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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCCTGTCGGTTGAGTTGGGACCTGGTATTCTTGGGAACATTTTTGATGGGATCCAGgtacttcaagttgtgaatgtggagtaatttcatttattttttaagctccttgcactccttgtctgttaactcttgtcatgtcctttttcctatcgtgtttgcag

Basic information

species Oryza sativa
transcript LOC_Os02g07870.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G128877_T03 (Zea mays), 5'ss of exon 1
-------------------------------------------CCCCTGTCGGTTGAGTTGGGACCTGGTATTCTTGGGAACATTTTTGATGGGATCCAGgtacttcaagttgtgaatgtggagtaatttcatttattttttaagctccttgcactccttgtctgttaactcttgtcatgtcctttttcctatcgtgtttgcag
                                           || || || ||||| ||||||||||| |||||||| || ||||||||||| |||||||| |         ||||||||      ||   |||    |         |||  ||  || |   || | | ||| | |  ||| |   |||| ||||||||||
TTGTTTTGCTATCCTTTAACACATAATGGCTATACCCATGCAGCCTCTATCAGTTGAATTGGGACCTGGAATTCTTGGAAATATTTTTGATGGTATCCAGgtgcgc-------tgaatgtgacagggttcattttgcggtcatctacttttgttcttgtttttcttttaat-ttgcccttacctctcctctattgtgtttgcag

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 4
CCCCTGTCGGTTGAGTTGGGACCTGGTATTCTTGGGAACATTTTTGATGGGATCCAGgtacttcaagttgtgaatgtggagtaatttcatttattttttaagctccttgcactccttgtctgttaactcttgtcatgtcctttttcctatcgtgtttgcag
|| || || ||||| ||||||||||| |||||||| ||||||||||| || ||||||||       ||  ||||   |            ||| ||||   ||   || ||    || | | ||  || || || |  |       ||||  |||||||||
CCTCTTTCAGTTGAATTGGGACCTGGAATTCTTGGAAACATTTTTGACGGTATCCAGgt-------gtgctgaacacgacagggc-----ttacttttgcggccatttaca----ttattttttgtctattatcctcactcgccctctattatgtttgcag

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G128877_T02 (Zea mays), 5'ss of exon 4
CCCCTGTCGGTTGAGTTGGGACCTGGTATTCTTGGGAACATTTTTGATGGGATCCAGgtacttcaagttgtgaatgtggagtaatttcatttattttttaagctccttgcactccttgtctgttaactcttgtcatgtcctttttcctatcgtgtttgcag
|| || || ||||| ||||||||||| |||||||| || ||||||||||| |||||||| |         ||||||||      ||   |||    |         |||  ||  || |   || | | ||| | |  ||| |   |||| ||||||||||
CCTCTATCAGTTGAATTGGGACCTGGAATTCTTGGAAATATTTTTGATGGTATCCAGgtgcgc-------tgaatgtgacagggttcattttgcggtcatctacttttgttcttgtttttcttttaat-ttgcccttacctctcctctattgtgtttgcag

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|58663310|gb|CK051996.1|CK051996
EST:     CGGTTGAGTTGGGACCTGGTATTCTTGGGAACATTTTTGATGGGATCCAG                         CGCCCTCTGAAAACTATTGCTATTAAATCTGGAGATGTGTACATTCCGCGT
genomic: CGGTTGAGTTGGGACCTGGTATTCTTGGGAACATTTTTGATGGGATCCAGgtacttcaag ... gtgtttgcagCGCCCTCTGAAAACTATTGCTATTAAATCTGGAGATGTGTACATTCCGCGT
EST: gi|58673192|gb|CK061878.1|CK061878
EST:     CGGTTGAGTTGGGACCTGGTATTCTTGGGAACATTTTTGATGGGATCCAG                         CGCCCTCTGAAAACTATTGCTATTAAATCTGGAGATGTGTACATTCCGCGT
genomic: CGGTTGAGTTGGGACCTGGTATTCTTGGGAACATTTTTGATGGGATCCAGgtacttcaag ... gtgtttgcagCGCCCTCTGAAAACTATTGCTATTAAATCTGGAGATGTGTACATTCCGCGT
EST: gi|58662103|gb|CK050783.1|CK050783
EST:     GGTTGAGTTGGGACCTGGTATTCTTGGAGAACATTTTTGATGGGATCCAG                         CGCCCTCTGAAAACTATTGCTATTAAATCTGGAGATGTGTACATTCCGCGT
genomic: GGTTGAGTTGGGACCTGGTATTCTTGG-GAACATTTTTGATGGGATCCAGgtacttcaag ... gtgtttgcagCGCCCTCTGAAAACTATTGCTATTAAATCTGGAGATGTGTACATTCCGCGT
EST: gi|58663588|gb|CK052274.1|CK052274
EST:     CGGTTGAGTTGGGACCTGGTATTCTTGGGAACATTTTTGATGGGATCCAG                         CGCCCTCTGAAAACTATTGCTATTAAATCTGGAGATGTGTACATTCCGCGT
genomic: CGGTTGAGTTGGGACCTGGTATTCTTGGGAACATTTTTGATGGGATCCAGgtacttcaag ... gtgtttgcagCGCCCTCTGAAAACTATTGCTATTAAATCTGGAGATGTGTACATTCCGCGT
EST: gi|58666816|gb|CK055502.1|CK055502
EST:     CGGTTGAGTTGGGACCTGGTATTCTTGGGAACATTTTTGATGGGATCCAG                         CGCCCTCTGAAAACTATTGCTATTAAATCTGGAGATGTGTACATTCCGCGT
genomic: CGGTTGAGTTGGGACCTGGTATTCTTGGGAACATTTTTGATGGGATCCAGgtacttcaag ... gtgtttgcagCGCCCTCTGAAAACTATTGCTATTAAATCTGGAGATGTGTACATTCCGCGT
EST: gi|27547953|gb|CA765929.2|CA765929
EST:     CGGTTGAGTTGGGACCTGGTATTCTTGGGAACATTTTTGATGGGATCCAG                         CGCCCTCTGAAAACTATTGCTATTAAATCTGGAGATGTGTACATTCCGCGT
genomic: CGGTTGAGTTGGGACCTGGTATTCTTGGGAACATTTTTGATGGGATCCAGgtacttcaag ... gtgtttgcagCGCCCTCTGAAAACTATTGCTATTAAATCTGGAGATGTGTACATTCCGCGT

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: 57 (upstream exon), 65 (downstream exon)
Score: 12

CCCCTGTCGGTTGAGTTGGGACCTGGTATTCTTGGGAACATTTTTGATGGGATCCAGgtacttcaag ... gtgtttgcagCGCCCTCTGAAAACTATTGCTATTAAATCTGGAGATGTGTACATTCCGCGTGGTGTCTCAGTTCCTGCCCTTGACAAAGATGCTTTGTGGCATTTTAAGC




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