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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagttatttacagtgcgtacattttttaccagaagacaatgaatcccactgcctcaacttgatttctgtgctttttagGTTAATCAAATTAGAGATTCTTTGGCAGTTATGGGCAACAACAGCACTGCTTTTAGCCTGCCCCAG

Basic information

species Oryza sativa
transcript LOC_Os03g58240.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g58240.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G305254_T04 (Zea mays), 3'ss of exon 10
gtacagttatt--------tacagtgc-gtacatttttta-ccagaagacaatgaatccca---ctgcctcaa-cttgatttctgtgc-tttttagGTTAATCAAATTAGAGATTCTTTGGCAGTTATGGGCAACAACAGCACTGCTTTTAGCCTGCCCCAG
||||||||  |        || ||| |  |||| |||||| ||| || |  ||   | | |   | |   |||  ||  ||||| ||  ||||||||| ||||||||  |||||||||||||||||||||||||| ||||||||||||||||| ||||||||
gtacagtttgtgtatgaaatatagtactatacaatttttaaccaaaaaatgatagctacaagctcagttacaaattttctttctatgtgtttttagGTCAATCAAATACGAGATTCTTTGGCAGTTATGGGCAACCACAGCACTGCTTTTAGCTTGCCCCAG

upper sequence: LOC_Os03g58240.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G321413_T01 (Zea mays), 3'ss of exon 4
---------gtacagttatttacagtgcgtacattttttaccagaagacaatgaatccca----ctgcctcaacttgatttctgtgctttttagGTTAATCAAATTAGAGATTCTTTGGCAGTTATGGGCAACAACAGCACTGCTTTTAGCCTGCCCCAG
         ||  |   | |         |||| |||| | |  ||     | | | | |    | |   ||| ||  |||||||  ||||||||| ||||||||  ||||||| |||||||||||||| ||||||||||||||||||||| |||| |||
gtgtagtttgtgtatgaaatctagtaatatacacttttgaaccaaaagttgttagttctaagctcagttacaaattc-tttctgta-tttttagGTCAATCAAATACGAGATTCGTTGGCAGTTATGGGGAACAACAGCACTGCTTTTAGCTTGCCTCAG

upper sequence: LOC_Os03g58240.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G019361_T03 (Zea mays), 3'ss of exon 10
-------------gtacagtt-atttacagtg-cgtacattttttaccagaagacaatgaatccca----ctgcctcaacttgatttctgtgctttttagGTTAATCAAATTAGAGATTCTTTGGCAGTTATGGGCAACAACAGCACTGCTTTTAGCCTGCCCCAG
              |  | || |  |  |||    |||| |||| | |  ||     | | | | |    |||   ||| ||  |||||||  ||||||||| ||||||||  ||||||| |||||||||||||| ||||||||||||||||||||| |||| |||
gtgtagtttgtgtatgaaattgaaatctagtaatatacacttttgaaccaaaagttgttagttctaagctctgttacaaattc-tttctgta-tttttagGTCAATCAAATACGAGATTCGTTGGCAGTTATGGGGAACAACAGCACTGCTTTTAGCTTGCCTCAG

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|29636549|gb|CB641558.1|CB641558
EST:     AAGTGGGGACAAATATATTGATGAG                         GTTAATCAAATTACAGATTCTTTGGCAGTTATGGGCAACAACAGCACTGCT
genomic: AAGTGGGGACAAATATATTGATGAGgtacagttat ... tgctttttagGTTAATCAAATTAGAGATTCTTTGGCAGTTATGGGCAACAACAGCACTGCT
EST: gi|29629845|gb|CB634854.1|CB634854
EST:     AAGTGGGGACAAATATATTGATGAG                         GTTAATCAAATTAGAGATTCTTTGGCAGTTATGGGCAACAACAGCACTGCT
genomic: AAGTGGGGACAAATATATTGATGAGgtacagttat ... tgctttttagGTTAATCAAATTAGAGATTCTTTGGCAGTTATGGGCAACAACAGCACTGCT
EST: gi|29666666|gb|CB662941.1|CB662941
EST:     AAGTGGGGACAAATATATTGATGAG                         GTTAATCAAATTAGAGATTCTTTGGCAGTTATGGGCAACAACAGCACTGCT
genomic: AAGTGGGGACAAATATATTGATGAGgtacagttat ... tgctttttagGTTAATCAAATTAGAGATTCTTTGGCAGTTATGGGCAACAACAGCACTGCT
EST: gi|29629844|gb|CB634853.1|CB634853
EST:     AAGTGGGGACAAATATATTGATGAG                         GTTAATCAAATTAGAGATTCTTTGGCAGTTATGGGCAACAACAGCACTGCT
genomic: AAGTGGGGACAAATATATTGATGAGgtacagttat ... tgctttttagGTTAATCAAATTAGAGATTCTTTGGCAGTTATGGGCAACAACAGCACTGCT

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: 20 (upstream exon), 66 (downstream exon)
Score: 9

GGGACAAATATATTGATGAGgtacagttat ... tgctttttagGTTAATCAAATTAGAGATTCTTTGGCAGTTATGGGCAACAACAGCACTGCTTTTAGCCTGCCCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttaccagaagacaatgaatcccactgcctcaacttgatttctgtgctttttagGTTAATCAAATTAGAGATTCTTTGGCAGTTATGGGCAACAACAGCACTGCTTTTAGCCTGCCCCAG
                                 acttgat  putative branch site (score: 9)
                                       tttctgtgcttttt  CT-rich tract
                                                ttttta  TA-rich tract