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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggctgactgagtaccttactatatatttatcttatggatcagctgccatctgcactgacacttcaaactaatcctgcggttcaattcaatagGTGTTATGATCTGGTTGCTAGCCATTATCTACTTTATATCTGGTGTACCTGGAGCCTATGTGTTATGGTATCGCCCCCTTTACAATGCGATGAG

Basic information

species Oryza sativa
transcript LOC_Os01g57220.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g57220.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G169773_T02 (Zea mays), 3'ss of exon 6
gtatggctgactgagtaccttactatatatttatcttatggatcagctgccatctgcactgacacttcaaactaatcctgcggttcaattcaatagGTGTTATGATCTGGTTGCTAGCCATTATCTACTTTATATCTGGTGTACCTGGAGCCTATGTGTTATGGTATCGCCCCCTTTACAATGCGATGAG
||||||     || | |   |||| | | |  ||||| || || |  ||| | |         || |  ||||||||| | || ||  || ||||||||| ||||||||||||||||| || |||||||| || |||||||| ||||| ||||||||| | ||||||||||| |||||||||||||||||
gtatgggcatatg-gcagtgtacttt-tctacatcttttgaatgaattgctacca--------acctggaactaatccagtggctcgcttgaatagGTGTCATGATCTGGTTGCTAGCAATCATCTACTTCATCTCTGGTGTCCCTGGGGCCTATGTGCTTTGGTATCGCCCGCTTTACAATGCGATGAG

upper sequence: LOC_Os01g57220.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA12G11820.2 (Glycine max), 3'ss of exon 7
gtatggctgactgagtaccttactatatatttatcttatggatcagctgccatctgcactgacacttcaaactaatcctgcggttcaattcaatagGTGTTATGATCTGGTTGCTAGCCATTATCTACTTTATATCTGGTGTACCTGGAGCCTATGTGTTATGGTATCGCCCCCTTTACAATGCGATGAG
                   ||    |  |  |   |  || ||||     | | |  | | |  |||  || |||       ||         |||||   |  |||||||| || || |||||||| ||||| |||||||  || ||| |||||||||| ||||||||||| |||||   ||| |||||
-----------------gtttgtcttgcaactggatattgcatcaat---cttgttaagtcatgctt--aattaacagacttgtctctccatgtaggtccaaccatctggtttcttgcaattatctattttatttctggtgctccagGATCCTATGTGTTGTGGTATCGCCCTCTTTATCGTGCTATGAG

upper sequence: LOC_Os01g57220.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA06G45160.1 (Glycine max), 3'ss of exon 7
gtatggctgactgagtaccttactatatatttatcttatggatcagctgccatctgcactgacacttcaaactaatcctgcggttcaattcaatagGTGTTATGATCTGGTTGCTAGCCATTATCTACTTTATATCTGGTGTACCTGGAGCCTATGTGTTATGGTATCGCCCCCTTTACAATGCGATGAG
            |  |  ||| | |  |   ||| | ||| ||||  |      ||    | ||     || | | |     ||         |||||   |  |||||||| || || |||||||| ||||| |||||||  || ||| |||||||||| ||||||||||| |||||   ||| |||||
------------gtttgtcttgcaac-tggatat-tgatgcatcaatt-----ttgttaagtcatgcttaatttaccgacttgtctttccatgtagGTCCAACCATCTGGTTTCTTGCTATTATCTATTTTATTTCTGGTGCTCCAGGATCCTATGTGTTGTGGTATCGCCCTCTTTATCGTGCTATGAG

upper sequence: LOC_Os01g57220.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT1G11180.2 (Arabidopsis thaliana), 3'ss of exon 6
----------------gtatggctgact-gagtaccttactatatatttatcttatggatcagctgccatctgcactgacacttcaaactaatcctgcggttcaattcaat-agGTGTTATGATCTGGTTGCTAGCCATTATCTACTTTATATCTGGTGTACCTGGAGCCTATGTGTTATGGTATCGCCCCCTTTACAATGCGATGAG
                 ||    || || | || ||||  ||  |    |  |  |   | |    || |||    | |          | ||  |    |||  ||   | ||| || |  || ||| | || ||| |||| ||||| ||||| ||||| || |||| |||||||||||||||||| || || |||  |||  | ||
gtctctttttgttctcttacacatgtcttgtgttcctttttagctggccaagtcttctgtgatggtccgtctctgtttatttacagtcttgattttttttttctcttttttcagGAGTAACAATTTGGCTTCTCGCCGTTATTTACTTCATATCGGGTGTTCCAGGAGGCTATGTGTTATGGTATCGGCCTCTCTACCGTGCCTTCAG

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|11370676|gb|AU164981.1|AU164981
EST:     TCTTTTCTGGAACATAATTGCAACTACAGCAGCATGGATTAAAGGGGCAG                         GTGTTATGATCTGGTTGCTAGCCATTATCTACTTTATATCTGGTGTACCTG
genomic: TCTTTTCTGGAACATAATTGCAACTACAGCAGCATGGATTAAAGGGGCAGgtatggctga ... aattcaatagGTGTTATGATCTGGTTGCTAGCCATTATCTACTTTATATCTGGTGTACCTG
EST: gi|3760903|gb|C98157.1|C98157
EST:     TCTTTTCTGGAACATAATTGCAACTACAGCAGCATGGATTAAAGGGGCAG                         GTGTTATGATCTGGTTGCTAGCCATTATCTACTTTATATCTGGTGTACCTG
genomic: TCTTTTCTGGAACATAATTGCAACTACAGCAGCATGGATTAAAGGGGCAGgtatggctga ... aattcaatagGTGTTATGATCTGGTTGCTAGCCATTATCTACTTTATATCTGGTGTACCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcagctgccatctgcactgacacttcaaactaatcctgcggttcaattcaatagGTGTTATGATCTGGTTGCTAGCCATTATCTACTTTATATCTGGTGTACCTGGAGCCTATGTGTTATGGTATCGCCCCCTTTACAATGCGATGAG
                            aactaat  putative branch site (score: 2)
                                             aattcaata  TA-rich tract