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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaaaagaactcatagcattggatgttagacatttcttttctatagagatcatacattatttctttgttgatcaatctaattcattatattctggaatagGTAAGCGAAGAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATTCAGGGAAG

Basic information

species Oryza sativa
transcript LOC_Os02g35470.4
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g35470.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G113453_T01 (Zea mays), 3'ss of exon 3
gtgagtaaaagaactcatagcattggatgttag---acatttcttttctatagagatcatacattatttctttgttgatcaatctaattcattatattctggaa--tagGTAAGCGAAGAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATTCAGGGAAG
|||||| |||   ||  | | | |   | ||||   | || |   |||| || ||   |||||  |   |||| || |    | | ||| ||| ||||   ||   |||||||| ||||| ||||||||||||||||||||  |||||||||| ||||| || |||||
gtgagtcaaatttctgtttg-acttatttttagtttatatgtaaattctgtatagtgtatacacaa---ctttattcacatgtttgattgattttatttatgatcctagGTAAGTGAAGAAGTAGAGCGTGCTTTAGCCAAACTGGGTCCTGCTAGAATCCAAGGAAG

upper sequence: LOC_Os02g35470.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G054109_T01 (Zea mays), 3'ss of exon 3
gtgagtaaaagaactcatagcattggatgttagacatttcttttctatagagatcatacat-tatttctttgttgatcaatctaattcattatattctggaa--tagGTAAGCGAAGAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATTCAGGGAAG
|||||| |||   ||  |||  ||   | ||||        ||| |||  | ||  |  ||  || || || ||||   || | |  |||| ||||   |    |||||||| ||||| ||||||||||||||||||||  |||||||||| |||||||| |||||
gtgagtcaaatttct-gtagagtt---ttttag--------tttatatgtaaattctctatacatatccttattgacatatttgacccattgtatttctggtcctagGTAAGTGAAGAAGTAGAGCGTGCTTTAGCCAAACTGGGTCCTGCTAGAATTCAAGGAAG
















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|58695876|gb|CK084563.1|CK084563
EST:     ATAGTTTGCAGAAGCTTTGTTCATCACTGGAGCCAATTCTTCGTAGAGTT                         GTAAGCGAAGAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATT
genomic: ATAGTTTGCAGAAGCTTTGTTCATCACTGGAGCCAATTCTTCGTAGAGTTgtgagtaaaa ... tctggaatagGTAAGCGAAGAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATT
EST: gi|29675099|gb|CB671374.1|CB671374
EST:     ATAGTTTGCAGAAGCTTTGTTCATCACTGGAGCCAATTCTTCGTAGAGTT                         GTAAGCGAAGAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATT
genomic: ATAGTTTGCAGAAGCTTTGTTCATCACTGGAGCCAATTCTTCGTAGAGTTgtgagtaaaa ... tctggaatagGTAAGCGAAGAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATT
EST: gi|29674900|gb|CB671175.1|CB671175
EST:     ATAGTTTGCAGAAGCTTTGTTCATCACTGGAGCCAATTCTTCGTAGAGTT                         GTAAGCGAAGAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATT
genomic: ATAGTTTGCAGAAGCTTTGTTCATCACTGGAGCCAATTCTTCGTAGAGTTgtgagtaaaa ... tctggaatagGTAAGCGAAGAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATT
EST: gi|29677880|gb|CB674155.1|CB674155
EST:     ATAGTTTGCAGAAGCTTTGTTCATCACTGGAGCCAATTCTTCGTAGAGTT                         GTAAGCGAAGAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATT
genomic: ATAGTTTGCAGAAGCTTTGTTCATCACTGGAGCCAATTCTTCGTAGAGTTgtgagtaaaa ... tctggaatagGTAAGCGAAGAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATT
EST: gi|29630082|gb|CB635091.1|CB635091
EST:     ATAGTTTGCAGAAGCTTTGTTCATCACTGGAGCCAATTCTTCGTAGAGTT                         GTAAGCGAAGAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATT
genomic: ATAGTTTGCAGAAGCTTTGTTCATCACTGGAGCCAATTCTTCGTAGAGTTgtgagtaaaa ... tctggaatagGTAAGCGAAGAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATT
EST: gi|58686392|gb|CK075079.1|CK075079
EST:     ATAGTTTGCAGAAGCTTTGTTCATCACTGGAGCCAATTCTTCGTAGAGTT                         GTAAGCGAAGAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATT
genomic: ATAGTTTGCAGAAGCTTTGTTCATCACTGGAGCCAATTCTTCGTAGAGTTgtgagtaaaa ... tctggaatagGTAAGCGAAGAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATT
EST: gi|29635770|gb|CB640779.1|CB640779
EST:     ATAGTTTGCAGAAGCTTTGTTCATCACTGGAGCCAATTCTTCGTAGAGTT                         GTAAGCGAAGAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATT
genomic: ATAGTTTGCAGAAGCTTTGTTCATCACTGGAGCCAATTCTTCGTAGAGTTgtgagtaaaa ... tctggaatagGTAAGCGAAGAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATT
EST: gi|29626070|gb|CB631081.1|CB631081
EST:     ATAGTTTGCAGAAGCTTTGTTCATCACTGGAGCCAATTCTTCGTAGAGTT                         GTAAGCGAAGAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATT
genomic: ATAGTTTGCAGAAGCTTTGTTCATCACTGGAGCCAATTCTTCGTAGAGTTgtgagtaaaa ... tctggaatagGTAAGCGAAGAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATT
EST: gi|29629686|gb|CB634695.1|CB634695
EST:     ATAGTTTGCAGAAGCTTTGTTCATCACTGGAGCCAATTCTTCGTAGAGTT                         GTAAGCGAAGAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATT
genomic: ATAGTTTGCAGAAGCTTTGTTCATCACTGGAGCCAATTCTTCGTAGAGTTgtgagtaaaa ... tctggaatagGTAAGCGAAGAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATT

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: 60 (upstream exon), 52 (downstream exon)
Score: 24

TGTCATTGTGGAAGCTCTTAAGGTGGATAGTTTGCAGAAGCTTTGTTCATCACTGGAGCCAATTCTTCGTAGAGTTgtgagtaaaa ... tctggaatagGTAAGCGAAGAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATTCAGGGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagatcatacattatttctttgttgatcaatctaattcattatattctggaatagGTAAGCGAAGAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATTCAGGGAAG
                             atctaat  putative branch site (score: 24)
                         atcaatctaattcatt  TA-rich tract