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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAGgtcagtatgttatcatacaggtgatttacattattttctactattttaaatttgttagaacttggaatgtgtgataattttatttgttattgccttgttc...

Basic information

species Oryza sativa
transcript LOC_Os09g24650.4
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g24650.3 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G113619_T04 (Zea mays), 5'ss of exon 9
CTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAGgtcagtatgttatcatacaggtgatttacattattttctactattttaaatttgttagaacttggaatgtgtgataattttatttgttat-tgccttgttc
|||||||| |||||||||||||| || ||||| || ||||| || |||||||||||| | |||||||||||||||||||||||| |||||||||||   | ||     | |||| |      || |||   |  ||    ||||   |  |  ||||    | |   | ||  |||  ||   ||   | |
CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaataatttctaaagtgaatatttgcatcttccttttcttattttttgaaggttccgggaacacctaacg-tatttcttgccatacaccgaatac

upper sequence: LOC_Os09g24650.3 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA20G04870.1 (Glycine max), 5'ss of exon 6
CTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAGgtcagtatgttatcatacaggtgatttacattattttctactattttaaatttgttagaacttggaatgtgtgataattttatttgttattgccttgttc-
|||||  |  | ||||||||||| |||||  |||| | |||||| |||||||||||| | ||||| ||||| |||||  ||||  |||| || ||| |    || |     ||| | |  ||  || | ||| |  ||| |  ||      |||   ||| |   ||| ||  || ||    ||   ||  
CTTTTCTTGCTTCGTGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCTTGGGCAATCAGTATTTTGCAACGCCGGCGACAAAGACAAgtaagt-ttcagtcttggttctgactaatttttgttccgactttgctaattcggtgttggtttgttctgttttgaaatcttgctttttggctccaactttg

upper sequence: LOC_Os09g24650.3 (Oryza sativa), 5'ss of exon 8
lower sequence: AT2G02960.2 (Arabidopsis thaliana), 5'ss of exon 7
CTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAGgtcagtatgtta-----tcatacaggtgatttac---attattttctactattttaaatttgttagaacttggaatgtgtgataatttt--atttgttattgccttgttc-----
||| | ||  | || |||||||||||||| || |||| |||||| |||||||||||  | |||||  | |||||||| |||||| ||||||| ||||   ||     |||| || |   ||| |   |   | || |  | || | | | | |||  | |   | || || |    | |  | ||  | |  ||   ||      
CTTGTCCTGCTCCGAGCTGCTGGATTTCTTCTTCCATGCTATATCATGGCTTGGGCCATCAGTATTCTACAGCGCCGAAGACAGAGACAGgttagtagtataagaactcatgcaaggatttttccggacagtcttttttttttcttactgttttatgaatcaaactgagtcactggtatcgacttaatgtaacccgattgaacag

upper sequence: LOC_Os09g24650.3 (Oryza sativa), 5'ss of exon 8
lower sequence: AT2G02960.5 (Arabidopsis thaliana), 5'ss of exon 5
----------CTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAGgtcagtatgtta-----tcatacaggtgatttac---attattttctactattttaaatttgttagaacttggaatgtgtgataatttt--atttgttattgccttgttc-----
          ||| | ||  | || |||||||||||||| || |||| |||||| |||||||||||  | |||||  | |||||||| |||||| ||||||| ||||   ||     |||| || |   ||| |   |   | || |  | || | | | | |||  | |   | || || |    | |  | ||  | |  ||   ||      
CTTATTTTAGCTTGTCCTGCTCCGAGCTGCTGGATTTCTTCTTCCATGCTATATCATGGCTTGGGCCATCAGTATTCTACAGCGCCGAAGACAGAGACAGgttagtagtataagaactcatgcaaggatttttccggacagtcttttttttttcttactgttttatgaatcaaactgagtcactggtatcgacttaatgtaacccgattgaacag

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|86431015|gb|CI083438.1|CI083438
EST:     AGCGCCGCAGACAGCGACAG                         GAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATACATTCTTCAGTCTGGG
genomic: AGCGCCGCAGACAGCGACAGgtcagtatgt ... gtttgttcagGAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
EST: gi|38471428|gb|CF955559.1|CF955559
EST:     ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAG                         GAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
genomic: ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAGgtcagtatgt ... gtttgttcagGAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
EST: gi|86831029|gb|CI295513.1|CI295513
EST:     ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAG                         GAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
genomic: ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAGgtcagtatgt ... gtttgttcagGAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
EST: gi|88982076|gb|CI027653.1|CI027653
EST:     ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAG                         GAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
genomic: ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAGgtcagtatgt ... gtttgttcagGAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
EST: gi|29626393|gb|CB631404.1|CB631404
EST:     ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAG                         GAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTTTTCAGTCTGGG
genomic: ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAGgtcagtatgt ... gtttgttcagGAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
EST: gi|218496676|gb|FG944369.1|FG944369
EST:     ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCTGCAGACAGCGACAG                         GAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
genomic: ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAGgtcagtatgt ... gtttgttcagGAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
EST: gi|88223285|gb|CI223134.1|CI223134
EST:     ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAG                         GAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
genomic: ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAGgtcagtatgt ... gtttgttcagGAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
EST: gi|16575403|gb|BI802699.1|BI802699
EST:     CTTGCAGCGCCGCAGACAGCGACAG                         GAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
genomic: CTTGCAGCGCCGCAGACAGCGACAGgtcagtatgt ... gtttgttcagGAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG

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), 73 (downstream exon)
Score: 7

CTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAGgtcagtatgt ... gtttgttcagGAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGGCAAGGAACCGGAGTGCATTTCACCATTGCACCGGATTCGCCGACCACAC




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