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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCATGGAATATTTGCATGGGAAGAATATAGTTCATTTTGATCTAAAGTGTGAGAACCTACTGGTCAACATGAGGGATCCACAACGACCAATCTGCAAAgtttgatccctgccctctcatcttcatttcctcagctcttgcttcaaatggttgttacctgactgtcatcccacctccattttctgctcag

Basic information

species Oryza sativa
transcript LOC_Os02g54510.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g54510.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G039106_T03 (Zea mays), 5'ss of exon 4
TGGCATGGAATATTTGCATGGGAAGAATATAGTTCATTTTGATCTAAAGTGTGAGAACCTACTGGTCAACATGAGGGATCCACAACGACCAATCTGCAAAgtttgatccctgccctctcatcttcat---ttcctcagctcttgcttcaaatggttgttacctgactgtcatcccacctccattttctgctcag------------------
|||||||||||||||||| |||||||||||||| |||||||| || ||||||||||| |||||||| ||||||||||||||||| |||||||||||||| ||||||||||| |||   | | | | |      ||      ||      |||  ||||  |    |||     |  |  |    |||| | ||                   
TGGCATGGAATATTTGCACGGGAAGAATATAGTCCATTTTGACCTGAAGTGTGAGAATCTACTGGTGAACATGAGGGATCCACAGCGACCAATCTGCAAGgtttgatcccttccccagcctttccctacgccgctttatctttctggggaattcttgtcgcaatgctggatatcttctcctgacttctccccaacacaaatactctgatcag

upper sequence: LOC_Os02g54510.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G052658_T01 (Zea mays), 5'ss of exon 5
TGGCATGGAATATTTGCATGGGAAGAATATAGTTCATTTTGATCTAAAGTGTGAGAACCTACTGGTCAACATGAGGGATCCACAACGACCAATCTGCAAAgtttgatccctgccctctcat-------cttcatttcctcagctcttgct-tca-aatggttgttacctgactgtcatcccacctc---cattttctgctcag
||||||||| ||||||||||||||||||||||| |||||||| || || |||||||| |||||||| |||||||||||||| || |||||||| ||||| ||||||||||   ||| ||         ||| || |     |   ||| | ||| |||||| | | ||||||| |   || | |||    | | |||| ||||
TGGCATGGAGTATTTGCATGGGAAGAATATAGTCCATTTTGACCTGAAATGTGAGAATCTACTGGTGAACATGAGGGATCCGCAGCGACCAATTTGCAAGgtttgatccccagcctttccctctgctgctttatctttctggaaattgttgtcacaatggtggat-cctgact-tgtcccaaactcaaatactctctgatcag

upper sequence: LOC_Os02g54510.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA13G01190.2 (Glycine max), 5'ss of exon 8
TGGCATGGAATATTTGCATGGGAAGAATATAGTTCATTTTGATCTAAAGTGTGAGAACCTACTGGTCAACATGAGGGATCCACAACGACCAATCTGCAAAgtttg-atccctgccctctcatcttcatttcctcag-ctcttgcttcaaatggt-tgttacctga--ctgtcatcccacctccattttctgctcag
||| ||||| ||||||||||| || || || |||||||||||| | || |||||||| ||| ||||||| ||||| ||||| ||||| || |||||||| ||    ||       |   ||  | || |    ||| |    ||   ||      || || | ||   ||  ||   |  |   |  | |  ||||
TGGGATGGAGTATTTGCATGGAAAAAACATTGTTCATTTTGATTTGAAATGTGAGAATCTATTGGTCAATATGAGAGATCCTCAACGGCCTATCTGCAAGgtacacataagaatacatacacatacactgatgcagacaaaagccaaaagcaacctgctagcggagattgaaatgagatttgtgtaattt-ttcag

upper sequence: LOC_Os02g54510.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA17G07320.1 (Glycine max), 5'ss of exon 11
TGGCATGGAATATTTGCATGGGAAGAATATAGTTCATTTTGATCTAAAGTGTGAGAACCTACTGGTCAACATGAGGGATCCACAACGACCAATCTGCAAAgtttg-atccctgccctctcatcttcatttcctcagctcttgcttcaaatggt-tgttacctga--ctgtcatcccacctccattttctgctcag
||| ||||| ||||||||||| || || || || ||||||||| | || |||||||| ||| ||||||| ||||| ||||| ||||| || |||||||| ||    ||       |  |||  |  | |    || |    ||   |       || || | ||   ||  ||   |  |   |  | |  ||||
TGGGATGGAGTATTTGCATGGAAAAAACATTGTGCATTTTGATTTGAAATGTGAGAATCTATTGGTCAATATGAGAGATCCTCAACGGCCTATCTGCAAGgtacacataagaatacattcacatatactgaggcaacaaaagccaaacgcaacctgctagcggagattgaaatgagatttgtgtaattt-ttcag

upper sequence: LOC_Os02g54510.2 (Oryza sativa), 5'ss of exon 6
lower sequence: AT5G57610.1 (Arabidopsis thaliana), 5'ss of exon 6
TGGCATGGAATATTTGCATGGGAAGAATATAGTTCATTTTGATCTAAAGTGTGAGAACCTACTGGTCAACATGAGGGATCCACAACGACCAATCTGCAAAgtttgatccctgccc-tctcatct-tcatttcctcagctcttgcttcaaatggttgttacctgactgtcatcccacctccattttctgctcag
||| ||||| |||||||| || ||||| || |||||||| ||| | ||||||||||| || || || |||||||| ||||| || || || || ||||| |||   |   | | | ||| |||| |||| |    |    |    | | ||| || | |  | | | |  |    | | | |||||    |||
TGGGATGGAGTATTTGCACGGAAAGAACATTGTTCATTTCGATTTGAAGTGTGAGAATCTTCTTGTGAACATGAGAGATCCTCAGCGTCCTATATGCAAGgttctgttgttactcatctgatctctcatataacaaagagtaagcttatatgtttctca--taaattttgt----ctttctttttccttccag

upper sequence: LOC_Os02g54510.2 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ30928 (Selaginella moellendorffii), 5'ss of exon 3
TGGCATGGAATATTTGCATGGGAAGAATATAGTTCATTTTGATCTAAAGTGTGAGAACCTACTGGTCAACATGAGGGATCCACAACGACCAATCTGCAAAgtt-tgatccctgccctctcatcttcatttcctcagctcttgcttcaaatggttgttacctgactgtcatcccacctccattttctgctcag
||| ||||| ||| | || || ||||| || |||||||| || || ||||| |||||  | ||||||||||||||||||||||| || ||| | ||||| ||  ||||  ||  | ||||   ||| ||  ||  |   |   |     ||   ||| || |                              
TGGGATGGAGTATCTACACGGAAAGAACATCGTTCATTTCGACCTGAAGTGCGAGAATTTGCTGGTCAACATGAGGGATCCACATCGGCCAGTGTGCAAGgtaatgatatct-tcgtctctcgttctttcactttgtagtgagtgactgtgcacgtttccag------------------------------

upper sequence: LOC_Os02g54510.2 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ17246 (Selaginella moellendorffii), 5'ss of exon 3
TGGCATGGAATATTTGCATGGGAAGAATATAGTTCATTTTGATCTAAAGTGTGAGAACCTACTGGTCAACATGAGGGATCCACAACGACCAATCTGCAAAgtt-tgatccctgccctctcatcttcatttcctcagctcttgcttcaaatggttgttacctgactgtcatcccacctccattttctgctcag
||| ||||| ||| | || || ||||| || |||||||| || || ||||| |||||  | ||||||||||||||||||||||| || ||| | ||||| ||  ||||  ||  | ||||   ||| ||  ||  |   |   |     ||   ||| || |                              
TGGGATGGAGTATCTACACGGAAAGAACATCGTTCATTTCGACCTGAAGTGCGAGAATTTGCTGGTCAACATGAGGGATCCACATCGGCCAGTGTGCAAGgtaatgatatct-tcgtctctcgttctttcgctttgtagtgagtgactgtgcacgtttccag------------------------------

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|396941216|gb|HO188425.1|HO188425
EST:     GGTCAACATGAGGGATCCACAACGACCAATCTGCAAA                         ATTGGTGATCTTGGACTATCAAAGGTGAAGCAGCACACTTTGGTGTCTGGC
genomic: GGTCAACATGAGGGATCCACAACGACCAATCTGCAAAgtttgatccc ... ttctgctcagATTGGTGATCTTGGACTATCAAAGGTGAAGCAGCACACTTTGGTGTCTGGC
EST: gi|66924155|gb|CX111003.1|CX111003
EST:     GTGAGAACCTACTGGTCAACATGAGGGATCCACAACGACCAATCTGCAAA                         ATTGGTGATCTTGGACTAT
genomic: GTGAGAACCTACTGGTCAACATGAGGGATCCACAACGACCAATCTGCAAAgtttgatccc ... ttctgctcagATTGGTGATCTTGGACTAT

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: 64 (upstream exon), 71 (downstream exon)
Score: 24

TGGCATGGAATATTTGCATGGGAAGAATATAGTTCATTTTGATCTAAAGTGTGAGAACCTACTGGTCAACATGAGGGATCCACAACGACCAATCTGCAAAgtttgatccc ... ttctgctcagATTGGTGATCTTGGACTATCAAAGGTGAAGCAGCACACTTTGGTGTCTGGCGGTGTTAGAGGAACCTTACCATGGATGGCACCAGAGCTTCTGAGTGGGA




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