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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccacttctcttccatttgcagccctccaattatgattggatcatgcaaagaagcagcaaagaacctaatgactgatttttttatttatttattttttggttccgcgtagGGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCAACTCTTTCATATGACGGGTTCTTGTCAATGGTCATTCCCTTCATTGTCC

Basic information

species Oryza sativa
transcript LOC_Os08g44390.4
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g44390.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G069922_T03 (Zea mays), 3'ss of exon 4
gtatgccacttctcttccatttgcagccctccaattatgattggatcatgcaaagaagcagcaaagaacctaatgactgatttttttatttatttattttttggttccgcgtagGGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCAACTCTTTCATATGACGGGTTCTTGTCAATGGTCATTCCCTTCATTGTCC
         |  | |     ||| |  |  |    |||   ||||       ||||||    | ||     ||| |||||      ||  |||| |       ||   | | |||||||||| || |||||||| ||||||||||| ||||||| ||||||||| |||||| |||| || || |||||||||||||| || |||||||| ||||
--------gtattttgttgattggatactacagcctatatatggagtgaatcaagaagggttacaggttgcaattactga------tacatattcac------gtcatgtgcagGGTTTAACCGAGAAATTCAAGGAGAAGGATACGCGCTACACCGGCTCGGCTACTCTTACATACGATGGTTTCTTGTCAATGGTGATCCCCTTCATCGTCC

upper sequence: LOC_Os08g44390.4 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv06s0080g00450.t01 (Vitis vinifera), 3'ss of exon 4
gtatgccacttctcttccatttgcagccctccaattatgattggatcatgcaaagaagcagcaaagaacctaatgactgatttttttatttatttattttttggttccgcgtagGGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCAACTCTTTCATATGACGGGTTCTTGTCAATGGTCATTCCCTTCATTGTCC
  ||||  |  |    | || |  ||  |   |  ||| |   || |    |              | | |     ||||| | |  |||| |      |    ||||    ||||||| |||||||||||||| ||||||||| |||| ||||  || || ||||| ||  | || || |  |||||||| ||| ||||||| ||  ||||  
--atgcggc--catcgctatatatagttcatgagatataa---gaactcttacgtcctgtttttttatcattgcctctgatctctaaatttgt---cactacaattcc----agGGTTTGACTGAAAAATTCAAGGAGAAGGATCCACGTTACACTGGTTCAGCAACACTCACCTACGATGCATTCTTGTCTATGATCATTCCATTTCTTGTAG
















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|88275704|gb|CI396308.1|CI396308
EST:     TGTGGAGTGTGGAATGATTGTTAAG                         GGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
genomic: TGTGGAGTGTGGAATGATTGTTAAGgtatgccact ... ttccgcgtagGGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
EST: gi|5003194|gb|AU068303.1|AU068303
EST:     TGTGGAGTGTGGAATGATTGTTAAG                         GGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
genomic: TGTGGAGTGTGGAATGATTGTTAAGgtatgccact ... ttccgcgtagGGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
EST: gi|88297877|gb|CI553506.1|CI553506
EST:     TGTGGAGTGTGGAATGATTGTTAAG                         GGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
genomic: TGTGGAGTGTGGAATGATTGTTAAGgtatgccact ... ttccgcgtagGGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
EST: gi|86879935|gb|CI339998.1|CI339998
EST:     TGTGGAGTGTGGAATGATTGTTAAG                         GGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
genomic: TGTGGAGTGTGGAATGATTGTTAAGgtatgccact ... ttccgcgtagGGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
EST: gi|88267292|gb|CI379227.1|CI379227
EST:     TGTGGAGTGTGGAATGATTGTTAAG                         GGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
genomic: TGTGGAGTGTGGAATGATTGTTAAGgtatgccact ... ttccgcgtagGGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
EST: gi|8251032|gb|AU091278.1|AU091278
EST:     TGTGGAGTGTGGAATGATTGTTAAG                         GGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
genomic: TGTGGAGTGTGGAATGATTGTTAAGgtatgccact ... ttccgcgtagGGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
EST: gi|87010793|gb|CI312485.1|CI312485
EST:     TGTGGAGTGTGGAATGATTGTTAAG                         GGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
genomic: TGTGGAGTGTGGAATGATTGTTAAGgtatgccact ... ttccgcgtagGGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
EST: gi|87033916|gb|CI188540.1|CI188540
EST:     TGTGGAGTGTGGAATGGTTGTTAAG                         GGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
genomic: TGTGGAGTGTGGAATGATTGTTAAGgtatgccact ... ttccgcgtagGGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
EST: gi|88250360|gb|CI348590.1|CI348590
EST:     TGTGGAGTGTGGAATGATTGTTAAG                         GGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
genomic: TGTGGAGTGTGGAATGATTGTTAAGgtatgccact ... ttccgcgtagGGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
EST: gi|88199342|gb|CI199192.1|CI199192
EST:     TGTGGAGTGTGGAATGATTGTTAAG                         GGTCTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
genomic: TGTGGAGTGTGGAATGATTGTTAAGgtatgccact ... ttccgcgtagGGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
EST: gi|88204649|gb|CI204498.1|CI204498
EST:     TGTGGAGTGTGGAATGATTGTTAAG                         GGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
genomic: TGTGGAGTGTGGAATGATTGTTAAGgtatgccact ... ttccgcgtagGGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
EST: gi|88903146|gb|CI088684.1|CI088684
EST:     TGTGGAGTGTGGAATGATTGTTAAG                         GGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
genomic: TGTGGAGTGTGGAATGATTGTTAAGgtatgccact ... ttccgcgtagGGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
EST: gi|88828498|gb|CI073368.1|CI073368
EST:     TGTGGAGTGTGGAATGATTGTTAAG                         GGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTATAGCGGCTCGGCA
genomic: TGTGGAGTGTGGAATGATTGTTAAGgtatgccact ... ttccgcgtagGGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
EST: gi|86529359|gb|CI169565.1|CI169565
EST:     TGTGGAGTGTGGAATGATTGTTAAG                         GGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
genomic: TGTGGAGTGTGGAATGATTGTTAAGgtatgccact ... ttccgcgtagGGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
EST: gi|86893216|gb|CI313376.1|CI313376
EST:     TGTGGAGTGTGGAATGATTGTTAAG                         GGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
genomic: TGTGGAGTGTGGAATGATTGTTAAGgtatgccact ... ttccgcgtagGGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
EST: gi|8251157|gb|AU091297.1|AU091297
EST:     TGTGGAGTGTGGAATGATTGTTAAG                         GGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
genomic: TGTGGAGTGTGGAATGATTGTTAAGgtatgccact ... ttccgcgtagGGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
EST: gi|86426420|gb|CI071517.1|CI071517
EST:     TGTGGAGTGTGGAATGATTGTTAAG                         GGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA
genomic: TGTGGAGTGTGGAATGATTGTTAAGgtatgccact ... ttccgcgtagGGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCA

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: 49 (upstream exon), 47 (downstream exon)
Score: 5

GTGTGGAATGATTGTTAAGgtatgccact ... ttccgcgtagGGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCAACTCTTTCATATGACGGGTTCTTGTCAATGGTCATTCCCTTCATTGTCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcaaagaacctaatgactgatttttttatttatttattttttggttccgcgtagGGTTTAACTGAAAAATTCAAAGAGAAGGATACACGCTACAGCGGCTCGGCAACTCTTTCATATGACGGGTTCTTGTCAATGGTCATTCCCTTCATTGTCC
               gactgat  putative branch site (score: 5)
       aacctaatgactgatt  TA-rich tract