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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTGGAAGAAAGTTATCTATGTCGACAGACTTGTGCAGCTGTTCAGATACGTACCACGTGAACAACTGACAATTCCTGATTTTGTCTTCCAgtatgtaatgtttctagaattttaagaggtctgctataaactagggtcaatactgacattctgacaattaaactctgcag

Basic information

species Oryza sativa
transcript LOC_Os03g05660.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g05660.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G100707_T01 (Zea mays), 5'ss of exon 13
GTCTGGAAGAAAGTTATCTATGTCGACAGACTTGTGCAGCTGTTCAGATACGTACCACGTGAACAACTGACAATTCCTGATTTTGTCTTCCAgtatgtaatgt------ttctagaattt-taagaggtctgctataaactagggtcaatactgacattctgacaattaaactctgcag
||||||||||||||| | ||||||||||||||||||||||| |||||||| |||||||||||||| || || |||||||||||||| |||||||| | ||| |      |  |||  ||| | ||||||| ||||   |||||  ||        |||  | |  | | ||  ||||||
GTCTGGAAGAAAGTTGTATATGTCGACAGACTTGTGCAGCTATTCAGATATGTACCACGTGAACAGCTCACCATTCCTGATTTTGTGTTCCAgtaagcaatctagtacttgttagcttttcttagaggtccgctagttactagactc--------catcttaaataatcaatcctgcag

upper sequence: LOC_Os03g05660.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA01G06730.1 (Glycine max), 5'ss of exon 15
GTCTGGAAGAAAGTTATCTATGTCGACAGACTTGTGCAGCTGTTCAGATACGTACCACGTGAACAACTGACAATTCCTGATTTTGTCTTCCAgt--atgtaatgtttctagaattttaagaggtctgctataaactagggtcaatactgacattc--tgacaattaaactctgcag------------------------------------------------------------------------------------------------------
|| |||||||||||  | ||||| || |||||  | ||||| |||||||| ||||| ||||||||| |||| || || ||||||||||| ||||  |    ||||||  |   | |||           ||    |    |  ||| ||  |||   |||  |  | || ||   |                                                                                                      
GTTTGGAAGAAAGTGGTATATGTTGATAGACTACTCCAGCTCTTCAGATATGTACCCCGTGAACAATTGACCATCCCAGATTTTGTCTTTCAgttgagtctatgttttcatg-tgttatatttataatcatttgttccttttcataatgctattacatgagtaacacacactctggtttaaatttattggaaattacaattaaataaaaagcgagacttagaagtaaatgtactttagattataggttctaattcattttgtacttttattctcaaag

upper sequence: LOC_Os03g05660.1 (Oryza sativa), 5'ss of exon 13
lower sequence: AT1G69340.1 (Arabidopsis thaliana), 5'ss of exon 14
GTCTGGAAGAAAGTTATCTATGTCGACAGACTTGTGCAGCTGTTCAGATACGTACCACGTGAACAACTGACAATTCCTGATTTTGTCTTCCAgtatgtaa----tgtttctagaattttaagaggtctgctataaactagggtcaat--actgac-attctgacaattaaactctgcag
|| |||||||||||| | ||||  ||| ||||| |||||||||||| |||||| || ||||| || |||||||| || || ||||| |||||||| ||      |  | ||   | | ||  |    |  |     || |  |   |  ||| || |  |      | |||   |||||
GTATGGAAGAAAGTTGTATATGCAGACCGACTTCTGCAGCTGTTCAAATACGTTCCTCGTGAGCAGCTGACAATCCCAGACTTTGTTTTCCAgtaagttcactctactcctcacactctagtaacgttattcagttctcgatttgttttacttactagaccttgtgtgaaaaattgcag

upper sequence: LOC_Os03g05660.1 (Oryza sativa), 5'ss of exon 13
lower sequence: Vv01s0011g00870.t01 (Vitis vinifera), 5'ss of exon 13
GTCTGGAAGAAAGTTATCTATGTCGACAGACTTGTGCAGCTGTTCAGATACGTACCACGTGAACAACTGACAATTCCTGATTTTGTCTTCCAgt---atgtaatgtttct----agaattttaagaggtctgctataaactagggtcaa--tactgacattctgacaattaaactctgcag-------------
|| |||||||||||  | ||||| ||| ||||  ||||||||||||||||||| |||||||| ||  ||||||| || || ||||| || ||||    | |  ||||  |    | ||| |  |   ||   | || | | |    |||  || | ||  ||  |||  |||  |    ||             
GTGTGGAAGAAAGTGGTATATGTTGACCGACTCATGCAGCTGTTCAGATACGTTCCACGTGAGCAGTTGACAATCCCCGACTTTGTGTTTCAgttgagttttctgttctttttcaaaatctggacttgttctcaattatcaataaccaagttagtaaccgtcccacatctaa--ttaaaaggcattcctgatag

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|88521495|gb|CI449188.1|CI449188
EST:     TTCAGATACGTACCACGTGAACAACTGACAATTCCTGATTTTGTCTTCCA                         GCATGATCTCGAAGTGAATGGTGGAAAGGGCATAATAATTGACCCTAGAAC
genomic: TTCAGATACGTACCACGTGAACAACTGACAATTCCTGATTTTGTCTTCCAgtatgtaatg ... aactctgcagGCATGATCTCGAAGTGAATGGTGGAAAGGGCATAATAATTGACCCTAGAAC
EST: gi|51946082|gb|CV152423.1|CV152423
EST:     TTCAGATACGTACCACGTGAACAACTGACAATTCCTGATTTTGTCTTCCA                         GCATGATCTCGAAGTGAATGGTGGAAAGGGCATAATAATTGACCCTAGAAC
genomic: TTCAGATACGTACCACGTGAACAACTGACAATTCCTGATTTTGTCTTCCAgtatgtaatg ... aactctgcagGCATGATCTCGAAGTGAATGGTGGAAAGGGCATAATAATTGACCCTAGAAC
EST: gi|86892252|gb|CI332265.1|CI332265
EST:     TTCAGATACGTACCACGTGAACAACTGACAATTCCTGATTTTGTCTTCCA                         GCATGATCTCGAAGTGAATGNTGGAAAGGGCATAATAATTGACCCTAGAAC
genomic: TTCAGATACGTACCACGTGAACAACTGACAATTCCTGATTTTGTCTTCCAgtatgtaatg ... aactctgcagGCATGATCTCGAAGTGAATGGTGGAAAGGGCATAATAATTGACCCTAGAAC
EST: gi|88510486|gb|CI437992.1|CI437992
EST:     TTCAGATACGTACCACGTGAACAACTGACAATTCCTGATTTTGTCTTCCA                         GCATGATCTCGAAGTGAATGGTGGAAAGGGCATAATAATTGACCCTAGGAA
genomic: TTCAGATACGTACCACGTGAACAACTGACAATTCCTGATTTTGTCTTCCAgtatgtaatg ... aactctgcagGCATGATCTCGAAGTGAATGGTGGAAAGGGCATAATAATTGACCCTA-GAA
EST: gi|88546733|gb|CI474403.1|CI474403
EST:     TTCAGATACGTACCACGTGAACAACTGACAATTCCTGATTTTGTCTTCCA                         GCATGATCTCGAAGTGAATGGTGGAAAGGGCATAATAATTGACCCTAGAAC
genomic: TTCAGATACGTACCACGTGAACAACTGACAATTCCTGATTTTGTCTTCCAgtatgtaatg ... aactctgcagGCATGATCTCGAAGTGAATGGTGGAAAGGGCATAATAATTGACCCTAGAAC

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: 48 (upstream exon), 64 (downstream exon)
Score: 3

GTCTGGAAGAAAGTTATCTATGTCGACAGACTTGTGCAGCTGTTCAGATACGTACCACGTGAACAACTGACAATTCCTGATTTTGTCTTCCAgtatgtaatg ... aactctgcagGCATGATCTCGAAGTGAATGGTGGAAAGGGCATAATAATTGACCCTAGAACAAAGCATGTCTACCAAAGACCATCAGGTTGATAAATATAGCCTGCTATA




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