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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTGCTAGTTACAAAGGAGCTCATCAAGATAGCAGATTTTGGACTTGCTCGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCGCTGgtgcgccatgcaattcttatacttgttaaactatatacacaacaacagaatttagataggagtattaaatatccacttgttcactatcaacatag

Basic information

species Oryza sativa
transcript LOC_Os06g02550.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g02555.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM5G864414_T02 (Zea mays), 5'ss of exon 9
ATTTGCTAGTTACAAAGGAGCTCATCAAGATAGCAGATTTTGGACTTGCTCGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCGCTGgtgcgccatgc---aattcttatacttgttaaactatatacacaacaacagaatttagataggagtattaaatatccacttgttcactatcaacatag
||||||| ||||||||||| |||||||||||||| |||||||| ||||||||||| ||||||||||| ||||| || || ||||||||||| ||||| ||||  |  |||    ||  | |||| ||  | ||   | || | || || |||||  | ||   | |      |||| ||| |                
ATTTGCTTGTTACAAAGGAACTCATCAAGATAGCGGATTTTGGGCTTGCTCGTGAAATTTCTTCTGAGCCACCTTATACGGAATATGTGTCCACTCGTTGgtaggttatgtttgaaggcctatattttcttaaa-gtgtagaaaataatagaataaacattctaatgcctgctatcaactag----------------

upper sequence: LOC_Os06g02555.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv02s0033g01110.t01 (Vitis vinifera), 5'ss of exon 6
ATTTGCTAGTTACAAAGGAGCTCATCAAGATAGCAGATTTTGGACTTGCTCGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCGCTGgtgcgc----------catgcaattcttatacttgttaa---actatatacacaacaacagaatttagataggagtattaaatatccacttgttcactatcaacatag-----------
| ||| | |||||||| ||  | || || || || |||||||| |||||||| |||||   |||| ||||||||||||| |||||||| || || ||||||| ||            |     || |     || ||||     |   | |   | |    ||| |   |   | ||||   | |  | ||  | |  |  || |||            
ACTTGTTGGTTACAAAAGATGTAATAAAAATTGCTGATTTTGGTCTTGCTCGGGAGATCAATTCTCAACCACCATACACGGAATATGTCTCTACACGCTGgtacgtgtttttgggttacttgtttgtcccctttattaatgtgttgcgtccttcaaatttcaatctccctgatattatttggt-tgtattttgttatcactaaaatatggacatggcag
















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|58674281|gb|CK062967.1|CK062967
EST:     CGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCGCTG                         GTACCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGT
genomic: CGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCGCTGgtgcgccatg ... atcaacatagGTACCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGT
EST: gi|58655521|gb|CK044201.1|CK044201
EST:     ATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCGCTG                         GTACCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGT
genomic: ATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCGCTGgtgcgccatg ... atcaacatagGTACCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGT
EST: gi|29638208|gb|CB643217.1|CB643217
EST:     CGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCGCTG                         GTACCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTT
genomic: CGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCGCTGgtgcgccatg ... atcaacatagGTACCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTT
EST: gi|58662294|gb|CK050974.1|CK050974
EST:     CGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCGCTG                         GTACCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGT
genomic: CGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCGCTGgtgcgccatg ... atcaacatagGTACCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGT
EST: gi|29641486|gb|CB646493.1|CB646493
EST:     CGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCGCTG                         GTACCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGT
genomic: CGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCGCTGgtgcgccatg ... atcaacatagGTACCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGT
EST: gi|58687727|gb|CK076414.1|CK076414
EST:     CGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCGCTG                         GTACCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGT
genomic: CGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCGCTGgtgcgccatg ... atcaacatagGTACCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGT
EST: gi|58677581|gb|CK066268.1|CK066268
EST:     CGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCGCTG                         GTACCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGT
genomic: CGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCGCTGgtgcgccatg ... atcaacatagGTACCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGT
EST: gi|58657844|gb|CK046524.1|CK046524
EST:     CGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCGCTG                         GTACCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGT
genomic: CGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCGCTGgtgcgccatg ... atcaacatagGTACCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGT
EST: gi|29658028|gb|CB654303.1|CB654303
EST:     CGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCGCTG                         GTACCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGT
genomic: CGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCGCTGgtgcgccatg ... atcaacatagGTACCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGT
EST: gi|58685041|gb|CK073728.1|CK073728
EST:     CGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCGCTG                         GTACCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGT
genomic: CGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCGCTGgtgcgccatg ... atcaacatagGTACCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGT
EST: gi|29685601|gb|CB681876.1|CB681876
EST:     CGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCGCTG                         GTACCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGT
genomic: CGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCGCTGgtgcgccatg ... atcaacatagGTACCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGT
EST: gi|58689016|gb|CK077703.1|CK077703
EST:     CGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCGCTG                         GTACCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGT
genomic: CGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCGCTGgtgcgccatg ... atcaacatagGTACCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGT

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: 75 (upstream exon), 53 (downstream exon)
Score: 92

ATTTGCTAGTTACAAAGGAGCTCATCAAGATAGCAGATTTTGGACTTGCTCGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCGCTGgtgcgccatg ... atcaacatagGTACCGTGCCCCTGAAGTTCTGCTCCAAGCTTCTGTTTACAACTCAGCAGTTG




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