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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCACACTAACCTGCGAAGAGTAACATACCTCGTCCTGGATGAGGCTGACCGCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttgttttagaatgcttatatcagttctggtgttttggctaactctccattttttctattgtgctaaacgtttttgttgttaatag

Basic information

species Oryza sativa
transcript LOC_Os01g68320.3
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68320.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G059020_T01 (Zea mays), 5'ss of exon 7
TCACACTAACCTGCGAAGAGTAACATACCTCGTCCTGGATGAGGCTGACCGCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttgttttagaatgcttatatcagttctggtgttttggctaactctccattttttctattgtgctaaacgtttttgttgttaatag
|||||| ||||| || ||||| |||||||| ||  |||||||||| ||||| ||||| || ||||| ||||||||||| ||||| |||||||| ||||| | |    |   |||||||       ||   | ||  | | |    |  || |||    | |      ||   |||  || || | |   |||
TCACACAAACCTACGTAGAGTGACATACCTTGTGTTGGATGAGGCGGACCGGATGCTAGATATGGGGTTTGAGCCCCAAATTCGAAAAATAGTAGCACAAgtacatttccgtttagaaatgcagaattcttactaatatct--attgtctttcctagctctaatgcttgtccaacacttctgctatccttag

upper sequence: LOC_Os01g68320.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G362850_T01 (Zea mays), 5'ss of exon 6
TCACACTAACCTGCGAAGAGTAACATACCTCGTCCTGGATGAGGCTGACCGCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttgttttagaatgcttatatcagttctggtgttttggctaactctccattttttctattgtgctaaacgtttttgttgttaatag
|||||| ||||| || ||||| |||||||| ||  |||||||||| ||||| ||||| || ||||| ||||||||||| ||||| |||||||| ||||||| |  | ||  |||||||       ||   | ||  | | |    |  ||  ||    | |      ||   |||  || || | |   |||
TCACACAAACCTACGTAGAGTGACATACCTTGTGTTGGATGAGGCGGACCGGATGCTAGATATGGGGTTTGAGCCCCAAATTCGGAAAATAGTAGCACAGgtacagtttcgtttagaaatgcagaattcttactaatatct--attgtcttgcctagctctaatgcttgtccaacacttctgctatccttag

upper sequence: LOC_Os01g68320.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA17G09270.1 (Glycine max), 5'ss of exon 5
TCACACTAACCTGCGAAGAGTAACATACCTCGTCCTGGATGAGGCTGACCGCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttgtt-ttagaatgcttata-tcagttctggtgttttggctaactctccattttttctattgtgctaaacgtttttgttgttaatag----------
 ||||| |||||||| ||||| || ||||| ||| | ||||| ||||| || ||||| |||||||||||||| || ||||| || ||||| || || |||| |  | |||    ||  |||    || | ||| |||     | ||  ||     | |    ||||||    |  |  | | || |  | ||||          
GCACACGAACCTGCGGAGAGTGACTTACCTTGTCTTAGATGAAGCTGATCGAATGCTAGACATGGGTTTTGAACCTCAGATACGGAAAATTGTAGCCCAGgtactgtttgcaactaacatgtaactagttagtactgagtaatggggaaaagaaacctcaaatctatt----tccatttgtgtgctactgatagtttaccaacc

upper sequence: LOC_Os01g68320.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA05G02590.1 (Glycine max), 5'ss of exon 5
TCACACTAACCTGCGAAGAGTAACATACCTCGTCCTGGATGAGGCTGACCGCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttgttttagaatgcttata-----tcagttctggtgttttggctaactctccattttttctattg----tgctaaacgtt---tttgttgttaatag
 ||||| ||||||   ||||| || ||||| ||| ||||||| ||||| || ||||| |||||||||||||| || ||||| || ||||| || || |||| |    || ||  |     | | ||     | ||| |||     | ||  ||     ||||   ||||||     |  | ||| ||   | || ||||     
GCACACAAACCTGAAGAGAGTGACTTACCTTGTCTTGGATGAAGCTGATCGAATGCTAGACATGGGTTTTGAACCTCAGATACGGAAAATTGTAGCCCAGgtac--ttttttgcaactaacctgtaacaagttagtactgagtagtggggaaaagaaacattgaatctatttccatttttgaaccttaagtgtgctgttgtc--

upper sequence: LOC_Os01g68320.3 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv17s0000g09130.t01 (Vitis vinifera), 5'ss of exon 5
TCACACTAACCTGCGAAGAGTAACATACCTCGTCCTGGATGAGGCTGACCGCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttgttttagaatgcttatatcagttctggtgttttggctaactctccatt---------ttttctattgtgctaaacgtttttgttgttaatag
 || || |||||||||||||| || ||||| ||  | |||||||||||||| ||| | |||||||| ||||| || |||||  | |||||  |  | || | |||| ||   ||    |||||   |      |   |  |  ||| | | | |||          ||||      |  ||| |  | ||    |  ||||
ACATACAAACCTGCGAAGAGTGACTTACCTTGTATTAGATGAGGCTGACCGAATGTTAGACATGGGATTTGAACCTCAGATCAGGAAAATTATTTCCCAAgtatggttt-ccttgctttgcttcctttctcatttacgagtcagcttaatttgcatcaggaataactttttggaaattataagcactgttcacttctatag

upper sequence: LOC_Os01g68320.3 (Oryza sativa), 5'ss of exon 5
lower sequence: EDP09760 (Chlamydomonas reinhardtii), 5'ss of exon 4
TCACACTAACCTGCGAAGAGTAACATACCTCGTCCTGGATGAGGCTGACCGCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggct-tgttttagaatgcttatatcagttctggtgttttggctaa---ctctccattttttctatt--gtgctaaacgtttttgttgttaatag--
   ||| ||||||||  | || |||||||| || ||||| ||||| ||||||||||| |||||||| |||||||| ||||| || || || ||||  ||||   |||   |     ||     | |||       ||      ||   |   |    ||      | |    | ||    |      |    |  ||   
CATCACCAACCTGCGGCGTGTGACATACCTGGTGCTGGACGAGGCGGACCGCATGCTGGACATGGGCTTTGAGCCGCAGATCCGCAAGATTGTGGACCAGgtggggcggcggggcggaggcggtgtatggagcggggcaaggcggggcagggcagggcagggcagcaagccggggccgggcacgacgggcagtcctacag

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|87023569|gb|CI286320.1|CI286320
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAA
EST: gi|29636635|gb|CB641644.1|CB641644
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29673236|gb|CB669511.1|CB669511
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29640324|gb|CB645333.1|CB645333
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29664446|gb|CB660721.1|CB660721
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29679220|gb|CB675495.1|CB675495
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29644134|gb|CB649141.1|CB649141
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|33797128|gb|CF324429.1|CF324429
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29638139|gb|CB643148.1|CB643148
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|88417599|gb|CI581622.1|CI581622
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29633338|gb|CB638347.1|CB638347
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29675369|gb|CB671644.1|CB671644
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|218485924|gb|FG959170.1|FG959170
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29661777|gb|CB658052.1|CB658052
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAA
EST: gi|29675371|gb|CB671646.1|CB671646
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29645557|gb|CB650564.1|CB650564
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29666768|gb|CB663043.1|CB663043
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29678103|gb|CB674378.1|CB674378
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29677571|gb|CB673846.1|CB673846
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29633337|gb|CB638346.1|CB638346
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCATACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29669296|gb|CB665571.1|CB665571
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29667787|gb|CB664062.1|CB664062
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29670396|gb|CB666671.1|CB666671
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA

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: 72 (upstream exon), 71 (downstream exon)
Score: 111

TCACACTAACCTGCGAAGAGTAACATACCTCGTCCTGGATGAGGCTGACCGCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG




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