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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaactaagggcctttgcattgcttatatttcaatataaatttacctagtagcttatcagctatttacctggagttactggcacgcgactttgctgaccaaagtcatcatgaacaaataattgattccatttttaactaagctctgtcaaccgcagGCCGAGTGTGCCATCATGGCTCTGAATTGCAGTGGGATGATTTTGGGTACACTGCCTGTCAG

Basic information

species Oryza sativa
transcript LOC_Os01g11120.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g11120.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G051043_T01 (Zea mays), 3'ss of exon 8
gtaagaactaagggcctttgcattgcttatatttcaatataaatttacctagtagcttatcagctatttacctggagttactggcacgcgactttgctgaccaaagtcatcatgaacaaataattgattccatttttaactaagctctgtcaaccgcagGCCGAGTGTGCCATCATGGCTCTGAATTGCAGTGGGATGATTTTGGGTACACTGCCTGTCAG
                                          |||   || ||| |      ||  | ||  ||   || ||  ||  |    |  | |   ||  |    ||         |||||||| |  |||   | | |||||  || | ||||| ||| ||||||||||||||||||||||||| |||||||||||||| ||||||||||||||
-----------------------------------------gattgtgctcgta-caggcatgccttctatttg---ttccttccatactgagtatccgcttaagatggagat---------attgattctaacttt---tgaactctg--aatcacagGCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAG

upper sequence: LOC_Os01g11120.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G069816_T01 (Zea mays), 3'ss of exon 8
gtaagaactaagggcctttgcattgcttatatttcaatataaatttacctagtagcttatcagctatttacctggagttac-tggcacgcgactttgctgaccaaagtcatcatgaacaaataattgattccattttta----actaagctctgtcaaccgcagGCCGAGTGTGCCATCATGGCTCTGAATTGCAGTGGGATGATTTTGGGTACACTGCCTGTCAG
                                                                |  | |    |   ||| |  ||   |  | |    |    |||   |    | | |||   | ||  ||| | |    | | | |||||  || | ||||| ||| ||||||||||||||||||||||||| |||||||||||||| || |||||||||||
-------------------------------------------------------------ttgtgctcatacaggcatacgttacatttgtttctttaaaattgagtatccgctta-agatagaggctttgattgtaacactattgaactctg--aatcacagGCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACTCTGCCTGTCAG
















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|86540303|gb|CI180509.1|CI180509
EST:     TAGGGGATAATGTACATTCTACAAGGATTGCTTTTGTTGAGTTTGTCCAT                         GCCGAGTGTGCCATCATGGCTCTGAATTGCAGTGGGATGATTTTGGGTACA
genomic: TAGGGGATAATGTACATTCTACAAGGATTGCTTTTGTTGAGTTTGTCCATgtaagaacta ... tcaaccgcagGCCGAGTGTGCCATCATGGCTCTGAATTGCAGTGGGATGATTTTGGGTACA
EST: gi|29678319|gb|CB674594.1|CB674594
EST:     TAGGGGATAATGTACATTCTACAAGGATTGCTTTTGTTGAGTTTGTCCAT                         GCCGAGTGTGCCATCATGGCTCTGAATTGCAGTGGGATGATTTTGGGTACA
genomic: TAGGGGATAATGTACATTCTACAAGGATTGCTTTTGTTGAGTTTGTCCATgtaagaacta ... tcaaccgcagGCCGAGTGTGCCATCATGGCTCTGAATTGCAGTGGGATGATTTTGGGTACA
EST: gi|58685262|gb|CK073949.1|CK073949
EST:     TAGGGGATAATGTACATTCTACAAGGATTGCTTTTGTTGAGTTTGTCCAT                         GCCGAGTGTGCCATCATGGCTCTGAATTGCAGTGGGATGATTTTGGGTACA
genomic: TAGGGGATAATGTACATTCTACAAGGATTGCTTTTGTTGAGTTTGTCCATgtaagaacta ... tcaaccgcagGCCGAGTGTGCCATCATGGCTCTGAATTGCAGTGGGATGATTTTGGGTACA
EST: gi|89167533|gb|CI108934.1|CI108934
EST:     TAGGGGATAATGTACATTCTACAAGGATTGCTTTTGTTGAGTTTGTCCAT                         GCCGAGTGTGCCATCATGGCTCTGAATTGCAGTGGGATGATTTTGGGTACA
genomic: TAGGGGATAATGTACATTCTACAAGGATTGCTTTTGTTGAGTTTGTCCATgtaagaacta ... tcaaccgcagGCCGAGTGTGCCATCATGGCTCTGAATTGCAGTGGGATGATTTTGGGTACA
EST: gi|86483597|gb|CI126230.1|CI126230
EST:     TAGGGGATAATGTACATTCTACAAGGATTGCTTTTGTTGAGTTTGTCCAT                         GCCGAGTGTGCCATCATGGCTCTGAATTGCAGTGGGATGATTTTGGGTACA
genomic: TAGGGGATAATGTACATTCTACAAGGATTGCTTTTGTTGAGTTTGTCCATgtaagaacta ... tcaaccgcagGCCGAGTGTGCCATCATGGCTCTGAATTGCAGTGGGATGATTTTGGGTACA
EST: gi|88851137|gb|CI373895.1|CI373895
EST:     TAGGGGATAATGTACATTCTACAAGGATTGCTTTTGTTGAGTTTGTCCAT                         GCCGAGTGTGCCATCATGGCTCTGAATTGCAGTGGGATGATTTTGGGTACA
genomic: TAGGGGATAATGTACATTCTACAAGGATTGCTTTTGTTGAGTTTGTCCATgtaagaacta ... tcaaccgcagGCCGAGTGTGCCATCATGGCTCTGAATTGCAGTGGGATGATTTTGGGTACA
EST: gi|88268986|gb|CI380284.1|CI380284
EST:     TAGGGGATAATGTACATTCTACAAGGATTGCTTTTGTTGAGTTTGTCCAT                         GCCGAGTGTGCCATCATGGCTCTGAATTGCAGTGGGATGATTTTGGGTACA
genomic: TAGGGGATAATGTACATTCTACAAGGATTGCTTTTGTTGAGTTTGTCCATgtaagaacta ... tcaaccgcagGCCGAGTGTGCCATCATGGCTCTGAATTGCAGTGGGATGATTTTGGGTACA
EST: gi|89182435|gb|CI113804.1|CI113804
EST:     TAGGGGATAATGTACATTCTACAAGGATTGCTTTTGTTGAGTTTGTCCAT                         GCCGAGTGTGCCATCATGGCTCTGAATTGCAGTGGGATGATTTTGGGTACA
genomic: TAGGGGATAATGTACATTCTACAAGGATTGCTTTTGTTGAGTTTGTCCATgtaagaacta ... tcaaccgcagGCCGAGTGTGCCATCATGGCTCTGAATTGCAGTGGGATGATTTTGGGTACA
EST: gi|58682423|gb|CK071110.1|CK071110
EST:     TAGGGGATAATGTACATTCTACAAGGATTGCTTTTGTTGAGTTTGTCCAT                         GCCGAGTGTGCCATCATGGCTCTGAATTGCAGTGGGATGATTTTGGGTACA
genomic: TAGGGGATAATGTACATTCTACAAGGATTGCTTTTGTTGAGTTTGTCCATgtaagaacta ... tcaaccgcagGCCGAGTGTGCCATCATGGCTCTGAATTGCAGTGGGATGATTTTGGGTACA

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: 45 (upstream exon), 73 (downstream exon)
Score: 27

GTCTCTCGTTTGAGACTTCTAGGGGATAATGTACATTCTACAAGGATTGCTTTTGTTGAGTTTGTCCATgtaagaacta ... tcaaccgcagGCCGAGTGTGCCATCATGGCTCTGAATTGCAGTGGGATGATTTTGGGTACACTGCCTGTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtcatcatgaacaaataattgattccatttttaactaagctctgtcaaccgcagGCCGAGTGTGCCATCATGGCTCTGAATTGCAGTGGGATGATTTTGGGTACACTGCCTGTCAG
                             ttttaac  putative branch site (score: 27)
                                        ctctgtc  putative PPT
             aaataattgattccat  TA-rich tract