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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTATGGCCAACTCTGCAGAGAAAATCAGACTTGCTGGAAATCAAAATGTTATGGTCTGTGAGCGTGGCACCATGTTTGGCTACAgttaaggaatatatattcttttggctatcttttctgtacattgctcaatttaagataacacaaagtgaaaagtcatagatgtaaatatatgatattggat...

Basic information

species Oryza sativa
transcript LOC_Os12g10784.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g10784.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G168510_T01 (Zea mays), 5'ss of exon 1
---------------GTTATGGCCAACTCTGCAGAGAAAATCAGACTTGCTGGAAATCAAAATGTTATGGTCTGTGAGCGTGGCACCATGTTTGGCTACAgttaaggaatatatattcttttggctatct--tttctgtacattgctcaatttaagataacacaaagtgaaaagtcatagatgtaaatatatgatattggat-----
               |||||||  |||||| |||||||| | || |||||||| |||| |||||| ||||||||||||||||| ||||||||||||||||||||||| ||       ||||||| | | |  |||||||   |||| || || || || | | | |   || | | |   ||   ||   | || | | | |     
CATTTACATCTCCAGGTTATGGTGAACTCTACAGAGAAAGTAAGGCTTGCTGGGAATCCAAATGTGATGGTCTGTGAGCGTGGTACCATGTTTGGCTACAgttaaggcat-------cttttggttctttattttctgtttgttgcccacttaaacatgaaaaagatacaacaattaatcataggaactaaggaaagtaggtaacat

upper sequence: LOC_Os12g10784.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G168510_T02 (Zea mays), 5'ss of exon 8
GTTATGGCCAACTCTGCAGAGAAAATCAGACTTGCTGGAAATCAAAATGTTATGGTCTGTGAGCGTGGCACCATGTTTGGCTACAgttaaggaatatatattcttttggctatct--tttctgtacattgctcaatttaagataacacaaagtgaaaagtcatagatgtaaatatatgatattggat-----
|||||||  |||||| |||||||| | || |||||||| |||| |||||| ||||||||||||||||| ||||||||||||||||||||||| ||       ||||||| | | |  |||||||   |||| || || || || | | | |   || | | |   ||   ||   | || | | | |     
GTTATGGTGAACTCTACAGAGAAAGTAAGGCTTGCTGGGAATCCAAATGTGATGGTCTGTGAGCGTGGTACCATGTTTGGCTACAgttaaggcat-------cttttggttctttattttctgtttgttgcccacttaaacatgaaaaagatacaacaattaatcataggaactaaggaaagtaggtaacat

upper sequence: LOC_Os12g10784.1 (Oryza sativa), 5'ss of exon 7
lower sequence: AT1G79500.2 (Arabidopsis thaliana), 5'ss of exon 8
GTTATGGCCAACTCTGCAGAGAAAATCAGACTTGCTGGAAATCAAAATGTTATGGTCTGTGAGCGTGGCACCATGTTTGGCTACAgttaaggaatatatattcttttggctatcttttctgtacattgctcaatttaagataacacaaagtgaaaagtca--tagatgtaaatatatgatattggat--------------------------------------------------------------------------------------------
|| ||||  || || || ||||| |||||||| ||||| |||| |||||||||||| |||||  | || |||||||| || |||||| |   |  || |    |||    |||  | ||     | |     |||  |||||     || |   | |  |      || || || |  | |||||||                                                                                            
GTCATGGAGAATTCAGCTGAGAAGATCAGACTGGCTGGGAATCCAAATGTTATGGTTTGTGAAAGAGGAACCATGTTCGGATACAgtaagttatcatct-ccttttcaaatattgtgtccacggaatttagtattgtagatattctcaaatctcatgcaaatctcttggaattaaaaaaaattggattgctgaagtatacattagagggtgctaaaacaattttttttctctgcctttacaattgactgactgatactctttttggttttgattatcag

upper sequence: LOC_Os12g10784.1 (Oryza sativa), 5'ss of exon 7
lower sequence: EFJ32189 (Selaginella moellendorffii), 5'ss of exon 6
GTTATGGCCAACTCTGCAGAGAAAATCAGACTTGCTGGAAATCAAAATGTTATGGTCTGTGAGCGTGGCACCATGTTTGGCTACAgttaaggaatatatattcttttggctatcttttctgtacattgctcaatttaagataacacaaagtgaaaagtcatagatgtaaatatatgatattggat
|| ||| |||| || || |  || ||||| ||||||||||||| ||| || |||||||||||||| |||||||||||||||||||||     | ||| | ||   ||  | |  | | |||   | || |     |    |  |    ||                                   
GTGATGACCAATTCAGCCGCTAAGATCAGGCTTGCTGGAAATCCAAACGTCATGGTCTGTGAGCGCGGCACCATGTTTGGCTACAgt----aagtattttttggattc-caaattctcctgctgagtggtgtggctggattttcgtgtag-----------------------------------

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|157651751|gb|EX451385.1|EX451385
EST:     TGGAAATCAAAATGTTATGGTCTGTGAGCGTGGCACCATGTTTGGCTACA                         ATGATCTAATTGTTGATCCAAGGAATTTTGAGTGGCTGAGAGAAGCTAATT
genomic: TGGAAATCAAAATGTTATGGTCTGTGAGCGTGGCACCATGTTTGGCTACAgttaaggaat ... tccgacacagATGATCTAATTGTTGATCCAAGGAATTTTGAGTGGCTGAGAGAAGCTAATT
EST: gi|4714258|gb|AU058225.1|AU058225
EST:     GGTCTGTGAGCGTGGCACCATGTTTGGCTACA                         ATGATCTAATTGTTGATCCAAGGAATTTTGAGTGGCTGAGAGAAGCTAATT
genomic: GGTCTGTGAGCGTGGCACCATGTTTGGCTACAgttaaggaat ... tccgacacagATGATCTAATTGTTGATCCAAGGAATTTTGAGTGGCTGAGAGAAGCTAATT
EST: gi|41883464|gb|BX928437.1|BX928437
EST:     TGGAAATCAAAATGTTATGGTCTGTGAGCGTGGCACCATGTTTGGCTACA                         ATGATCTAATTGTTGATCCAAGGAATCTTGAGTGGGTGAGAGAAGCTTATT
genomic: TGGAAATCAAAATGTTATGGTCTGTGAGCGTGGCACCATGTTTGGCTACAgttaaggaat ... tccgacacagATGATCTAATTGTTGATCCAAGGAATTTTGAGTGGCTGAGAGAAGCTAATT
EST: gi|11442603|gb|BF430506.1|BF430506
EST:     TGGAAATCAAAATGTTATGGTCTGTGAGCGTGGCACCATGTTTGGCTACA                         ATGATCTAATTGTTGATCCAAGGAATTTTGAGTGGCTGAGAGAAGCTAATT
genomic: TGGAAATCAAAATGTTATGGTCTGTGAGCGTGGCACCATGTTTGGCTACAgttaaggaat ... tccgacacagATGATCTAATTGTTGATCCAAGGAATTTTGAGTGGCTGAGAGAAGCTAATT
EST: gi|33688394|gb|CF316633.1|CF316633
EST:     GGAAATCAAAAATGTTATGGTCTGTGAGCGTGGCACCATGTTTGGCTACA                         ATGATCTAATTGTTGATCCAAGGAATTTTGAGTGGCTGAGAGAAGCTAATT
genomic: GGAAATC-AAAATGTTATGGTCTGTGAGCGTGGCACCATGTTTGGCTACAgttaaggaat ... tccgacacagATGATCTAATTGTTGATCCAAGGAATTTTGAGTGGCTGAGAGAAGCTAATT

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: 61 (upstream exon), 59 (downstream exon)
Score: 14

GTTATGGCCAACTCTGCAGAGAAAATCAGACTTGCTGGAAATCAAAATGTTATGGTCTGTGAGCGTGGCACCATGTTTGGCTACAgttaaggaat ... tccgacacagATGATCTAATTGTTGATCCAAGGAATTTTGAGTGGCTGAGAGAAGCTAATTGTCCAGTT




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