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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttgttcttgtgtaattataatatatctattaatgctctctccttttaagctaagtaggatggcactgaatgaacaataataaacttagatttcattaattaacacagtgaactagtagttactgtgaatatttgctgtgcaagatagcccatgctaaattttccctcgatttgcagAATTCAGCTTGGGCAACCAGCTACTGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAG

Basic information

species Oryza sativa
transcript LOC_Os06g04800.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g04800.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G152775_T04 (Zea mays), 3'ss of exon 3
gtaagtttgttcttgtgtaattataatatatctattaatgctctctccttttaagctaagtaggatggcactgaatgaacaataataaacttagatttcattaattaacacagtgaactagtagttactgtgaatat--ttgctgtgcaagat--agcccatgctaaattttccctcgatttgcagAATTCAGCTTGGGCAACCAGCTACTGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAG
                                                           ||| | | || ||  ||  ||||    | | | |  | |  ||   |||  || |  |||    | ||||    || |  ||| |    | |||  |||  |||||||| || ||| |  | |||||||| |||||||| ||||||||||| || ||||||||||||||||| ||||||||| | |||||||||||||||
-----------------------------------------------------------gtaagtttgctcttcatacacaacctaacattaatctcttgtttgataaatcaatatactgaatgatacttaagatctctttgataaatatgatggagctgatgctaaaattaccccct-tgtgcagAATCCAGCTTGGACAACCAGCTACCGTTAAAGTTGCAGCCAACTTGATTAGGTTGCTAGCTTATCAGAACAAG

upper sequence: LOC_Os06g04800.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G374881_T02 (Zea mays), 3'ss of exon 3
gtaagtttgttcttgtgtaattataatatatctattaatgctctctccttttaagctaagtaggatggcactgaatgaacaataataaacttagatt-tcattaattaacacagtgaactagtagttactgtgaatatttgctgtgcaagatagcccatgctaaattttccctcgatttgcagAATTCAGCTTGGGCAACCAGCTACTGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAG
||||||||||||||    |   | ||  || |  |    | ||| || |||   | | | ||       |||||||||          ||||| ||| || || |  || |   ||   ||  | |||||    |||| ||   ||| || |||   |||||||| || |||||  | |||||||| |||||||| |||||||||||||| ||||||||||| ||||| ||||||||| | ||||||||||| |||
gtaagtttgttctt---catacacaacttaacagtattcgatctttcattt---gatgaataaat--atactgaatgat---------acttaaattctctttgaacaatatgatggtata-caattacttgagatatctgacatgcgaggtagttgatgctaaagttaccctcc-tatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAGGTTGCTAGCTTATCAGAATAAG

upper sequence: LOC_Os06g04800.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G152775_T02 (Zea mays), 3'ss of exon 3
gtaagtttgttcttgtgtaattataatatatctattaatgctctctccttttaagctaagtaggatggcactgaatgaacaataataaacttagatttcattaattaacacagtgaactagtagttactgtgaatat--ttgctgtgcaagat--agcccatgctaaattttccctcgatttgcagAATTCAGCTTGGGCAACCAGCTACTGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAG---------------------------
                                                           ||| | | || ||  ||  ||||    | | | |  | |  ||   |||  || |  |||    | ||||    || |  ||| |    | |||  |||  |||||||| || ||| |  | |||||||| |||||||| ||||||||||| || ||||||||||||||||| ||||||||| | |||||||||||||||                           
-----------------------------------------------------------gtaagtttgctcttcatacacaacctaacattaatctcttgtttgataaatcaatatactgaatgatacttaagatctctttgataaatatgatggagctgatgctaaaattaccccct-tgtgcagAATCCAGCTTGGACAACCAGCTACCGTTAAAGTTGCAGCCAACTTGATTAGGTTGCTAGCTTATCAGAACAAGGTATGTTCCATAGCATTCCAGCACGTA

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|58594926|gb|CF993234.1|CF993234
EST:     GACACACAAGTCATTTCGGATTATGTACGCTATTTTCTCCACCAACACAC                         AATTCAGCTTGGGCAACCAGCTACTGTGAAAGTTGCAGCCAACTTAATTAG
genomic: GACACACAAGTCATTTCGGAATATGTACGCTATTTTCTCCACCAACACACgtaagtttgt ... cgatttgcagAATTCAGCTTGGGCAACCAGCTACTGTGAAAGTTGCAGCCAACTTAATTAG
EST: gi|88723743|gb|CI747253.1|CI747253
EST:     GACACACAAGTCATTTCGGAATATGTACGCTATTTTCTCCACCAACACAC                         AATTCAGCTTGGGCAACCAGCTACTGTGAAAGTTGCAGCCAACTTAATTAG
genomic: GACACACAAGTCATTTCGGAATATGTACGCTATTTTCTCCACCAACACACgtaagtttgt ... cgatttgcagAATTCAGCTTGGGCAACCAGCTACTGTGAAAGTTGCAGCCAACTTAATTAG
EST: gi|55410106|gb|CV722482.1|CV722482
EST:     GACACACAAGTCATTTCGGAATATGTACGCTATTTTCTCCACCAACACAC                         AATTCAGCTTGGGCAACCAGCTACTGTGAAAGTTGCAGCCAACTTAATTAG
genomic: GACACACAAGTCATTTCGGAATATGTACGCTATTTTCTCCACCAACACACgtaagtttgt ... cgatttgcagAATTCAGCTTGGGCAACCAGCTACTGTGAAAGTTGCAGCCAACTTAATTAG
EST: gi|29630183|gb|CB635192.1|CB635192
EST:     ACACACAAGTCATTTCGGATTATGTACGCCTATTTTCTCCACCAACACAC                         AATTCAGCTTGGGCAACCAGCTACTGTGAAAGTTGCAGCCAACTTAATTAG
genomic: ACACACAAGTCATTTCGGAATATGTACG-CTATTTTCTCCACCAACACACgtaagtttgt ... cgatttgcagAATTCAGCTTGGGCAACCAGCTACTGTGAAAGTTGCAGCCAACTTAATTAG

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), 75 (downstream exon)
Score: 26

GCTGCCGACACACAAGTCATTTCGGAATATGTACGCTATTTTCTCCACCAACACACgtaagtttgt ... cgatttgcagAATTCAGCTTGGGCAACCAGCTACTGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtgaatatttgctgtgcaagatagcccatgctaaattttccctcgatttgcagAATTCAGCTTGGGCAACCAGCTACTGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAG
                              tgctaaa  putative branch site (score: 26)
                                     ttttccctcgattt  CT-rich tract
                                 taaatttt  TA-rich tract