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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTACAGGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAGTAAAGgtacgtgctactgttcctctacaaattttcaacagactaatctggtagcaagttatactgagcatttctttcttcatgtaacttcttcag

Basic information

species Oryza sativa
transcript LOC_Os06g37180.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g37180.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G181151_T02 (Zea mays), 5'ss of exon 3
AGTACAGGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAGTAAAGgtacgtgctactgttcct-------------ctac-----aaattttcaacagactaatctggtagcaagttatactgagcatttctttcttcatgtaacttcttcag
||||||||||||| ||||||||||| || |||||||||||||||||||||||||||||  || |   | |  |              ||||     | ||||| |||||   | |||| ||||   |||| ||  |    | |   | ||| |  | |||  ||
AGTACAGGACTGTATCTGGTGTGGCCGGGCCTCTGGTTATCTTGGATAAAGTAAAGgtgtgtacagttttctccaatatgatgataactaccatgtagattttgaacagctcagtctgctagcctcttatgctttgttcctttgcttgcatatc-catctatag

upper sequence: LOC_Os06g37180.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G094497_T01 (Zea mays), 5'ss of exon 3
AGTACAGGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAGTAAAGgtacgtgctactgttcct------------------ctacaaattttcaacagactaatctggtagcaagttatactgagcatttctttcttcatgtaact-tcttcag
||||||||||||| |||||||| || || |||||||| || |||||||||||||||||  |  |   | |  |                   || || ||||| |||||   | |||| ||||   |||||||      | ||||  |  |||| |  || | ||
AGTACAGGACTGTATCTGGTGTTGCTGGGCCTCTGGTCATATTGGATAAAGTAAAGgtgtgcacagttttctccaatatgatgctaactaccctgcagattttgaacagctcattctgctagcctcttatact------tcctttgcttgtgtatccatcattag
















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|55410497|gb|CV722873.1|CV722873
EST:     GGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAGTAAAG                         GGCCCAAAGTACCAGGAAATTGTAAACATCCGATTGGGAGATGGCACCACT
genomic: GGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAGTAAAGgtacgtgcta ... acttcttcagGGCCCAAAGTACCAGGAAATTGTAAACATCCGATTGGGAGATGGCACCACT
EST: gi|29633929|gb|CB638938.1|CB638938
EST:     GGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAGTAAAG                         GGCCCAAAGTACCAGGAAATTGTAAACATCCGATTGGGAGATGGCACCACT
genomic: GGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAGTAAAGgtacgtgcta ... acttcttcagGGCCCAAAGTACCAGGAAATTGTAAACATCCGATTGGGAGATGGCACCACT
EST: gi|42591928|gb|CK738414.1|CK738414
EST:     GGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAGTAAAG                         GGCCCAAAGTACCAGGAAATTGTAAACATCCGATTGGGAGATGGCACCACT
genomic: GGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAGTAAAGgtacgtgcta ... acttcttcagGGCCCAAAGTACCAGGAAATTGTAAACATCCGATTGGGAGATGGCACCACT
EST: gi|29641774|gb|CB646781.1|CB646781
EST:     GGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAGTAAAG                         GGCCCAAAGTACCAGGAAATTGTAAACATCCGATTGGGAGATGGCACCACT
genomic: GGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAGTAAAGgtacgtgcta ... acttcttcagGGCCCAAAGTACCAGGAAATTGTAAACATCCGATTGGGAGATGGCACCACT
EST: gi|29631355|gb|CB636364.1|CB636364
EST:     GGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAGTAAAG                         GGCCCAAAGTACCAGGAAATTGTAAACATCCGATTGGGAGATGGCACCACT
genomic: GGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAGTAAAGgtacgtgcta ... acttcttcagGGCCCAAAGTACCAGGAAATTGTAAACATCCGATTGGGAGATGGCACCACT
EST: gi|29683215|gb|CB679490.1|CB679490
EST:     GGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAGTAAAG                         GGCCCAAAGTACCAGGAAATTGTAAACATCCGATTGGGAGATGGCACCACT
genomic: GGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAGTAAAGgtacgtgcta ... acttcttcagGGCCCAAAGTACCAGGAAATTGTAAACATCCGATTGGGAGATGGCACCACT
EST: gi|29630856|gb|CB635865.1|CB635865
EST:     GGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAGTAAAG                         GGCCCAAAGTACCAGGAAATTGTAAACATCCGATTGGGAGATGGCACCACT
genomic: GGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAGTAAAGgtacgtgcta ... acttcttcagGGCCCAAAGTACCAGGAAATTGTAAACATCCGATTGGGAGATGGCACCACT
EST: gi|29617703|gb|CB622715.1|CB622715
EST:     GGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAGTAAAG                         GGCCCAAAGTACCAGGAAATTGTAAACATCCGATTGGGAGATGGCACCACT
genomic: GGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAGTAAAGgtacgtgcta ... acttcttcagGGCCCAAAGTACCAGGAAATTGTAAACATCCGATTGGGAGATGGCACCACT
EST: gi|29675287|gb|CB671562.1|CB671562
EST:     GGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAGTAAAG                         GGCCCAAAGTACCAGGAAATTGTAAACATCCGATTGGGAGATGGCACCACT
genomic: GGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAGTAAAGgtacgtgcta ... acttcttcagGGCCCAAAGTACCAGGAAATTGTAAACATCCGATTGGGAGATGGCACCACT
EST: gi|29669854|gb|CB666129.1|CB666129
EST:     GGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAGTAAAG                         GGCCCAAAGTACCAGGAAATTGTAAACATCCGATTGGGAGATGGCACCACT
genomic: GGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAGTAAAGgtacgtgcta ... acttcttcagGGCCCAAAGTACCAGGAAATTGTAAACATCCGATTGGGAGATGGCACCACT
EST: gi|29630446|gb|CB635455.1|CB635455
EST:     GGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAGTAAAG                         GGCCCAAAGTACCAGGAAATTGTAAACATCCGATTGGGAGATGGCACCACT
genomic: GGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAGTAAAGgtacgtgcta ... acttcttcagGGCCCAAAGTACCAGGAAATTGTAAACATCCGATTGGGAGATGGCACCACT
EST: gi|29681069|gb|CB677344.1|CB677344
EST:     GGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAGTAAAG                         GGCCCAAAGTACCAGGAAATTGTAAACATCCGATTGGGAGATGGCACCACT
genomic: GGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAGTAAAGgtacgtgcta ... acttcttcagGGCCCAAAGTACCAGGAAATTGTAAACATCCGATTGGGAGATGGCACCACT
EST: gi|29642143|gb|CB647150.1|CB647150
EST:     GGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAGTAAAG                         GGCCCAAAGTACCAGGAAATTGTAAACATCCGATTGGGAGATGGCACCACT
genomic: GGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAGTAAAGgtacgtgcta ... acttcttcagGGCCCAAAGTACCAGGAAATTGTAAACATCCGATTGGGAGATGGCACCACT

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: 54 (upstream exon), 55 (downstream exon)
Score: 127

AGTACAGGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAGTAAAGgtacgtgcta ... acttcttcagGGCCCAAAGTACCAGGAAATTGTAAACATCCGATTGGGAGATGGCACCACTCGCCGTGGCCAAGTTCTGGAAGTTGACGGTGAAAAGGCTGTTGTGCAG




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