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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgtccccttgaagcgaataggaagaagttgaatgaactcttcatatatattgttctactagttactggaaacatttgatgtgcaagacagttcatgctaaattttccctccattttcagAATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAG

Basic information

species Oryza sativa
transcript LOC_Os02g53060.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g53060.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G152775_T04 (Zea mays), 3'ss of exon 3
gtaagttgtccccttgaagcgaataggaagaagttgaatgaactcttcatatat-attgttctactagttactggaaacat--ttgatgtgcaagac--agttcatgctaaattttccctccattttcagAATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAG
||||||| | | ||| |  |  | |     |  || |        || ||| || | | | ||    | ||||  | |  |  |||||    | ||   || | |||||||| || ||| |  | | |||||| |||||||| || ||||||||||| ||||||||||||||||| ||||||||| | |||||||||||||||
gtaagtt-tgctcttcatac--acaacctaacattaatctcttgtttgataaatcaatatactgaatgatacttaagatctctttgataaatatgatggagctgatgctaaaattaccccct-tgtgcagAATCCAGCTTGGACAACCAGCTACCGTTAAAGTTGCAGCCAACTTGATTAGGTTGCTAGCTTATCAGAACAAG

upper sequence: LOC_Os02g53060.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G374881_T02 (Zea mays), 3'ss of exon 3
---------------------------------gtaagttgtccccttga--agcgaataggaagaa-gttgaatgaactcttcat-----atatattgttctactagttactggaaacatttgatgtgcaagacagttcatgctaaattttccctccattttcagAATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAG
                                  |   |  | |  ||||  |   ||||    ||| | |   | || |||   |     ||||  || | ||| | ||||| || | || |||  ||| ||  |||| |||||||| || |||||| | | |||||| |||||||| || |||||||| || ||||||||||| ||||| ||||||||| | ||||||||||| |||
gtaagtttgttcttcatacacaacttaacagtattcgatctttcatttgatgaataaatatactgaatgatacttaaattctctttgaacaatatgatggtatac-aattacttgagatatctgacatgcgaggtagttgatgctaaagttaccctcc-tatgcagAATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAGGTTGCTAGCTTATCAGAATAAG

upper sequence: LOC_Os02g53060.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G152775_T02 (Zea mays), 3'ss of exon 3
gtaagttgtccccttgaagcgaataggaagaagttgaatgaactcttcatatat-attgttctactagttactggaaacat--ttgatgtgcaagac--agttcatgctaaattttccctccattttcagAATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAG---------------------------
||||||| | | ||| |  |  | |     |  || |        || ||| || | | | ||    | ||||  | |  |  |||||    | ||   || | |||||||| || ||| |  | | |||||| |||||||| || ||||||||||| ||||||||||||||||| ||||||||| | |||||||||||||||                           
gtaagtt-tgctcttcatac--acaacctaacattaatctcttgtttgataaatcaatatactgaatgatacttaagatctctttgataaatatgatggagctgatgctaaaattaccccct-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|88330848|gb|CI636860.1|CI636860
EST:     GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACAC                         AATTCAGCTTGGGCAGC
genomic: GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACACgtaagttgtc ... ccattttcagAATTCAGCTTGGGCAGC
EST: gi|88421759|gb|CI621403.1|CI621403
EST:     GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACAC                         AATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG
genomic: GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACACgtaagttgtc ... ccattttcagAATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG
EST: gi|86496862|gb|CI139495.1|CI139495
EST:     TTATGTACGCTATTTTCTCCACCAACACAC                         AATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG
genomic: TTATGTACGCTATTTTCTCCACCAACACACgtaagttgtc ... ccattttcagAATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG
EST: gi|218499779|gb|FG945547.1|FG945547
EST:     GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACAC                         AATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG
genomic: GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACACgtaagttgtc ... ccattttcagAATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG
EST: gi|8527814|gb|AU092629.1|AU092629
EST:     GATACACAAGTAATTNCCGATTATGTACGCTATTTTCTCCACCAACACAC                         AATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG
genomic: GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACACgtaagttgtc ... ccattttcagAATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG
EST: gi|88573296|gb|CI664867.1|CI664867
EST:     GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACAC                         AATTCAGCTTGGGCAGCCAGCTACCGTGAAAGT
genomic: GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACACgtaagttgtc ... ccattttcagAATTCAGCTTGGGCAGCCAGCTACCGTGAAAGT
EST: gi|58588610|gb|CF986918.1|CF986918
EST:     GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACAC                         AATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG
genomic: GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACACgtaagttgtc ... ccattttcagAATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG
EST: gi|88358083|gb|CI605008.1|CI605008
EST:     GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACAC                         AATTCAGCTTGGGC
genomic: GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACACgtaagttgtc ... ccattttcagAATTCAGCTTGGGC
EST: gi|58692319|gb|CK081006.1|CK081006
EST:     GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACAC                         AATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG
genomic: GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACACgtaagttgtc ... ccattttcagAATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG
EST: gi|25799545|gb|CA755506.1|CA755506
EST:     GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACAC                         AATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG
genomic: GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACACgtaagttgtc ... ccattttcagAATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG
EST: gi|88309396|gb|CI655764.1|CI655764
EST:     GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACAC                         AATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG
genomic: GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACACgtaagttgtc ... ccattttcagAATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG
EST: gi|38477245|gb|CF961378.1|CF961378
EST:     GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACAC                         AATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG
genomic: GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACACgtaagttgtc ... ccattttcagAATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG
EST: gi|218498714|gb|FG963991.1|FG963991
EST:     GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACAC                         AATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG
genomic: GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACACgtaagttgtc ... ccattttcagAATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG
EST: gi|88390264|gb|CI605717.1|CI605717
EST:     GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAAAACAC                         AATTCACCTTGGGCAGCCAGCTACCGTGAAAGTTGC
genomic: GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACACgtaagttgtc ... ccattttcagAATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGC
EST: gi|218498950|gb|FG948071.1|FG948071
EST:     GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACAC                         AATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG
genomic: GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACACgtaagttgtc ... ccattttcagAATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG
EST: gi|38472737|gb|CF956869.1|CF956869
EST:     GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACAC                         AATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG
genomic: GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACACgtaagttgtc ... ccattttcagAATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG
EST: gi|33803228|gb|CF327486.1|CF327486
EST:     GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACAC                         AATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG
genomic: GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACACgtaagttgtc ... ccattttcagAATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG
EST: gi|88302060|gb|CI667906.1|CI667906
EST:     GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACAC                         AATTCAGCTTGGGCAGCCA
genomic: GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACACgtaagttgtc ... ccattttcagAATTCAGCTTGGGCAGCCA
EST: gi|218504275|gb|FG947024.1|FG947024
EST:     GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACAC                         AATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG
genomic: GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACACgtaagttgtc ... ccattttcagAATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG
EST: gi|13165514|gb|AU174311.1|AU174311
EST:     GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACAC                         AATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAG
genomic: GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACACgtaagttgtc ... ccattttcagAATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAG
EST: gi|88342591|gb|CI655593.1|CI655593
EST:     GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACAC                         AATTCAGCTTGGGCAGCCAGCTACCGTGAA
genomic: GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACACgtaagttgtc ... ccattttcagAATTCAGCTTGGGCAGCCAGCTACCGTGAA
EST: gi|218486985|gb|FG965418.1|FG965418
EST:     GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACAC                         AATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG
genomic: GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACACgtaagttgtc ... ccattttcagAATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG
EST: gi|14191702|gb|AU183913.1|AU183913
EST:     GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACAC                         AATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG
genomic: GATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACACgtaagttgtc ... ccattttcagAATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAG

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: 74 (upstream exon), 70 (downstream exon)
Score: 56

GCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACACgtaagttgtc ... ccattttcagAATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggaaacatttgatgtgcaagacagttcatgctaaattttccctccattttcagAATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAG
                              tgctaaa  putative branch site (score: 56)
                                     ttttccctccattttc  CT-rich tract
                                 taaatttt  TA-rich tract