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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACTCGTTTTGTCTCAAGGAAACCAGCAAAGACTATAGTAGCTACAATTGAAGTTGTTGCTGAGACTATGGGTCTTAAGGTCCACTCTCAGAATTACAAGgtaattacaaaacattttcttcaacaagcaactcatttcttactcttgatgtaatgatacttattgctaactcttttctgcag

Basic information

species Oryza sativa
transcript LOC_Os06g40370.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g40370.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G137569_T03 (Zea mays), 5'ss of exon 10
AACTCGTTTTGTCTCAAGGAAACCAGCAAAGACTATAGTAGCTACAATTGAAGTTGTTGCTGAGACTATGGGTCTTAAGGTCCACTCTCAGAATTACAAGgtaattacaaaacattttcttcaacaagcaact------catttctt--actcttgatgtaatgatacttattgctaactcttt------tctgcag
||| |||||||||||||| |||||||| |||||||||||||||||||||||||||||||| ||| | ||| |||| ||||||||||| |||||||||||||||      ||||||   |||||| ||  | ||      || |  ||  ||||||| |  |     |  |  || ||  | |||      | |||||
AACGCGTTTTGTCTCAAGAAAACCAGCTAAGACTATAGTAGCTACAATTGAAGTTGTTGCCGAGTCAATGAGTCTCAAGGTCCACTCCCAGAATTACAAGgtacacttgaaacatcg-cttcaaaaaatatctgctggacaatcatttgactcttg-ttcatctccatgtgctggtacatgtttactaactttgcag

upper sequence: LOC_Os06g40370.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G171507_T02 (Zea mays), 5'ss of exon 13
AACTCGTTTTGTCTCAAGGAAACCAGCAAAGACTATAGTAGCTACAATTGAAGTTGTTGCTGAGACTATGGGTCTTAAGGTCCACTCTCAGAATTACAAGgtaattacaaaacattttcttcaacaagcaactcatttcttactcttga-----tgtaatgatacttattgctaactcttttctgcag------------------
||| ||||| |||||||| || ||||| |||||| |||||||||||||||| |||||||||||| | |||||||| ||||||||||| | ||| |||||||||      ||||||    ||||| || || ||  |   | |   ||||     |||  ||   |    |||| | |   |  | |                    
AACACGTTTCGTCTCAAGAAAGCCAGCCAAGACTGTAGTAGCTACAATTGAGGTTGTTGCTGAGTCAATGGGTCTCAAGGTCCACTCCCGGAACTACAAGgtacacttgaaacatcga-ttcaa-aaacatctgctggataatcattgagcttttgtcttgtctccatctgctgaattgctgatacgtattttactaactttgcag

upper sequence: LOC_Os06g40370.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA17G12250.2 (Glycine max), 5'ss of exon 11
AACTCGTTTTGTCTCAAGGAAACCAGCAAAGACTATAGTAGCTACAATTGAAGTTGTTGCTGAGACTATGGGTCTTAAGGTCCACTCTCAGAATTACAAGgta-attacaaaacattttcttcaacaagcaactcatttcttact--cttgatgtaatgatactta--ttgctaactctt--ttctgcag----------
|||||||||||||||  | |||||||||||   |||| |  || ||||||||| |||||| ||| | ||||||||||||||||| ||||  |||||||||||| |   | |    | | ||| |    | || |  ||  |   |  |      | | ||| ||||  ||| |||    |  |  ||             
AACTCGTTTTGTCTCCCGTAAACCAGCAAAAGTTATAATTTCTTCAATTGAAGCTGTTGCAGAGTCAATGGGTCTTAAGGTCCATTCTCGCAATTACAAGgtataactcgacttgtctactttacactgtaaatgtttaatggataacacaggctcaagatgcttaatttgataataactggtgttgtgatgtaccaggc

upper sequence: LOC_Os06g40370.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA13G23500.1 (Glycine max), 5'ss of exon 11
AACTCGTTTTGTCTCAAGGAAACCAGCAAAGACTATAGTAGCTACAATTGAAGTTGTTGCTGAGACTATGGGTCTTAAGGTCCACTCTCAGAATTACAAGgtaa------------ttacaaaacattttc----ttcaacaagcaactca--tttcttactcttgatgtaatgatacttattgctaactcttttctgcag
|||||||||||||||  | |||||||||||   |||| |  || ||||||||| |||||| ||| | ||||||||||||||||| ||||  ||||||||||||              |||   ||||| |     || ||     ||| ||   |   ||  ||| || | || |||  |  || |      | || |   
AACTCGTTTTGTCTCCCGTAAACCAGCAAAAGTTATAATTTCTTCAATTGAAGCTGTTGCAGAGTCAATGGGTCTTAAGGTCCATTCTCGCAATTACAAGgtataactccacttgtctactttacattgtaaatgtttaatggataacacaggctcaatatgcttaatttgataataactggtgttgtgatgtatcaggc-

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|699698|gb|D45989.1|D45989
EST:     AAGTTGTTGCTGAGACTATGGGTCTTAAGGTCCACTCTCAGGATTACAAG                         TTGCGTCTTGAAGGTGTATCTTCAAACAGGATGAGCCCCCTTGCTGTTGTN
genomic: AAGTTGTTGCTGAGACTATGGGTCTTAAGGTCCACTCTCAGAATTACAAGgtaattacaa ... ttttctgcagTTGCGTCTTGAAGGTGTATCTTCAAACAGAATGAGCCCGTTTGCTGTTGTT
EST: gi|58586866|gb|CF985174.1|CF985174
EST:     AAGTTGTTGCTGAGACTATGGGTCTTAAGGTCCACTCTCAGAATTACAAG                         TTGCGTCTTGAAGGTGTATCTTCAAACAGAATGAGCCCGTTTGCTGTTGTT
genomic: AAGTTGTTGCTGAGACTATGGGTCTTAAGGTCCACTCTCAGAATTACAAGgtaattacaa ... ttttctgcagTTGCGTCTTGAAGGTGTATCTTCAAACAGAATGAGCCCGTTTGCTGTTGTT
EST: gi|218485351|gb|FG957642.1|FG957642
EST:     AAGTTGTTGCTGAGACTATGGGTCTTAAGGTCCACTCTCAGAATTACAAG                         TTGCGTCTTGAAGGTGTATCTTCAAACAGAATGAGCCCGTTAGCTGTTGTT
genomic: AAGTTGTTGCTGAGACTATGGGTCTTAAGGTCCACTCTCAGAATTACAAGgtaattacaa ... ttttctgcagTTGCGTCTTGAAGGTGTATCTTCAAACAGAATGAGCCCGTTTGCTGTTGTT
EST: gi|86505939|gb|CI148572.1|CI148572
EST:     TCAGAATTACAAG                         TTGCGTCTTGAAGGTGTATCTTCAAACAGAATGAGCCCGTTTGCTGTTGTT
genomic: TCAGAATTACAAGgtaattacaa ... ttttctgcagTTGCGTCTTGAAGGTGTATCTTCAAACAGAATGAGCCCGTTTGCTGTTGTT
EST: gi|88226354|gb|CI226270.1|CI226270
EST:     ACTCTCAGAATTACAAG                         TCGCGTCTTGAAGGTGTATCTTCAAACAGAATGAGCCCGTTTGCTGTTGTT
genomic: ACTCTCAGAATTACAAGgtaattacaa ... ttttctgcagTTGCGTCTTGAAGGTGTATCTTCAAACAGAATGAGCCCGTTTGCTGTTGTT
EST: gi|87020107|gb|CI277839.1|CI277839
EST:     AAGTTGTTGCTGAGACTATGGGTCTTAAGGTCCACTCTCAGAATTACAAG                         TTGCGTCTTGAAGGTGTATCTTCAAACAGAATGAGCCCGTTTGCTGTTGTT
genomic: AAGTTGTTGCTGAGACTATGGGTCTTAAGGTCCACTCTCAGAATTACAAGgtaattacaa ... ttttctgcagTTGCGTCTTGAAGGTGTATCTTCAAACAGAATGAGCCCGTTTGCTGTTGTT

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), 56 (downstream exon)
Score: 17

AACTCGTTTTGTCTCAAGGAAACCAGCAAAGACTATAGTAGCTACAATTGAAGTTGTTGCTGAGACTATGGGTCTTAAGGTCCACTCTCAGAATTACAAGgtaattacaa ... ttttctgcagTTGCGTCTTGAAGGTGTATCTTCAAACAGAATGAGCCCGTTTGCTGTTGTTCTACAG




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