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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATATGAGAGGTCAGAAGATCCTATTTATGTTTTGGATAATAACATACCAATAGATCCCCAATACTACCTTGAGAACCAAATCAGCAAAgtatgtccagaacacatttcttgatattcgaaaattcgcttcctccaattctaacaaacttttaattgctag

Basic information

species Oryza sativa
transcript LOC_Os11g08330.1
intron # 26
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g08330.1 (Oryza sativa), 5'ss of exon 26
lower sequence: GRMZM2G115245_T01 (Zea mays), 5'ss of exon 10
GCATATGAGAGGTCAGAAGATCCTATTTATGTTTTGGATAATAACATACCAATAGATCCCCAATACTACCTTGAGAACCAAATCAGCAAAgtatgtccagaacacatttcttgatattcgaaaattcgcttcctccaattctaacaaactttt--aattgctag---------------
||||||||||  ||||||||||| |||||||||||||| ||||| ||||| || ||||| ||||||||||||||||||||||| ||||| || ||| |   |  | |  | |  |||||  |   || |  | ||   ||   |     ||||  || ||                   
GCATATGAGAAATCAGAAGATCCGATTTATGTTTTGGACAATAATATACCCATTGATCCTCAATACTACCTTGAGAACCAAATTAGCAAGgtttgtgccctatgcttcacctagtattcatagcctctccccttctgctttccatttttttttgtaactgaccacttgtcaatcggcag

upper sequence: LOC_Os11g08330.1 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA06G16110.1 (Glycine max), 5'ss of exon 26
GCATATGAGAGGTCAGAAGATCCTATTTATGTTTTGGATAATAACATACCAATAGATCCCCAATACTACCTTGAGAACCAAATCAGCAAAgtatgtccagaacacatttcttgatattcgaaaattcgct----tcctccaattctaacaaactt--ttaattgctag
||||||||||| ||||| |||||||| |||||  | || || |||||||| |||||||| || ||||| |||||||| ||||| ||||| ||  ||  |    |  ||  | ||| ||   || ||| |     |  ||   |  | |  | |||  || ||    ||
GCATATGAGAGATCAGAGGATCCTATCTATGTGCTAGAGAACAACATACCCATAGATCCTCATTACTATCTTGAGAATCAAATTAGCAAGgttggttta--ttagtttattagatgttttgaatttctccaatgttttctgctatttattagcttcattcatgtgcag

upper sequence: LOC_Os11g08330.1 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA04G38800.2 (Glycine max), 5'ss of exon 10
GCATATGAGAGGTCAGAAGATCCTATTTATGTTTTGGATAATAACATACCAATAGATCCCCAATACTACCTTGAGAACCAAATCAGCAAAgtatgtccagaacacatttcttgatattcgaaaattcgcttcctccaattctaacaaacttttaattgctag-------------
||||| ||||  ||||| |||||||| |||||| | || || ||||||||||||||||| || ||||| |||||||| ||||| ||||| ||  ||  |  ||   ||  | ||| ||      || | || ||| |||  | ||     |||| | |||               
GCATACGAGAAATCAGAGGATCCTATCTATGTTCTAGAGAACAACATACCAATAGATCCTCAGTACTATCTTGAGAATCAAATTAGCAAGgttggtttatgac--tttattggatgtt------ttggatttctctaatgtttactgttctttattagcttcattcatattgcag

upper sequence: LOC_Os11g08330.1 (Oryza sativa), 5'ss of exon 26
lower sequence: PP1S54_271V6.1 (Physcomitrella patens), 5'ss of exon 26
GCATATGAGAGGTCAGAAGATCCTATTTATGTTTTGGATAATAACATACCAATAGATCCCCAATACTACCTTGAGAACCAAATCAGCAAAgtatgtccagaacacatttcttgatattcgaaaattcgcttcctccaattctaac----aaacttttaattgctag-------------------------
|| ||||||| |||||||||||| || ||||||||||| ||||| || || || ||||| ||||||||| | || |||||  | || || ||  |||   ||   || | ||  |     ||| |  |  |  |    ||   ||    ||| | ||   | |                            
GCGTATGAGAAGTCAGAAGATCCAATCTATGTTTTGGAGAATAATATTCCGATTGATCCACAATACTACTTGGAAAACCAGCTGAGTAAGgtgcgtcttcaatg-atgtgtttttggcttaaagtcagacttttatggtttgcacttggaaattattctctacagacctgtgtgcaggggcgtttaatgtt

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|58654042|gb|CK042722.1|CK042722
EST:     ATAACATACCAATAGATCCCCAATACTACCTTGAGAACCAAATCAGCAAA                         CCACTTTTGAGGATCTTTGAGCCGATTCTGAAGAATGCCAGTAGAGAGCTG
genomic: ATAACATACCAATAGATCCCCAATACTACCTTGAGAACCAAATCAGCAAAgtatgtccag ... taattgctagCCACTTTTGAGGATCTTTGAGCCGATTCTGAAGAATGCCAGTAGAGAGCTG
EST: gi|87006736|gb|CI285770.1|CI285770
EST:     ATAACATACCAATAGATCCCCAATACTACCTTGAGAACCAAATCAGCAAA                         CCACTTTTGAGGATCTTTGAGCCGATTCTGAAGAATGCCAGTAGAGAGCTG
genomic: ATAACATACCAATAGATCCCCAATACTACCTTGAGAACCAAATCAGCAAAgtatgtccag ... taattgctagCCACTTTTGAGGATCTTTGAGCCGATTCTGAAGAATGCCAGTAGAGAGCTG

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: 73 (upstream exon), 63 (downstream exon)
Score: 7

GCATATGAGAGGTCAGAAGATCCTATTTATGTTTTGGATAATAACATACCAATAGATCCCCAATACTACCTTGAGAACCAAATCAGCAAAgtatgtccag ... taattgctagCCACTTTTGAGGATCTTTGAGCCGATTCTGAAGAATGCCAGTAGAGAGCTGCTTCATGGAAGTCACACCAGGGCTGTTTCAATCTCAACTCCTTCAAATA




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