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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattcatgatcttatattggttattacgtactaattatttaccatgtatattctaagccgttgatttgaatgcag

Basic information

species Oryza sativa
transcript LOC_Os11g04980.1
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g04980.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GRMZM2G176546_T01 (Zea mays), 5'ss of exon 10
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattcatgatcttatattggttat-tacgtactaattatttaccatgtatattctaagccg-ttgatttgaatgcag
||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||| || |||||||| ||||| || || |||||||||||||||||| |||||  | | |||| ||| |    |  | ||||   ||| | || ||||||  |  ||| || |  |||||
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatatttatgattctgtgttggctatatgaccatcagttatg-gccaagcatgttctaaatctcttgtttcggttgcag

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GLYMA20G28200.1 (Glycine max), 5'ss of exon 19
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgta---atattcatgatcttatattggttattacgtactaattatttaccatgtatattctaagccgttgatttgaatgcag
||||| || || ||||| || ||||| || ||||| ||||| ||||||||||| || || ||||| || ||||| ||| | ||||| |||||| |||||||||   | ||  || ||          | | |  ||  |  | ||||    |   |  |  | ||   |  |||   || ||
AAGAATATCTTTAAGTTGGCACAAGGGGAGTACATTGCTCCTGAGAAGATTGAAAACGTATATGCCAAATGCAAATTTGTGGCGCAATGCTTTGTATATGgtatggaaataaatcattcccacaaattcagtgtgtg-tggtcatttgtactagcttgttgatgcttcttttttctttgtag

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GLYMA10G39540.1 (Glycine max), 5'ss of exon 19
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaat---attcatgatcttatattggttattacgtactaattatttaccatgtatattctaagccgttgatttgaatgcag
||||| || || ||||| || ||||| || ||||| ||||| ||||||||||| ||||| || || || ||||| ||| | |||||||||||| ||||||||||    ||  || ||          |   |  ||  | ||  |||    |   |     | ||   |  ||||  || ||
AAGAATATCTTTAAGTTGGCACAAGGCGAGTACATTGCTCCTGAGAAGATTGAAAATGTATACGCCAAATGCAAATTTGTGGCGCAGTGCTTTGTATATGgtaaggaaataaatcattcccacaaattcggtgtgtg-tgatcgtttgtactagcttgctgatgcttcttttttgtttgtag

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 5'ss of exon 19
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 5'ss of exon 19
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattcatgatcttatattggttattacgt-actaattatttaccatgtatattctaagccgttgatttgaatgcag
||||||||||| ||||| || |||||||| ||||||||||| ||||| ||||||||||| |||||||| ||||| ||| |||| ||||||||| |||||||||| |   ||||  || ||    |   |   | |    ||   | |    |   |  |   | | ||||          
AAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAAAATTGAGAATGTATATGCTAAATGCAAATTTGTTGCCCAGTGCTTTGTATATGgtaagaaaaatgagattttacaaatctctctttcatcttttgcctgctgactgcttatttctctgatgatag--------

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 5'ss of exon 19
lower sequence: Vv14s0128g00720.t01 (Vitis vinifera), 5'ss of exon 19
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattcatgatcttatattggttattacgtactaattatttaccatgtatattctaagccgttgatttgaatgcag
|||||||| |||||| | || || || ||||| ||||| || ||||| ||||||||||| ||||| |||||||| ||| || | || || ||||| ||||||||     |||   ||   |||   |||  |  ||    |  ||   | | | | || | | | | | |||| |  ||
AAGAACATCTTCAAGCTGGCACAGGGTGAATATATAGCACCAGAGAAAATTGAGAATGTATATGCCAAGTGCAAATTTGTTTCCCAATGTTTTATCTATGgtaaggcagatggagtttacttgcagattgggccctccccagctaagttctctttgctga-ctgcttaattgattttag

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 5'ss of exon 19
lower sequence: PP1S408_23V6.1 (Physcomitrella patens), 5'ss of exon 21
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattcatgatcttatattggttattacgtactaattatttaccatgtatattctaagccgttgatttgaatgcag----------------------
||||| || || ||||| ||||||||||| ||||| || || |||||||| |||||||||||   |    |    || ||  | ||||| |  ||| |||||| | |||||  | | |     |  | |    | |  || |   | |   |  ||  ||   ||  |  ||| |  ||                      
AAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAAGATCGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATACATGgta-tgttcattttttaaatggaggaactcttcatttcttgtggtctaaacaagttgcaactggtgtagatgacttaagatttttttttcatctgaaatga

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 5'ss of exon 19
lower sequence: PP1S33_126V6.1 (Physcomitrella patens), 5'ss of exon 22
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattcatgatctta-------tattggttattac-gtactaattatttaccatgtatattctaagccgttgatttgaatgcag---------------
||||| || |||||||| ||||| ||||| ||||| || ||||||||||||||||| |||||        |   ||| ||||| |||||||||||  |||||    |||||    |||        ||   || | |  ||   | | || | |  |||   |   |  || | | |      |  |               
AAGAATATCTTCAAGTTGGCTCAGGGAGAGTACATTGCGCCCGAGAAGATTGAGAACGTCTACCTGCGAAGTCGGTTCATTGCACAGTGCTTTATTCATGgtg-cgttcattcaattaatggaggcatcccttctcattgtctcagtcatctgct-tgtggttgaaacaccatggttactggggttgtgggtgctttaagag

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 5'ss of exon 19
lower sequence: PP1S12_178V6.2 (Physcomitrella patens), 5'ss of exon 21
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgta-----at---attcatgatcttatatt---ggttattacgtactaattatt--taccatgtatattctaagccgttgat-ttgaatgcag--------------------------------------------------------------------------
||||||||||||||||||||||||||||||||||| || || || |||||||||||  | |||  |    |   ||||||| ||||||| ||  ||||||||      ||   ||  | | ||  || ||     | ||| |    || || ||  |   | | | |     |||   || | ||   |  |                                                                           
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATTGCACCGGAAAAGATTGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATGgtgcgttcatttaatcgacggtcgcatctttttaatgattgcacgttactttttcgtgtgacggaaacgtgtagcaactggtgttacgtatactggaaaaactaccaactcattgaaatccaatcattcttaccaatcgtataattggttggtggtgaattgcacag

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 5'ss of exon 19
lower sequence: EFJ33980 (Selaginella moellendorffii), 5'ss of exon 20
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattcatgatcttatattggttattacgtactaattatttaccatgtatattctaagccgttgatttgaatgcag
||||||||||| ||| | || || || ||||||||||| || |||||||||||||||||||||  |||  |||||||  |||| ||||| ||  | || ||| | |   |  || || | |||  | |  ||  |   ||    || || | | ||| |                    
AAGAACATTTTTAAGCTTGCACAGGGTGAATACATAGCGCCAGAGAAGATTGAGAATGTCTATCATAAAAGCAAGTTCGTTGCTCAGTGTTTCGTCTACGgtgaga---acaattttgttttgtgtctagcgagcggttttgacacaat-tctcttcgattgtaacag-----------

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 5'ss of exon 19
lower sequence: EFJ37488 (Selaginella moellendorffii), 5'ss of exon 20
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattcatgatcttatat---tggttatt-------acgtactaattatttaccatgtatatt--ctaagccgttgatttgaatgcag-----------------------------------
||||||||||| ||| | || || || ||||||||||| || |||||||||||||||||||||   ||  |||||||  |||| ||||| ||  | || ||| | |   ||  | || | |   | |  | |        || |   ||   |  |    ||   |  | |||   |     |   ||                                      
AAGAACATTTTTAAGCTTGCACAGGGTGAATACATAGCGCCAGAGAAGATTGAGAATGTCTATCAAAAAAGCAAGTTCGTTGCTCAGTGTTTCGTCTACGgtgagaacaattttgttttgtgtctagcgagtccacctggcgaaaggatcggtcgctgaatagcatggcaaagttttctccctatgtgtgactcggttttgacacaattctcttcgattgtaacag

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|66919239|gb|CX106087.1|CX106087
EST:     TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATG                         GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
genomic: TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattca ... ttgaatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
EST: gi|29671404|gb|CB667679.1|CB667679
EST:     CAAGTTTATTGCGCAGTGCTTTATATATG                         GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
genomic: CAAGTTTATTGCGCAGTGCTTTATATATGgtaatattca ... ttgaatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
EST: gi|58590451|gb|CF988759.1|CF988759
EST:     TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATG                         GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
genomic: TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattca ... ttgaatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
EST: gi|58595336|gb|CF993644.1|CF993644
EST:     TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATG                         GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
genomic: TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattca ... ttgaatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
EST: gi|29679208|gb|CB675483.1|CB675483
EST:     TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATG                         GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
genomic: TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattca ... ttgaatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
EST: gi|29679210|gb|CB675485.1|CB675485
EST:     TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATG                         GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
genomic: TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattca ... ttgaatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
EST: gi|29665943|gb|CB662218.1|CB662218
EST:     TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATG                         GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
genomic: TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattca ... ttgaatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
EST: gi|29665942|gb|CB662217.1|CB662217
EST:     TGAGAATGTCTATGTTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATG                         GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
genomic: TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattca ... ttgaatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
EST: gi|29674249|gb|CB670524.1|CB670524
EST:     TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATG                         GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
genomic: TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattca ... ttgaatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
EST: gi|29670549|gb|CB666824.1|CB666824
EST:     TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATG                         GTGATAGTNTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
genomic: TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattca ... ttgaatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
EST: gi|29622335|gb|CB627346.1|CB627346
EST:     GTTTATTGCGCAGTGCTTTATATATG                         GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
genomic: GTTTATTGCGCAGTGCTTTATATATGgtaatattca ... ttgaatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG

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: 40 (upstream exon), 69 (downstream exon)
Score: 12

AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattca ... ttgaatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGGTGTTGAAGGCTTGGGCTGCATCGGAAGGAATCCAG




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