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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatatgtagtttgttattgggtttacagtgatttcgaaagttgaactgttatttggatttcaggaattcatgtattaacaccattagtgttttgaacaattttatttactgctgtctgtctggagttaaccgtgtattgtgaaataatctaaagtacattctttttcaccatatacagGAGAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAG

Basic information

species Oryza sativa
transcript LOC_Os07g47290.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g47290.3 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G081682_T01 (Zea mays), 3'ss of exon 13
gtacatatgtagtttgttattgggtttacagtgatttcgaaagttgaactgttatttggatttcaggaattcatgtattaacaccattagtgttttg--aacaattttattt-actgctgtctgtctggagttaaccgtgtattgtgaaataatctaaagtacattctttttcaccatatacagGAGAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAG
                                                         | | |  | |  ||||| | ||   |   | | |   |||  | ||| ||| | | | ||  |  ||| ||   ||||| || | || | |||  |    |  |   | || | ||||   | | |||||| |||||||| |||||||| |||||||| ||||||||||||||||| ||
---------------------------------------------------------gtaatataagttttcatatttttggaatgtgaatacattgtcagcaagtttctgtgagtgaagcttgtgtgagtttaactgtttgttctaaaagtac---acctttttactgtctcacatgacatagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAG

upper sequence: LOC_Os07g47290.3 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G005493_T01 (Zea mays), 3'ss of exon 13
gtacatatgtagtttgttattgggtttacagtgatttcgaaagttgaactgttatttggatttcaggaattcatgtattaacaccattagtgttttgaacaattttatttac-tgctgtctgtctggagttaaccgtgtattgtgaaataatctaaagtacattctttttcaccatatacagGAGAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAG
                                                  || || |  |||||   | ||   | ||   ||      |  || | | ||||||| |  |  ||  |  ||| ||   ||| |  | | || ||||   |    |  |   |||| | ||||     |||||||| |||||||| |||||||| |||||||| ||||||||||||||||||||
--------------------------------------------------gtaatataaatttccatattttcaggatgtccat-----gcattgttaccaattttctacaagtgaagcttgtgtgagtttagctttctgttctgaatgtac---actttttttctgtatcacatggcacagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAG
















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|29667757|gb|CB664032.1|CB664032
EST:     TACAGAAATATGGTCTAACAG                         GAGAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATA
genomic: TACAGAAATATGGTCTAACAGgtacatatgt ... ccatatacagGAGAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATA
EST: gi|29625367|gb|CB630378.1|CB630378
EST:     ACAGAAATATGGTCTAACAG                         GAGAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATA
genomic: ACAGAAATATGGTCTAACAGgtacatatgt ... ccatatacagGAGAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATA
EST: gi|12622805|gb|AU173018.1|AU173018
EST:     TTGGGATGTTGCAACCACATTCTCTTTCCTACAGAAATATGGTCTAACAG                         GAGAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATA
genomic: TTGGGATGTTGCAACCACATTCTCTTTCCTACAGAAATATGGTCTAACAGgtacatatgt ... ccatatacagGAGAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATA
EST: gi|29661148|gb|CB657423.1|CB657423
EST:     AGAAATATGGTCTAACAG                         GAGAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATA
genomic: AGAAATATGGTCTAACAGgtacatatgt ... ccatatacagGAGAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATA
EST: gi|5004160|gb|AU069309.1|AU069309
EST:     CCACATTCTCTTTCCTACAGAAATATGGTCTAACAG                         GAGAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATA
genomic: CCACATTCTCTTTCCTACAGAAATATGGTCTAACAGgtacatatgt ... ccatatacagGAGAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATA
EST: gi|29665147|gb|CB661422.1|CB661422
EST:     TGGGATGTTGCAACCACATTCTCTTTCCTACAGAAATATGGTCTAACAG                         GAGAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATA
genomic: TGGGATGTTGCAACCACATTCTCTTTCCTACAGAAATATGGTCTAACAGgtacatatgt ... ccatatacagGAGAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATA
EST: gi|29637953|gb|CB642962.1|CB642962
EST:     TTGGGATGTTGCAACCACATTCTCTTTCCTACAGAAATATGGTCTAACAG                         GAGAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATA
genomic: TTGGGATGTTGCAACCACATTCTCTTTCCTACAGAAATATGGTCTAACAGgtacatatgt ... ccatatacagGAGAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATA
EST: gi|88306647|gb|CI671406.1|CI671406
EST:     TTGGGATGTTGCAACCACATTCTCTTTCCTACAGAAATATGGTCTAACAG                         GAGAATTCAAGATAAATGTTGAATGCAACCACGCCTACTCTATCTGGACAT
genomic: TTGGGATGTTGCAACCACATTCTCTTTCCTACAGAAATATGGTCTAACAGgtacatatgt ... ccatatacagGAGAATTCAAGATAAATGTTGAATGCAACCACGC-TACTCTATCTGGACAT
EST: gi|29620969|gb|CB625980.1|CB625980
EST:     TTGGGATGTTGCAACCACATTCTCTTTCCTACAGAAATATGGTCTAACAG                         GAGAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATA
genomic: TTGGGATGTTGCAACCACATTCTCTTTCCTACAGAAATATGGTCTAACAGgtacatatgt ... ccatatacagGAGAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATA

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: 55 (upstream exon), 73 (downstream exon)
Score: 64

GTACGATTGGGATGTTGCAACCACATTCTCTTTCCTACAGAAATATGGTCTAACAGgtacatatgt ... ccatatacagGAGAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttaaccgtgtattgtgaaataatctaaagtacattctttttcaccatatacagGAGAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAG
                       atctaaa  putative branch site (score: 64)
                                 cattctttttcacc  putative PPT
                  aaataatctaaagta  TA-rich tract