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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACACTGGAGAAATTCTTGGAGTTCACATATTAGGTTTGCATGCTGCTGACCTCATCCACGAGGCATCAAACGCCATTGCCCTCGGAACTCGTGTACAAgtaagtgacgagcattttattgtttatgaatggattgcatttgctcaacgctgtttacatcccccag

Basic information

species Oryza sativa
transcript LOC_Os01g23610.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G145595_T01 (Zea mays), 5'ss of exon 13
TGACACTGGAGAAATTCTTGGAGTTCACATATTAGGTTTGCATGCTGCTGACCTCATCCACGAGGCATCAAACGCCATTGCCCTCGGAACTCGTGTACAAgtaagt--gacgagcattttattgtttatgaatggatt--gcatttg----ctcaacgctgtttacatcccccag-----------------------------
|||||| |||||||||||||||||||| || || || |||||||||||||| |||||||| ||||||||||| ||||||||||| ||||| | ||| || || |||  | |  ||||| | ||   | || |    ||  ||||||     |||  |    |    | | |  |                              
TGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGCTTGCATGCTGCTGATCTCATCCATGAGGCATCAAATGCCATTGCCCTTGGAACCCATGTGCAGgtgagtttgtcatgcattctgttagctgtgtagcatttctgcatttttgttctctgcataatgctaaacgcttaaatttgcacataaccttttgtaccctgcag

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA15G15310.1 (Glycine max), 5'ss of exon 13
TGACACTGGAGAAATTCTTGGAGTTCACATATTAGGTTTGCATGCTGCTGACCTCATCCACGAGGCATCAAACGCCATTGCCCTCGGAACTCGTGTACAAgtaagtga--cgagcatt-ttattgtttatgaatggattgcatttgctcaacgctgtttacatcccccag------------------------------------------------------------------------------------
|||||||||||| || || |||||||| ||||| || |||||||||||||| ||||||||||||||||| || || || ||  | ||||| ||| | || |||| |    | | |||   | |    | |||  |  | | ||||  |      || || |||   |                                                                                       
TGACACTGGAGAGATACTGGGAGTTCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCATTAGGAACACGTATTCAGgtaaattttcctaccatagctgtcacatgtgagagactgggatttagttcgtaatggttgcatgtgctgcatttggtttatttttgtcgatagcaacaagaaactttttatccgtctatatggtaactcccaacattgttgtgctacaatgcag

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 13
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 5'ss of exon 13
TGACACTGGAGAAATTCTTGGAGTTCACATATTAGGTTTGCATGCTGCTGACCTCATCCACGAGGCATCAAACGCCATTGCCCTCGGAACTCGTGTACAAgt--------aagtgacgagcattttattgtttatgaatggattgcatttgctcaacgctgtttacatcccccag-----------------
||||| ||| ||||| ||||||||||| ||||| || |||||||||||||| || ||||| || ||||||||||| |||||  | ||||| ||| | || ||        ||   |    |  |    | || || |  ||| |  |  |  | | |  | |||   |  |   |                 
TGACAATGGTGAAATCCTTGGAGTTCATATATTTGGATTGCATGCTGCTGATCTTATCCATGAAGCATCAAACGCGATTGCTTTAGGAACACGTATTCAGgtctggctgcaaactaacctctctccggtattgatcataggactttagattgtgagctttttttgtgtgtctttgtgtgatgataaatgcag

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 13
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 5'ss of exon 13
TGACACTGGAGAAATTCTTGGAGTTCACATATTAGGTTTGCATGCTGCTGACCTCATCCACGAGGCATCAAACGCCATTGCCCTCGGAACTCGTGTACAAgtaagtgac---gagcattttattgttta---tgaat---ggattgcatttgctcaacgctgtttacatcccccag------------------------
||||| |||||| ||||||||||| ||||| || || ||||||||||| ||||| ||||| || ||||| || || || || || || || ||| | || ||| ||      | |||    |   ||||   || ||    || ||  | |    |||| |  |  ||   |  |                         
TGACAATGGAGAGATTCTTGGAGTGCACATCTTTGGGTTGCATGCTGCAGACCTTATCCATGAAGCATCCAATGCTATAGCACTAGGCACACGTATTCAGgtatgtttttctgtgcaaagcaaaatttagagtgcatttgagagtgattctagaaaacgtttatagcaattctaacacttgaatgataaaaattttcaag

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|88851216|gb|CI373974.1|CI373974
EST:     AACGCCACTGCCCTCGGAACTCGTGTACAA                         GACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGGTCTGGAT
genomic: AACGCCATTGCCCTCGGAACTCGTGTACAAgtaagtgacg ... catcccccagGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGAT
EST: gi|29637258|gb|CB642267.1|CB642267
EST:     ACCTCATCCACGAGGCATCAAACGCCATTGCCCTCGGAACTCGTGTACAA                         GACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGAT
genomic: ACCTCATCCACGAGGCATCAAACGCCATTGCCCTCGGAACTCGTGTACAAgtaagtgacg ... catcccccagGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGAT
EST: gi|86887058|gb|CI325873.1|CI325873
EST:     ACCTCATCCACGAGGCATCAAACGCCATTGCCCTCGGAACTCGTGTACAA                         GACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGAT
genomic: ACCTCATCCACGAGGCATCAAACGCCATTGCCCTCGGAACTCGTGTACAAgtaagtgacg ... catcccccagGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGAT
EST: gi|22304992|gb|BQ906214.1|BQ906214
EST:     GCCCTCGGAACTCGTGTACAA                         GACATCAAGTTTGCTGTTCATGCACACCC-ACTTTGTCTGAGGTTCTGGAT
genomic: GCCCTCGGAACTCGTGTACAAgtaagtgacg ... catcccccagGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGAT
EST: gi|88518587|gb|CI446241.1|CI446241
EST:     TTGCCCTCGGAAGTCGTGTACAA                         GACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGAT
genomic: TTGCCCTCGGAACTCGTGTACAAgtaagtgacg ... catcccccagGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGAT

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: 60 (upstream exon), 72 (downstream exon)
Score: 31

TGACACTGGAGAAATTCTTGGAGTTCACATATTAGGTTTGCATGCTGCTGACCTCATCCACGAGGCATCAAACGCCATTGCCCTCGGAACTCGTGTACAAgtaagtgacg ... catcccccagGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAG




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