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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGAGGTTTCCCATGTGCTTAATTTTTGGTGGTGATGGAAGCTATATGTCTCCATACTACCTACACAGTGATACATTGTTATCTAACCTTCTTGGCCAGgtaaaaataagattaacttaatagggatgttaatgacattcctggtgttccaaacttccaattatatcatcacataggacagttcactttgttccacatt...

Basic information

species Oryza sativa
transcript LOC_Os04g10380.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g10380.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G015291_T01 (Zea mays), 5'ss of exon 9
GAAGAGGTTTCCCATGTGCTTAATTTTTGGTGGTGATGGAAGCTATATGTCTCCATACTACCTACACAGTGATACATTGTTATCTAACCTTCTTGGCCAGgtaaaaataagattaacttaatagggatgttaatgacattcctggtgttccaaacttccaattatatcatcaca-taggacagttcactttgttccacatt
||||||||||||||||||  ||||||||||||||||||||||||||||||| |||||||| ||||| |||||||||||| |||| || |||||||||||||||||  | |||||    | ||    ||   | | |  ||   |      | | || |  |  || |  |     | |  ||| ||| |  || |  ||  
GAAGAGGTTTCCCATGTGTCTAATTTTTGGTGGTGATGGAAGCTATATGTCCCCATACTATCTACATAGTGATACATTGCTATCAAATCTTCTTGGCCAGgtaaat-tcagattttgctgatgataataccatttatgtttgggactgctccagctccagaaaatttggtgttggtggagcaggtcattaggtgctccaaa

upper sequence: LOC_Os04g10380.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA11G04290.1 (Glycine max), 5'ss of exon 17
GAAGAGGTTTCCCATGTGCTTAATTTTTGGTGGTGATGGAAGCTATATGTCTCCATACTACCTACACAGTGATACATTGTTATCTAACCTTCTTGGCCAGgtaaaaataagattaacttaatagggatgttaatgacattcctggtgttccaaacttccaattatatcatcacataggacagttcactttgttccacatt-
|||||| |||||||||||| ||||||||||||| ||||| ||||| ||| | || ||  | || |||| ||||||| ||||  | ||||| ||||| ||||||         || | | | |    |||||  |||   |   |    |       || |   ||| | | |||||  |      |  ||| |   ||   
GAAGAGATTTCCCATGTGCATAATTTTTGGTGGGGATGGGAGCTACATGGCACCTTATAATCTTCACAATGATACACTGTTGACCAACCTCCTTGGTCAGgtatc-------ttgattcattgttaatgttg-tgaagatttagtcaattatgttctctatacatagc-tgacatactaatcccaaacttgatatccacag

upper sequence: LOC_Os04g10380.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA01G41140.1 (Glycine max), 5'ss of exon 17
GAAGAGGTTTCCCATGTGCTTAATTTTTGGTGGTGATGGAAGCTATATGTCTCCATACTACCTACACAGTGATACATTGTTATCTAACCTTCTTGGCCAGgtaaaaataagattaacttaatagggatgttaatgacattcctggtgttccaaacttccaattatatcatcacataggacagttcactttgttccacatt-
|||||| |||||||||||| ||||||||||||| ||||| ||||| ||| | || ||  | || |||| ||||||| ||||  | ||||| ||||| ||||||         ||   | | |    |||||  | | |||   | |  |       || |   ||| | | |||||  |      |  ||| |   ||   
GAAGAGATTTCCCATGTGCATAATTTTTGGTGGGGATGGGAGCTACATGGCACCTTATAATCTTCACAATGATACACTGTTGACCAACCTCCTTGGTCAGgtatc-------ttgtttcattgttaatgttgttaagattta-gttagttatgttctctatacatagc-tgacatactaatcccaaacttgatatccacag

upper sequence: LOC_Os04g10380.1 (Oryza sativa), 5'ss of exon 17
lower sequence: Vv02s0012g00460.t01 (Vitis vinifera), 5'ss of exon 17
GAAGAGGTTTCCCATGTGCTTAATTTTTGGTGGTGATGGAAGCTATATGTCTCCATACTACCTACACAGTGATACATTGTTATCTAACCTTCTTGGCCAGgtaaaaataagattaacttaatagggatgttaatgacattcctggtgttccaaacttccaattatatcatcacataggacagttcactttgttccacatt
|||||| || ||||||||| | ||||| ||||||||||||||||||||||| || ||  | ||  ||||||| ||||| ||  | || ||||||||||||||     ||  |  | | |  |     | ||  ||   ||     |      |||      | || ||| ||  |     |  |   | | | ||     
GAAGAGATTCCCCATGTGCATCATTTTCGGTGGTGATGGAAGCTATATGTCCCCTTATAATCTTTACAGTGACACATTATTGACAAATCTTCTTGGCCAGgt----ttattagcagcctcttt----tatttctgttcttttgaatagctataacaattgttcatttcaacattttcactatgtttttgtatacccag--

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|29624393|gb|CB629404.1|CB629404
EST:     CTCCATACTACCTACACAGTGATACATTGTTATCTAACCTTCTTGGCCAG                         TATGTGTCAACTGCGATCTGGAACAGATTGGTTGCGGGC
genomic: CTCCATACTACCTACACAGTGATACATTGTTATCTAACCTTCTTGGCCAGgtaaaaataa ... ctttctctagTATGTGTCAACTGCGATCTGGAACAGATTGGTTGCGGGC




















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: 70 (upstream exon), 72 (downstream exon)
Score: 10

GAAGAGGTTTCCCATGTGCTTAATTTTTGGTGGTGATGGAAGCTATATGTCTCCATACTACCTACACAGTGATACATTGTTATCTAACCTTCTTGGCCAGgtaaaaataa ... ctttctctagTATGTGTCAACTGCGATCTGGAACAGATTGGTTGCGGGCTTGAATGCTCAGTTGAGGACAGTACGGCAAGGGAACATCCGATCAACTTTGGGACCTGTTG




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