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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAAGTTGGCGCAGAGCATGACCTCTCGCCCCATGAAGGGAATGTTGACTGGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtcagtgcctgttgttgataatgtaatctaatttgttctggttgtgaatgagcattcttttctgagtctgacattcatacgctggctcag

Basic information

species Oryza sativa
transcript LOC_Os12g42876.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g42876.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G149751_T03 (Zea mays), 5'ss of exon 11
CCAAGTTGGCGCAGAGCATGACCTCTCGCCCCATGAAGGGAATGTTGACTGGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtcagtgcctgttgttgataatgtaatctaatttgttctggttgtgaatgagcattctt-ttctgagtctgacattcatac-gctggctcag--------
| |||  ||| ||||||||||| |||||||| |||||||| ||| ||||||| || ||||||||||| |||||||| || ||| ||||||||||||||||||||||  ||   |   | || |   | | |||| |  || |         |  ||||| ||| |  | ||  | | |    |||    |          
CGAAGACGGCACAGAGCATGACGTCTCGCCCAATGAAGGGGATGCTGACTGGCCCAGTCACAATCCTCAACTGGTCCTTCGTCCGGAATGACCAGCCGAGgtcagtaactagagc-aagaacg--gtttgatttctggtgctcagagcaccgttttcttcttccgtttttggtactgacgttgctcctcccatcttccag

upper sequence: LOC_Os12g42876.1 (Oryza sativa), 5'ss of exon 10
lower sequence: EFJ05611 (Selaginella moellendorffii), 5'ss of exon 9
CCAAGTTGGCGCAGAGCATGACCTCTCGCCCCATGAAGGGAATGTTGACTGGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtcagtgcctgttgttgataatgtaatctaatttgttctggttgtgaatgagcattcttttctgagtctgacattcatacgctggctcag
|    |   |||||||| | ||     | ||||||||||||||| | || || ||||| |||||  | |||||||| || ||||| |||||||||||||||| ||    |||  ||   |  |  ||||    |   ||||   |   |   |||||    | |                          
CTTCCTACTCGCAGAGCCTCACTAAGAGGCCCATGAAGGGAATGCTCACGGGACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAGgtgagcttttgtctttctcatcgacatctttgctaa-ctggccttacgttt-cattcaccacag--------------------------

upper sequence: LOC_Os12g42876.1 (Oryza sativa), 5'ss of exon 10
lower sequence: EFJ28889 (Selaginella moellendorffii), 5'ss of exon 9
CCAAGTTGGCGCAGAGCATGACCTCTCGCCCCATGAAGGGAATGTTGACTGGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtcagtgcctgttgttgataatgtaatctaatttgttctggttgtgaatgagcattcttttctgagtctgacattcatacgctggctcag
|    |   |||||||| | ||     | ||||||||||||||| | || || ||||| |||||  | |||||||| || ||||| |||||||||||||||| ||    |||  ||   |  |  ||||    |   |||||  |   |   ||||| ||    |                         
CTTCCTACTCGCAGAGCCTCACTAAGAGGCCCATGAAGGGAATGCTCACGGGACCCGTGACAATTTTGAACTGGTCCTTCGTCAGAAATGACCAGCCGAGgtgagcttttgtctttctcatcgacatctttgctaa-ctggtcttacgttt-cattcattcaccacag----------------------

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|58655717|gb|CK044397.1|CK044397
EST:     GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
genomic: GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtcagtgcct ... gctggctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
EST: gi|218488071|gb|FG946100.1|FG946100
EST:     CGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
genomic: CGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtcagtgcct ... gctggctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
EST: gi|58695495|gb|CK084182.1|CK084182
EST:     GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
genomic: GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtcagtgcct ... gctggctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
EST: gi|84117659|gb|CD151426.1|CD151426
EST:     GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAAGAGGTCGAGGA
genomic: GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtcagtgcct ... gctggctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
EST: gi|58603308|gb|CK013836.1|CK013836
EST:     GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
genomic: GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtcagtgcct ... gctggctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
EST: gi|163927443|gb|EG713883.1|EG713883
EST:     GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
genomic: GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtcagtgcct ... gctggctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
EST: gi|86830872|gb|CI293836.1|CI293836
EST:     GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
genomic: GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtcagtgcct ... gctggctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
EST: gi|163926579|gb|EG713595.1|EG713595
EST:     GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
genomic: GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtcagtgcct ... gctggctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
EST: gi|218486915|gb|FG967742.1|FG967742
EST:     GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
genomic: GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtcagtgcct ... gctggctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
EST: gi|38470366|gb|CF954497.1|CF954497
EST:     GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGA
genomic: GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtcagtgcct ... gctggctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGA
EST: gi|29657694|gb|CB653969.1|CB653969
EST:     GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAAGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
genomic: GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtcagtgcct ... gctggctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
EST: gi|218496339|gb|FG945901.1|FG945901
EST:     GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
genomic: GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtcagtgcct ... gctggctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
EST: gi|29619039|gb|CB624051.1|CB624051
EST:     GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
genomic: GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtcagtgcct ... gctggctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
EST: gi|58601334|gb|CK011862.1|CK011862
EST:     GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
genomic: GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtcagtgcct ... gctggctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
EST: gi|33676339|gb|CF304578.1|CF304578
EST:     CAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTACTCTTGCCATCAAGAAGGAGGTCGAGGA
genomic: CAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtcagtgcct ... gctggctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
EST: gi|33680371|gb|CF308610.1|CF308610
EST:     TGTCAGGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
genomic: TGTCAGGAATGACCAGCCGAGgtcagtgcct ... gctggctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
EST: gi|55408443|gb|CV720819.1|CV720819
EST:     GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
genomic: GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtcagtgcct ... gctggctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
EST: gi|396941259|gb|HO188468.1|HO188468
EST:     GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
genomic: GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtcagtgcct ... gctggctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
EST: gi|29612828|gb|CB617841.1|CB617841
EST:     GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
genomic: GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtcagtgcct ... gctggctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
EST: gi|218478250|gb|FG951121.1|FG951121
EST:     GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
genomic: GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtcagtgcct ... gctggctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
EST: gi|58680570|gb|CK069257.1|CK069257
EST:     GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
genomic: GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtcagtgcct ... gctggctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
EST: gi|33683114|gb|CF311353.1|CF311353
EST:     GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
genomic: GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtcagtgcct ... gctggctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
EST: gi|2428679|gb|C73142.1|C73142
EST:     GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
genomic: GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtcagtgcct ... gctggctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
EST: gi|29638193|gb|CB643202.1|CB643202
EST:     GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
genomic: GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtcagtgcct ... gctggctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
EST: gi|29689518|gb|CB685793.1|CB685793
EST:     GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
genomic: GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtcagtgcct ... gctggctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA

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: 74 (upstream exon), 74 (downstream exon)
Score: 377

CCAAGTTGGCGCAGAGCATGACCTCTCGCCCCATGAAGGGAATGTTGACTGGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtcagtgcct ... gctggctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGACCTTGAGGCTGGTGGTATTCAG




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