                         GGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
genomic: GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
EST: gi|40492104|gb|BX900098.1|BX900098
EST:     GTTAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAG                         GGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
genomic: GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
EST: gi|86881135|gb|CI339296.1|CI339296
EST:     GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAG                         GGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
genomic: GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
EST: gi|86426354|gb|CI071451.1|CI071451
EST:     GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAG                         GGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
genomic: GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
EST: gi|86412826|gb|CI067231.1|CI067231
EST:     NNNNNNNNCATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAG                         GGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
genomic: -TAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
EST: gi|88527296|gb|CI455440.1|CI455440
EST:     GGAGATNTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAG                         GGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
genomic: GGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
EST: gi|88531440|gb|CI459916.1|CI459916
EST:     GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAG                         GGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
genomic: GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
EST: gi|88275435|gb|CI395286.1|CI395286
EST:     GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAG                         GG-ACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
genomic: GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
EST: gi|89175817|gb|CI042838.1|CI042838
EST:     GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAG                         GGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
genomic: GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
EST: gi|88226693|gb|CI226609.1|CI226609
EST:     GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAG                         GGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
genomic: GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
EST: gi|88218295|gb|CI218144.1|CI218144
EST:     GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAG                         GGAACAAGCTGCCATTAGATTGAAAGATGTAAAAATTGAGAAGCTGGAGGA
genomic: GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
EST: gi|86543524|gb|CI183730.1|CI183730
EST:     GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAG                         GGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
genomic: GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
EST: gi|86495057|gb|CI137690.1|CI137690
EST:     GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAG                         GGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
genomic: GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
EST: gi|88255261|gb|CI354085.1|CI354085
EST:     GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAG                         GGAACAAGCTGCCATTAGATTGAAAGATTAAAAAATTGAGAAGCTGGAGGA
genomic: GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
EST: gi|89165864|gb|CI102954.1|CI102954
EST:     GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAG                         GGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
genomic: GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
EST: gi|87014873|gb|CI271472.1|CI271472
EST:     GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAG                         GGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
genomic: GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
EST: gi|218484344|gb|FG954469.1|FG954469
EST:     GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAG                         GGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
genomic: GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
EST: gi|86490088|gb|CI132721.1|CI132721
EST:     GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAG                         GGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
genomic: GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
EST: gi|89164799|gb|CI101887.1|CI101887
EST:     GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAG                         GGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
genomic: GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
EST: gi|86492775|gb|CI135408.1|CI135408
EST:     GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAG                         GGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
genomic: GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
EST: gi|86529860|gb|CI170066.1|CI170066
EST:     GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAG                         GGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA
genomic: GTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGA

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: 66 (upstream exon), 71 (downstream exon)
Score: 30

ATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctc ... tttattatagGGAACAAGCTGCCATTAGATTGAAAGATGAAAAAATTGAGAAGCTGGAGGAGGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAGgtattttctctgatatctttcaaattatcacaggaacgacttatgaatcaattcttgtttacaatcatgtcctattccagctaggtaacttagtagaata

- - - - - - - - - - -  CATGGA
- - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA