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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGTAGCTGTCAAGAAATTCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAAgtaggtgaaactatatatattttatatatcttagagctttactggctatagcgtggattcatttatttgtcatttttaattgatttttgctgcaatgttttgatttgccatatactttctttttacaag

Basic information

species Oryza sativa
transcript LOC_Os03g06410.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g06410.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G175563_T01 (Zea mays), 5'ss of exon 6
GAAGTAGCTGTCAAGAAATTCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAAgtaggtgaaactatatatattttatatatcttagagctttactggctatagcgtggattcatttatttgtcatttttaattgatttttgctgcaatgttttgatttgcc-atatactttctttttacaag
||||||||||| || |||||||||||||||||||| ||||| |||||| ||||||| ||  |||||||||||||||||  | ||| | |||    |||||| ||| ||| ||   || |   |   |  ||||   | |    |    |  ||| ||| |  | ||||| ||| | |  |||||||   |||| |||||
GAAGTAGCTGTAAAAAAATTCTTGGATCAAGATTTTTATGGCGATGCTCTGGATGAGTTTAGGAGTGAAgtaggtgaacttttatctgtttc---tatcttggagttttcctaaataaactat---tcaattttcatatttactcagttcaattgttgatttattgttt-gatatacggatatact---ttttgacaag

upper sequence: LOC_Os03g06410.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G044180_T02 (Zea mays), 5'ss of exon 7
GAAGTAGCTGTCAAGAAATTCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAAgtaggtgaaactatatatattttatatatcttagagctttactggctatagcgtggattcatttatttgtcatttttaattgatttttgctgcaatgttttgatttgccatatactttctttttacaag
||||||||||| || |||||||||||||||||||| ||||| |||||| ||||||| ||  |||||||||||||||||  | ||| | |||    |||||| ||| ||| ||   || |          ||| | || |||| ||||  | | ||    ||     || |  ||||  |||                 
GAAGTAGCTGTAAAAAAATTCTTGGATCAAGATTTTTATGGCGATGCTCTGGATGAGTTTAGGAGTGAAgtaggtgaacttttatctgtttc---tatcttggagttttcctaaataaa--------ctattcaattttcatattta-ctcagttcaattgttgatttattgtttgatata-----------------

upper sequence: LOC_Os03g06410.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G038982_T01 (Zea mays), 5'ss of exon 6
GAAGTAGCTGTCAAGAAATTCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAAgtaggtgaaactatatatattttatatatcttagagctttactggctatagcgtggattcatttatttgtcatttttaattgattt-ttgctgcaatgttttgatttgcc-atatactttctttttacaag
||||||||||| || ||||||||||||||||||||||||||||||||| ||||||| ||  |||||||||||||||||  | ||| | |||    |||||| ||| |||  |   || |      ||||| ||||      |  | | |  | || |||||  | ||||| ||| | |  || |||||| | |  |||||
GAAGTAGCTGTAAAAAAATTCTTGGATCAAGATTTCTATGGTGATGCTCTGGATGAGTTTAGGAGTGAAgtaggtgaacttttatctgtttc---tatcttggagttttcgtaaataaa----taattcaattatcatatttactcagtccagttgttgctttattgttt-gatatacggatgtactttatctg-acaag

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|88571349|gb|CI662722.1|CI662722
EST:     TCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAA                         GTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGT
genomic: TCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAAgtaggtgaaa ... tttttacaagGTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGT
EST: gi|569642|gb|D40491.1|D40491
EST:     TCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAA                         GTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGT
genomic: TCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAAgtaggtgaaa ... tttttacaagGTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGT
EST: gi|2799344|gb|AA752333.1|AA752333
EST:     AGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAA                         GTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGT
genomic: AGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAAgtaggtgaaa ... tttttacaagGTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGT
EST: gi|58596848|gb|CK007376.1|CK007376
EST:     TCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAA                         GTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGT
genomic: TCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAAgtaggtgaaa ... tttttacaagGTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGT
EST: gi|569641|gb|D40490.1|D40490
EST:     TCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAA                         GTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGT
genomic: TCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAAgtaggtgaaa ... tttttacaagGTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGT
EST: gi|571627|gb|D41138.1|D41138
EST:     TCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAA                         GTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGT
genomic: TCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAAgtaggtgaaa ... tttttacaagGTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGT
EST: gi|58688165|gb|CK076852.1|CK076852
EST:     TCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAA                         GTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGT
genomic: TCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAAgtaggtgaaa ... tttttacaagGTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGT

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: 69 (upstream exon), 70 (downstream exon)
Score: 25

GAAGTAGCTGTCAAGAAATTCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAAgtaggtgaaa ... tttttacaagGTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGTGCTGTTACTCGTCCTCCAAACTTATCTATTGTATCTGAGTATCTTCCAA




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