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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCAAGGGCTGGATTTTATGAGAAACCCATTGCGACTTTGGACTTTGCTTCGTTGTATCCATCCATCATGATGGCATATAACCTATGCTACTGTACTTTGgtaaaaattagtttcttaatttctgattataatacctactacatacagcagaaacatttgttctctgatattattgggtattcacaaagctcatgtttactgtttgaag

Basic information

species Oryza sativa
transcript LOC_Os11g08330.1
intron # 15
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 15
lower sequence: GLYMA06G16110.1 (Glycine max), 5'ss of exon 15
GGCAAGGGCTGGATTTTATGAGAAACCCATTGCGACTTTGGACTTTGCTTCGTTGTATCCATCCATCATGATGGCATATAACCTATGCTACTGTACTTTGgtaaaaattagtttctt-----------------aatttctga---ttataatacctactacatacagcagaaaca----tttgttctctgatattattgggtattcacaaagctcatgtttactgtttgaag--------------------------
||||||||||||||||||||| ||||| ||||| ||||| || ||||| || ||||||||||| || |||||||| |||||  |||| || || ||| ||||||| |||  ||| ||                 |  ||||||   || |  |  ||   | | | |  |  |  |    ||| |||     | |  ||   |    |    | | |   ||  |  ||                              
GGCAAGGGCTGGATTTTATGAAAAACCAATTGCTACTTTAGATTTTGCATCCTTGTATCCATCTATTATGATGGCCTATAATTTATGTTATTGCACTCTGgtaaatatttctttttttttttagtttttccttaagcttctgagttttgttgtttctttaaaaaaaattatgagtactactttattcatcagtttagttcaattcgtatgggggtaacaattggtacttttttttttttttgttttactgttctttaag

upper sequence: LOC_Os11g08330.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA04G38800.1 (Glycine max), 5'ss of exon 15
GGCAAGGGCTGGATTTTATGAGAAACCCATTGCGACTTTGGACTTTGCTTCGTTGTATCCATCCATCATGATGGCATATAACCTATGCTACTGTACTTTGgtaaaaatt--agtttcttaatt--------tctgattataa----tacctactacatacagcagaaacatttgttctctgatatt-attgggtattcacaaagctcatgt--ttactgtttgaag---------------------------------
||||||||||||||||||||| ||||| ||||| ||||| || ||||| || ||||||||||| || |||||||| |||||| |||| || || ||| ||||||| |||  | ||| || |||          |||   |||    |   |  |   || |  | ||  ||  || ||    |||| ||  | |     |||  |  |||   | ||   | | ||                                 
GGCAAGGGCTGGATTTTATGAAAAACCAATTGCTACTTTAGATTTTGCATCCTTGTATCCATCTATTATGATGGCCTATAACTTATGTTATTGCACTCTGgtaaatatttcattttttttattagtttttccttgagcttaagttttgttttttctttataa-aaaattatgagtactactttattcatcagattagttcaattcgtatggagtaacaactggtagataattttgtttttgtttttactgtttgttaag

upper sequence: LOC_Os11g08330.1 (Oryza sativa), 5'ss of exon 15
lower sequence: AT5G63960.1 (Arabidopsis thaliana), 5'ss of exon 15
GGCAAGGGCTGGATTTTATGAGAAACCCATTGCGACTTTGGACTTTGCTTCGTTGTATCCATCCATCATGATGGCATATAACCTATGCTACTGTACTTTGgtaaaaattagtttcttaatttctgattataatacctactacatacagcagaaacatttgttctctgatattattgggtattcacaaagctcatgtttac-tgtttgaag
 |||||  | || || ||||| || || ||||| |||||||| ||||||||  |||| || || || |||||||||||||| || |||||||| || |||||||   ||  |||  || |||||  ||  |||  ||| |   |  | ||   |   ||  |      ||||| |  |    ||  |    ||||||    | |||||||
AGCAAGAACAGGTTTCTATGAAAAGCCAATTGCAACTTTGGATTTTGCTTCACTGTACCCGTCAATTATGATGGCATATAATCTGTGCTACTGCACCTTGgtaa---ttcttttgatattttct--tttcaatttctatttattttatcatctattgtttatacaccttattaatttgggagcattatttccatgttcttgtctttgaag

upper sequence: LOC_Os11g08330.1 (Oryza sativa), 5'ss of exon 15
lower sequence: PP1S54_271V6.1 (Physcomitrella patens), 5'ss of exon 15
GGCAAGGGCTGGATTTTATGAGAAACCCATTGCGACTTTGGACTTTGCTTCGTTGTATCCATCCATCATGATGGCATATAACCTATGCTACTGTACTTTGgtaaaaa-ttagtttcttaatttctgattataatacctactacatacagcagaaacatttgttctctgatattattgggtattcacaaagctcatgtttactgtttgaag----
 || |  || || |  ||||| || || ||||| |||||||| ||||| || ||||| || |||||||||||||| || || || || ||||| ||||||||||    |||   || |   ||     | | |     | |   |  | |     |    |||   | ||  |    | ||  || |  | ||   ||| |||     |     
TGCTAAAGCAGGGTACTATGACAAGCCAATTGCCACTTTGGATTTTGCATCATTGTACCCCTCCATCATGATGGCGTACAATCTTTGTTACTGCACTTTGgtaacctcttacaatcgtggcttgatgctttgaagtgcatt---tgtacctatgccgac-gtttcataattct-ccagatacgcatatcgatctgattttctgaaaacattcag

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|58673981|gb|CK062667.1|CK062667
EST:     CGTTGTATCCATCCATCATGATGGCATATAACCTATGCTACTGTACTTTG                         GTCCCCCCTGAGGATGCCCGCAAACTCAACCTGCCTCCTGAAAGTGTCAAC
genomic: CGTTGTATCCATCCATCATGATGGCATATAACCTATGCTACTGTACTTTGgtaaaaatta ... ctgtttgaagGTCCCCCCTGAGGATGCCCGCAAACTCAACCTGCCTCCAGAAAGTGTCAAC
EST: gi|58606275|gb|CK034308.1|CK034308
EST:     CGTTGTATCCATCCATCATGATGGCATATAACCTATGCTACTGTACTTTG                         GTCCCCCCTGAGGATGCCCGCAAACTCAACCTGCCTCCTGAAAGTGTCAAC
genomic: CGTTGTATCCATCCATCATGATGGCATATAACCTATGCTACTGTACTTTGgtaaaaatta ... ctgtttgaagGTCCCCCCTGAGGATGCCCGCAAACTCAACCTGCCTCCAGAAAGTGTCAAC

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: 35 (upstream exon), 68 (downstream exon)
Score: 5

GGCAAGGGCTGGATTTTATGAGAAACCCATTGCGACTTTGGACTTTGCTTCGTTGTATCCATCCATCATGATGGCATATAACCTATGCTACTGTACTTTGgtaaaaatta ... ctgtttgaagGTCCCCCCTGAGGATGCCCGCAAACTCAACCTGCCTCCAGAAAGTGTCAACAAAACCCCATCTGGTGAAACATTTGTGAAACCAGATGTGCAAAAG




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