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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatgctgtttgtttatagccacaagcaatctatttattctcttatcaacttgctaggggctggtttctgatagctgaatctgtttctcagATGGAATGAAGCTGTACATTTCAGACAACAAGGTGATTCTGACAGAGGGTTTCGATGGCGTTGTTCCTGTGAAGTACTTCGAGAAAATTGAAACATGGCC

Basic information

species Oryza sativa
transcript LOC_Os06g04300.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g04300.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G092568_T01 (Zea mays), 3'ss of exon 7
gtatgatgctgtttgtttatagccacaagcaatctatttattctcttatcaacttgctaggggctggtttctgatagctgaatctgtttctcagATGGAATGAAGCTGTACATTTCAGACAACAAGGTGATTCTGACAGAGGGTTTCG------ATGGCGTTGTTCCTGTGAAGTACTTCGAGAAAATTGAAACATGGCC
|||  ||    |   |  | |    |   |||   | || ||   || ||    |||||| ||||| | |   | | || ||| |||  | ||||||| |||||||| || |||||||||||||| |||||  ||||||| ||||| |      |||||||||| |||||||| ||||| || | ||| |||||      
gtactatataatgcttacaaataggcccccaaaaaaattctttcgttttctgagtgctagaggctgatat--aacacctaaatttgtcgcgcagATGGGATGAAGCTTTATATTTCAGACAACAAAGTGATCTTGACAGAAGGTTTTGGTTTTGATGGCGTTGTCCCTGTGAAATACTTTGAAAGAATCGAAAC------

upper sequence: LOC_Os06g04300.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G092568_T02 (Zea mays), 3'ss of exon 4
--------gtatgatgctgtttgtttatagccacaagcaatctatttattctcttatcaacttgctaggggctggtttctgatagctgaatctgtttctcagATGGAATGAAGCTGTACATTTCAGACAACAAGGTGATTCTGACAGAGGGTTTCG------ATGGCGTTGTTCCTGTGAAGTACTTCGAGAAAATTGAAACATGGCC
        |||  ||    |   |  | |    |   |||   | || ||   || ||    |||||| ||||| | |   | | || ||| |||  | ||||||| |||||||| || |||||||||||||| |||||  ||||||| ||||| |      |||||||||| |||||||| ||||| || | ||| |||||      
acttaaaggtactatataatgcttacaaataggcccccaaaaaaattctttcgttttctgagtgctagaggctgatat--aacacctaaatttgtcgcgcagATGGGATGAAGCTTTATATTTCAGACAACAAAGTGATCTTGACAGAAGGTTTTGGTTTTGATGGCGTTGTCCCTGTGAAATACTTTGAAAGAATCGAAAC------

upper sequence: LOC_Os06g04300.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G061783_T04 (Zea mays), 3'ss of exon 4
gtatgatgctgtttgtttatagccacaagcaatctatttattctcttatcaacttgctaggggctggtttctgatagctgaatctgtttctcagATGGAATGAAGCTGTACATTTCAGACAACAAGGTGATTCTGACAGAGGGTTTCGATGGCGTTGTTCCTGTGAAGTACTTCGAGAAAATTGAAACATGGCC
|||  ||    |   |  | |    |   |||   |||| ||   || ||    |||||| ||||  | |   | | || ||| |||| | ||| ||| |||||||| || |||||||||||||| |||||  ||||||| ||||| |||||||| || || ||||| ||||| || | | | |||||||||||
gtactatataatgcttacaaataggctcccaaaaaatttctttcgttttctgagtgctagaggctaatat--aacacctaaatttgttgcgcagGTGGGATGAAGCTTTATATTTCAGACAACAAAGTGATCTTGACAGAAGGTTTTGATGGCGTCGTCCCGGTGAAATACTTTGAAAGAGTCGAAACATGGCC

upper sequence: LOC_Os06g04300.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA17G29450.1 (Glycine max), 3'ss of exon 7
--gtatgatgctgtttgtttatagccacaagcaatctatttattct-cttatcaacttgctaggggctggtttctgatagctgaatctgtt---tctcagATGGAATGAAGCTGTACATTTCAGACAACAAGGTGATTCTGACAGAGGGTTTCGATGGCGTTGTTCCTGTGAAGTACTTCGAGAAAATTGAAACATGGCC
   | |     | ||||||  | |     ||  |   |  | | |  |  || |  || ||    |||  ||    |||  |   |   |    | |||||  | || ||||| |||||||| ||||||||||||||  |||| || ||||| ||||| |||||||||  |||||| || || |  || ||| |||||||
aaatgttggattttttgttgtttgttgatagtgagtaaaatctacaacaaataagattactgatcgctacttctctatatattttttcatcctatttcagAAAGTATAAAGCTTTACATTTCTGACAACAAGGTGATCTTGACGGAAGGTTTTGATGGTGTTGTTCCTCCGAAGTATTTTGAAAGGATAGAATCATGGCC

upper sequence: LOC_Os06g04300.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA17G37310.1 (Glycine max), 3'ss of exon 9
------------------------------------------------------------gtatgatgctgtttgtt-tatagccacaagcaatctatttattctcttatcaacttgctaggggctggtttctgatagctgaatctgtt---tctcagATGGAATGAAGCTGTACATTTCAGACAACAAGGTGATTCTGACAGAGGGTTTCGATGGCGTTGTTCCTGTGAAGTACTTCGAGAAAATTGAAACATGGCC
                                                             | |     | |||||| | ||   | |   | |  | |      |  || |   | ||    |||  ||    |||  |   |   |    | ||||| || |||||||| |||||||| ||||||||||||||  |||| || ||||| ||||| ||||||||||  ||||| || || || || ||| |||||||
gtatgatatgacaatattccaaacatgttctgaactgaatgtctacaagttcatcttgaaatgttggattttttgttgtctattgatagtgagtaaaatctacaacaaataagactactgatagctacttctctatatattttttcatcctatttcagAAGGTATGAAGCTTTACATTTCTGACAACAAGGTGATCTTGACGGAAGGTTTTGATGGTGTTGTTCCTGCCAAGTATTTTGAAAAGATAGAATCATGGCC

upper sequence: LOC_Os06g04300.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv15s0048g00300.t01 (Vitis vinifera), 3'ss of exon 7
----------------------gtatgatgctgtttgtttatag--ccacaagcaatc-tatttattctcttatcaac-----------ttgctaggggctggtttctgatagctgaatctgtttctcagATGGAATGAAGCTGTACATTTCAGACAACAAGGTGATTCTGACAGAGGGTTTCGATGGCGTTGTTCCTGTGAAGTACTTCGAGAAAATTGAAACATGGCC
                         || | |   |  | ||      || ||  |||| ||||| |     ||| |              | |||  |  |  || |   |  || | ||  ||    ||||||||||||||| |||||||||||||||||||| ||  |||| || ||||| ||||| ||||| ||||| |||||||| || || || ||| | |||||
gtatacccttaaattcaaaatgagttggtccaactcctataggagttcagaatgaatcctatttgtaacagtatgagagatgtagaacactactaatgcttttttccccgtctctaattcaattgt--agATGGAATGAAGCTCTACATTTCAGACAACAAGGTCATCTTGACCGAAGGTTTTGATGGTGTTGTGCCTGTCAAGTACTTTGAAAAGATAGAATCTTGGCC

upper sequence: LOC_Os06g04300.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv15s0048g00280.t01 (Vitis vinifera), 3'ss of exon 7
----------------------gtatgatgctgtttgtttatag--ccacaagcaatc-tatttattctcttatcaacttgctaggg----gctggtttctgatagctgaatctgtttct----cagATGGAATGAAGCTGTACATTTCAGACAACAAGGTGATTCTGACAGAGGGTTTCGATGGCGTTGTTCCTGTGAAGTACTTCGAGAAAATTGAAACATGGCC
                         || | |   |  | ||      || ||  |||| ||| | |     ||| |      |||       ||  |   |  |  | |  |||  |||      ||||||||||||||| |||||||||||||||||||| ||  |||| || ||||| ||||| ||||| ||||| |||||||| || || || ||| | |||||
gtatacctttaaattcaaaatgaattggtccaactcctataggagttcagaatgaatcctatctgtaacagtataagagatgtagaacactactaatgctttttccccgtctctaattcaattgtagATGGAATGAAGCTCTACATTTCAGACAACAAGGTCATCTTGACCGAAGGTTTTGATGGTGTTGTGCCTGTCAAGTACTTTGAAAAGATAGAATCTTGGCC

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|3760634|gb|C97888.1|C97888
EST:     GCAGAGTGTTAACATCTTGATATATTTGGATGTCAGTATGGCACTGCAAG                         ATGGAATGAAGCTGTACATTTCAGACAACAAGGTGATTCTGACAGAGGGTT
genomic: GCAGAGTGTTAACATCTTGATATATTTGGATGTCAGTATGGCACTGCAAGgtatgatgct ... tgtttctcagATGGAATGAAGCTGTACATTTCAGACAACAAGGTGATTCTGACAGAGGGTT
EST: gi|568278|gb|D39115.1|D39115
EST:     GGCACTGCAAG                         ATGGAATGAAGCTGTACATTTCAGACAACAAGGTGATTCTGACAGAGGGTT
genomic: GGCACTGCAAGgtatgatgct ... tgtttctcagATGGAATGAAGCTGTACATTTCAGACAACAAGGTGATTCTGACAGAGGGTT
EST: gi|86593712|gb|CI266392.1|CI266392
EST:     GCAGAGTGTTAACATCTTGATATATTTGGATGTCAGTATGGCACTGCAAG                         ATGGAATGAAGCTGTACATTTCAGACAACAAGGTGATTCTGACAGAGGGTT
genomic: GCAGAGTGTTAACATCTTGATATATTTGGATGTCAGTATGGCACTGCAAGgtatgatgct ... tgtttctcagATGGAATGAAGCTGTACATTTCAGACAACAAGGTGATTCTGACAGAGGGTT
EST: gi|568243|gb|D39080.1|D39080
EST:     GGCACTGCAAG                         ATGGAATGAAGCTGTACATTTCAGACAACAAGGTGATTCTGACAGAGGGTT
genomic: GGCACTGCAAGgtatgatgct ... tgtttctcagATGGAATGAAGCTGTACATTTCAGACAACAAGGTGATTCTGACAGAGGGTT
EST: gi|88480820|gb|CI418091.1|CI418091
EST:     GCAGAGTGTTAACATCTTGATATATTTGGATGTCAGTATGGCACTGCAAG                         ATGGAATGAAGCTGTACATTTCAGACAACAAGGTGATTCTGACAGAGGGTT
genomic: GCAGAGTGTTAACATCTTGATATATTTGGATGTCAGTATGGCACTGCAAGgtatgatgct ... tgtttctcagATGGAATGAAGCTGTACATTTCAGACAACAAGGTGATTCTGACAGAGGGTT
EST: gi|86828407|gb|CI276947.1|CI276947
EST:     GCAGAGTGTTAACATCTTGAAATATTTGGATGTCAGTATGGCACTGCAAG                         ATGGAATGAAGCTGTACATTTCAGACAACAAGGTGATTCTGACAGAGGGTT
genomic: GCAGAGTGTTAACATCTTGATATATTTGGATGTCAGTATGGCACTGCAAGgtatgatgct ... tgtttctcagATGGAATGAAGCTGTACATTTCAGACAACAAGGTGATTCTGACAGAGGGTT
EST: gi|286303|gb|D15111.1|D15111
EST:     GCAGAGTGTTAACATCTTGATATATTTGGATGTCAGTATGGCACTGCAAG                         ATGGAATGAAGCTGTACATTTCAGACAACAAGGTGATTCTGACAGAGGGTT
genomic: GCAGAGTGTTAACATCTTGATATATTTGGATGTCAGTATGGCACTGCAAGgtatgatgct ... tgtttctcagATGGAATGAAGCTGTACATTTCAGACAACAAGGTGATTCTGACAGAGGGTT

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: 56 (upstream exon), 20 (downstream exon)
Score: 1

GTATGCGGCAGAGTGTTAACATCTTGATATATTTGGATGTCAGTATGGCACTGCAAGgtatgatgct ... tgtttctcagATGGAATGAAGCTGTACATTTCAGACAACAAGGTGATTCTGACAGAGGGTTTCGATGGCGTTGTTCCTGTGAAGTACTTCGAGAAAATTGAAACATGGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctcttatcaacttgctaggggctggtttctgatagctgaatctgtttctcagATGGAATGAAGCTGTACATTTCAGACAACAAGGTGATTCTGACAGAGGGTTTCGATGGCGTTGTTCCTGTGAAGTACTTCGAGAAAATTGAAACATGGCC
                             ttctgat  putative branch site (score: 1)
                                           tctgtttctc  putative PPT
      ttatcaa  TA-rich tract