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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGACTGGCCGAATTTCTGTCAGTGATTATGTGAGAGTGACAAGCACAGAATGgtatattgaagaaattcactagctatcattttaaacaacaaattccccactattcaacgaagtacaatgatcaaattactcaaatcttttcag

Basic information

species Oryza sativa
transcript LOC_Os01g59340.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g59340.2 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G020002_T01 (Zea mays), 5'ss of exon 11
GAGACTGGCCGAATTTCTGTCAGTGATTATGTGAGAGTGACAAGCACAGAATGgta-tattgaagaaattcact--agcta----tcattttaaac---aacaaattccc-----------cactattcaac------------gaagtacaatgat-caaattactcaaatcttttcag
   ||||||   |||||||| |  || ||||| ||||||||||||||||||||||| |||  |  ||||   ||  | | |    | | |||| |    | || |||  |           || | ||||||             ||  |||||| | ||||||||||||   |||||||
---ACTGGCAAGATTTCTGTAACCGACTATGTCAGAGTGACAAGCACAGAATGgtactatacattaaatctgctcaaaccagggtttagtttagaagtaaccagattgtcatatcaaaatgcattgttcaactagcaaaaaaaaaaaaaacaatggtacaaattactcaaccattttcag

upper sequence: LOC_Os01g59340.2 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G020002_T02 (Zea mays), 5'ss of exon 11
GAGACTGGCCGAATTTCTGTCAGTGATTATGTGAGAGTGACAAGCACAGAATGgta-tattgaagaaattcact--agcta----tcattttaaac---aacaaattccc-----------cactattcaac------------gaagtacaatgat-caaattactcaaatcttttcag
|||||||||   |||||||| |  || ||||| ||||||||||||||||||||||| |||  |  ||||   ||  | | |    | | |||| |    | || |||  |           || | ||||||             ||  |||||| | ||||||||||||   |||||||
GAGACTGGCAAGATTTCTGTAACCGACTATGTCAGAGTGACAAGCACAGAATGgtactatacattaaatctgctcaaaccagggtttagtttagaagtaaccagattgtcatatcaaaatgcattgttcaactagcaaaaaaaaaaaaaacaatggtacaaattactcaaccattttcag
















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|86873138|gb|CI328518.1|CI328518
EST:     GTCAGTGATTATGTGAGAGTGACAAGCACAGAATG                         TGCCAAGATTTTCAACATATACCCTCGGAAAGGAGCAATTGCTGGAAGGAT
genomic: GTCAGTGATTATGTGAGAGTGACAAGCACAGAATGgtatattgaa ... atcttttcagTGCCAAGATTTTCAACATATACCCTCGGAAAGGAGCAATT-CTGGAAGGAT
EST: gi|86431074|gb|CI083497.1|CI083497
EST:     TATGTGAGAGTGACAAGCACAGAATG                         TGCCAAGATTTTCAACATATACCCTCGGAAAGGAGCAATTCTGGAAGGATC
genomic: TATGTGAGAGTGACAAGCACAGAATGgtatattgaa ... atcttttcagTGCCAAGATTTTCAACATATACCCTCGGAAAGGAGCAATTCTGGAAGGATC
EST: gi|87026885|gb|CI259538.1|CI259538
EST:     ACTGGCCGAATTTCTGTCAGTGATTATGTGAGAGTGACAAGCACAGAATG                         TGCCAAGATTTTCAACATATACCCTCGGAAAGGAGCAATTCTGGAAGGATC
genomic: ACTGGCCGAATTTCTGTCAGTGATTATGTGAGAGTGACAAGCACAGAATGgtatattgaa ... atcttttcagTGCCAAGATTTTCAACATATACCCTCGGAAAGGAGCAATTCTGGAAGGATC

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: 53 (upstream exon), 63 (downstream exon)
Score: 33

GAGACTGGCCGAATTTCTGTCAGTGATTATGTGAGAGTGACAAGCACAGAATGgtatattgaa ... atcttttcagTGCCAAGATTTTCAACATATACCCTCGGAAAGGAGCAATTCTGGAAGGATCTGATGCAGATATTATCATCCTGAATCCCGAGAGGAGCTTTGTCATGGGT




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