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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatttaccttgtgatgtgttggttattgttatatttatcagtaaattgaagtactgtaaactagtatatttgaatgtttattaccttttaataccgctttaatatctttgtgtttgatatgagttacaatgttgcgtagATTGGGAAAGGATCAAGAGGAGATGTTACTATATTGCCTACTCTTGTTGTGAACAATCGGCAATACCGAG

Basic information

species Oryza sativa
transcript LOC_Os10g20630.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g20630.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G328265_T01 (Zea mays), 3'ss of exon 4
gtgaatttaccttg--tgatgtgttggttattgtta--tatttatcagtaaattgaagtac------------tgtaaactagtatattt------gaatgttt-attaccttttaataccgctttaatatctttgtgtttgatatgagttacaatgttgcgtagATTGGGAAAGGATCAAGAGGAGATGTTACTATATTGCCTACTCTTGTTGTGAACAATCGGCAATACCGAG
||||| | |||| |  |  | ||| | || | ||      ||||| |||||| | ||| ||            | |||| ||  | | |       || | ||| |||  | ||| |     ||| | ||||| || |||  || || |||   || |||  |||||||||||||| |||||| |||||||||||||||||||||| |||||||||||||| |||||||| ||||
gtgaagtgacctagcatattatgtagtttgtcgtggaccttttattagtaaaataaagcacacatatttattttttaaaatataacagtcactgcagactatttcattgaccttttaccgtccttcattatctatgagtt-aatttgtgttgttatattgtatagATTGGGAAAGGTTCAAGAAGAGATGTTACTATATTGCCTACACTTGTTGTGAACAACCGGCAATATCGAG

upper sequence: LOC_Os10g20630.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AC211785.2_FGT003 (Zea mays), 3'ss of exon 1
gtgaatttaccttg--tgatgtgttggttattgtta--tatttatcagtaaattgaagtac------------tgtaaactagtatattt------gaatgttt-attaccttttaataccgctttaatatctttgtgtttgatatgagttacaatgttgcgtagATTGGGAAAGGATCAAGAGGAGATGTTACTATATTGCCTACTCTTGTTGTGAACAATCGGCAATACCGAG
||||| | |||| |  |  | ||| | || | ||      ||||| |||||| | ||| ||            | |||| ||  | | |       || | ||| |||  | ||| |     ||| | ||||| || |||  || || |||   || |||  |||||||||||||| ||||||||||||||||||||||||||||| |||||||||||||| |||||||| ||||
gtgaagtgacctagcatattatgtagtttgtcgtggaccttttattagtaaaataaagcacacatatttattttttaaaatataacactcactgcagactatttcattgaccttttaccgtccttcattatctatgagtt-aatttgtgttgttatattgtatagATTGGGAAAGGTTCAAGAGGAGATGTTACTATATTGCCTACACTTGTTGTGAACAACCGGCAATATCGAG

upper sequence: LOC_Os10g20630.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G303631_T01 (Zea mays), 3'ss of exon 3
gtgaatttaccttg--tgatgtgttggttattgttata--tttatcagtaaattgaagtac------------tgtaaactagtatattt------gaatgttt-attaccttttaataccgctttaatatctttgtgtttgatatgagttacaatgttgcgtagATTGGGAAAGGATCAAGAGGAGATGTTACTATATTGCCTACTCTTGTTGTGAACAATCGGCAATACCGAG
||||| | |||| |  |  | ||| | || | ||      ||||| |||||| | ||| ||            | |||| ||  | | |       || | ||| |||  | ||| |     ||| | ||||| || |||  || || | |   || |||  |||||||||||||| ||||||||||||||||||||||||||||| |||||||||||||| |||||||| ||||
gtgaagtgacctagcatattatgtagtttgtcgtggagcttttattagtaaaataaagcacacagatttattttttaaaatataacagtcactgcagactatttcattgaccttttaccgtccttcattatctatgagtt-aatttgtgctgttatattgtatagATTGGGAAAGGTTCAAGAGGAGATGTTACTATATTGCCTACACTTGTTGTGAACAACCGGCAATATCGAG

upper sequence: LOC_Os10g20630.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA11G00370.1 (Glycine max), 3'ss of exon 3
gtgaatttaccttgtgatgtgttggttattgttatatttatcagtaaattgaagtactgtaaactagtatatttgaatgtttattaccttttaataccgctttaatatctttgtgtttgatatgagttacaatgttgcgtagATTGGGAAAGGATCAAGAGGAGATGTTACTATATTGCCTACTCTTGTTGTGAACAATCGGCAATACCGAG
                                                     ||| ||||   ||  ||   |     || ||| | ||  |  |  ||  |||||| |   ||||| | |    |   | | ||| ||||||||| || |||||  |||| |||||||| |||||||||||||||||||| || ||||| ||||| ||||
-----------------------------------------------------gtattgtactttataattgctattaattcatt-cattgcatcagtgcagtaatatatagatgtttaaca---atattagttttg-gtagATTGGAAAGGGATCGCGAGGTGATGTTACCATATTGCCTACTCTTGTTGTCAATAATCGACAATATCGAG

upper sequence: LOC_Os10g20630.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA01G45380.1 (Glycine max), 3'ss of exon 3
gtgaatttaccttgtgatgtgttggttattgttatatttatcagtaaattgaagtactgtaaactagtatatttgaatgtttattaccttttaataccgctttaatatctttgtgtttgatatgagttacaatgttgcgtagATTGGGAAAGGATCAAGAGGAGATGTTACTATATTGCCTACTCTTGTTGTGAACAATCGGCAATACCGAG
                                                     |||||||   ||  |||| |||  | |||| | | || ||  |  ||  |||||| |   ||||| | |  | |    |  ||  ||||||||| || |||||  |||| |||||||| ||||||||||||||||| || || ||||| ||||| ||||
-----------------------------------------------------gtactgt---cttttataattgc-tatttagttcattgtatcagtgcagtaatatatagatgtttaacaaaatt----agtttttgtagATTGGAAAGGGATCGCGAGGTGATGTTACCATATTGCCTACTCTTGTGGTCAATAATCGACAATATCGAG

upper sequence: LOC_Os10g20630.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv03s0091g00740.t01 (Vitis vinifera), 3'ss of exon 3
-------------gtgaatttaccttgtgatgtgttg--gttattgttatatttatcagtaaattgaagtactgtaaactagtatatttgaatgtttattaccttttaataccgctttaatatctttgtgtttgatatgagttacaatgttgcgtagATTGGGAAAGGATCAAGAGGAGATGTTACTATATTGCCTACTCTTGTTGTGAACAATCGGCAATACCGAG
              |  || ||  || |  | | |||  ||  ||     |    |  ||   |||  |  ||     ||  ||||    | ||| |      |  | || ||  || |||       ||||||| | ||      |  |     || ||||||||||| ||||||| ||||| ||||||||||| || ||||||||||||||| | ||||| ||||
gtaagcatctcttcttcatatattttttattttattgaagtgcttcagcaacccttttgttgtttgttgggcttctggcttttatacgc-attgtcttgagattggttattccagttcaatcaaacactgtttgacaagaac----acttcctacagGTTGGGAAAGGAACAAGAGGCGATGTCACTATATTGCCCACCCTTGTTGTGAACAATAGACAATATCGAG

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|58684519|gb|CK073206.1|CK073206
EST:     CAAATGCTGATTCGGACCACCCCTTGCTTAAAATGGAGCAGGATGCACAG                         ATTGGGAAAGGATCAAGAGGAGATGTTACTATATTGCCTACTCTTGTTGTG
genomic: CAAATGCTGATTCGGACCACCCCTTGCTTAAAATGGAGCAGGATGCACAGgtgaatttac ... tgttgcgtagATTGGGAAAGGATCAAGAGGAGATGTTACTATATTGCCTACTCTTGTTGTG
EST: gi|58594426|gb|CF992734.1|CF992734
EST:     AAATGCTGATTCGGACCACCCCTTGCTTAAAATGGAGCAGGATGCACGAG                         ATTGGGAAAGGATCAAGAGGAGATGTTACTATATTGCCTACTCTTGTTGT
genomic: AAATGCTGATTCGGACCACCCCTTGCTTAAAATGGAGCAGGATGCAC-AGgtgaatttac ... tgttgcgtagATTGGGAAAGGATCAAGAGGAGATGTTACTATATTGCCTACTCTTGTTGT
EST: gi|300215523|gb|HO088149.1|HO088149
EST:     CAAATGCTGATTCGGACCACCCCTTGCTTAAAATGGAGCAGGATGCACAG                         ATTGGGAAAGGATCAAGAGGAGATGTTACTATATTGCCTACTCTTGTTGTG
genomic: CAAATGCTGATTCGGACCACCCCTTGCTTAAAATGGAGCAGGATGCACAGgtgaatttac ... tgttgcgtagATTGGGAAAGGATCAAGAGGAGATGTTACTATATTGCCTACTCTTGTTGTG
EST: gi|29674931|gb|CB671206.1|CB671206
EST:     CAAATGCTGATTCGGACCACCCCTTGCTTAAAATGGAGCAGGATGCACAG                         ATTGGGAAAGGATCAAGAGGAGATGTTACTATATTGCCTACTCTTGTTGTG
genomic: CAAATGCTGATTCGGACCACCCCTTGCTTAAAATGGAGCAGGATGCACAGgtgaatttac ... tgttgcgtagATTGGGAAAGGATCAAGAGGAGATGTTACTATATTGCCTACTCTTGTTGTG

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: 72 (upstream exon), 67 (downstream exon)
Score: 108

GTTTAGATGTAAAGAAGGTTGACAAGTGCATGGGAGATCCAAATGCTGATTCGGACCACCCCTTGCTTAAAATGGAGCAGGATGCACAGgtgaatttac ... tgttgcgtagATTGGGAAAGGATCAAGAGGAGATGTTACTATATTGCCTACTCTTGTTGTGAACAATCGGCAATACCGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttaataccgctttaatatctttgtgtttgatatgagttacaatgttgcgtagATTGGGAAAGGATCAAGAGGAGATGTTACTATATTGCCTACTCTTGTTGTGAACAATCGGCAATACCGAG
             tttaatatctttgt  TA-rich tract