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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgcttgatcattgtatcagatggtgttatttcctttgttgattttttagtctgttctgaaacatttagtgtctctcattttcagCATACACCAAAGCTCTTGAGGATGCTTTAGCTGTCCTTGACAAAATTGCAATGCATGTTGACGTGAATGACC

Basic information

species Oryza sativa
transcript LOC_Os06g34690.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G069765_T05 (Zea mays), 3'ss of exon 6
---gtattgcttgatcatt-gtatcagatggtgttatttcctttgttgattttttagtctg---ttctgaaacatttagtgtctctcattttcagCATACACCAAAGCTCTTGAGGATGCTTTAGCTGTCCTTGACAAAATTGCAATGCATGTTGACGTGAATGACC
     ||| ||| ||  |  |||    |   |  ||      |   || |||||   |||    ||||||||| | || | | ||| || ||||||||| |||||||| ||||| |||||| | ||||| ||||||||||||||||||  |||||| |||||||| |
gtaagattcctttattctcagtactgcactttactagggtaatacctgttttttatatcttaacttctgaaacttgta-tttttcttatcttcagCATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATC

upper sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G175510_T01 (Zea mays), 3'ss of exon 6
-----------gtattgcttg-atcattgtatcagatggtgttattt--cctttgttgattttttagtctgttctgaaacatttagtgtctctcattttcagCATACACCAAAGCTCTTGAGGATGCTTTAGCTGTCCTTGACAAAATTGCAATGCATGTTGACGTGAATGACC
            ||||    | |     || |   | |||  || ||  | ||| ||  |  | |  | | ||||| |||  |||   | |||||| |||||||||||||||||| ||||| |||||| | ||||| |||||||||||||||||||  ||||| |||||||| |
gtaagattcctttattctcagtactgcagtttactagggtaatacttgacttttattcttgatctcttgtcttctggaac--ttatattttctcatcttcagCATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATC

upper sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G069765_T03 (Zea mays), 3'ss of exon 6
---gtattgcttgatcatt-gtatcagatggtgttatttcctttgttgattttttagtctg---ttctgaaacatttagtgtctctcattttcagCATACACCAAAGCTCTTGAGGATGCTTTAGCTGTCCTTGACAAAATTGCAATGCATGTTGACGTGAATGACC----------------------------
     ||| ||| ||  |  |||    |   |  ||      |   || |||||   |||    ||||||||| | || | | ||| || ||||||||| |||||||| ||||| |||||| | ||||| ||||||||||||||||||  |||||| |||||||| |                            
gtaagattcctttattctcagtactgcactttactagggtaatacctgttttttatatcttaacttctgaaacttgta-tttttcttatcttcagCATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATCGTAAGTTTACAGTGAACATATATTTTGT

upper sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA16G33380.1 (Glycine max), 3'ss of exon 7
gtattgcttgatcattgtatcagatggt-gttatttcctttgttgattttttagtctgttctgaaacatttagtg-------tctctcattttcagCATACACCAAAGCTCTTGAGGATGCTTTAGCTGTCCTTGACAAAATTGCAATGCATGTTGACGTGAATGACC
   |  ||| ||  |  || | | |  |   ||||||  |  |  ||  | ||   |  | |  |  | | | ||       | | | || | |||||||  |||||||| | ||||||||| | ||||| ||||||||||||||||||| | |  | |   | || |
--gtaacttaatagtgttaactgttaatcagtatttctctcctacatggtataaaattgtttatattaatgaatgctacaattttgtaatatgcagCATATGCCAAAGCTTTGGAGGATGCTATTGCTGTTCTTGACAAAATTGCAATGCCTATCAATGCTCAGGATC

upper sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA09G28650.1 (Glycine max), 3'ss of exon 7
gtattgcttgatcattgta---tcagatggtgttatttcctttgttgatttttta--gtctgttctga--aacatttagtgtctctcattttcagCATACACCAAAGCTCTTGAGGATGCTTTAGCTGTCCTTGACAAAATTGCAATGCATGTTGACGTGAATGACC
   |  ||| ||  |  ||   | |    |||||  |  | |    | | |   |  || | |  | |  ||   |     | | | || | ||||||| | ||||||| | ||||||||| | ||||||||||||||||||||||||| | |||| |   | || |
--gtaacttaatagtgttactgttaatcagtgtttctctcctacaaggtataaaattgtttatattaatgaatgctacaattttgtaatctgcagCATATAACAAAGCTTTGGAGGATGCTATTGCTGTCCTTGACAAAATTGCAATGCCTATTGATGCTCAGGATC

upper sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv07s0130g00410.t01 (Vitis vinifera), 3'ss of exon 6
gtattgcttgatcattgtatcagatggtgttatttcctttgttgattttttagtctgttctgaa-acatttagtgtctctcattttcagCATACACCAAAGCTCTTGAGGATGCTTTAGCTGTCCTTGACAAAATTGCAATGCATGTTGACGTGAATGACC
|||||   |    ||||  |  ||      | | |   ||||| | ||     ||| || |||  |     | | | | |  | |  ||||||||  |||||||| ||||||||| | ||||| ||||||||||||||||||    | || ||||| ||||
gtatt--ctagaaattgattgtgacacgactctctaagttgttaaattaaacttctcttttgattatggaaactttatttgttgtgtagCATACAATAAAGCTCTGGAGGATGCTATTGCTGTGCTTGACAAAATTGCAATGTCCATAGATGTGAAGGACC

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|29661337|gb|CB657612.1|CB657612
EST:     TGCAGAAGCATTCATTGATAAGCACTACCACCCAACTGTTATTTGCCGAG                         CATACACCAAAGCTCTTGAGGATGCTTTAGCTGTCCTTGACAAAATTGCAA
genomic: TGCAGAAGCATTCATTGATAAGCACTACCACCCAACTGTTATTTGCCGAGgtattgcttg ... tcattttcagCATACACCAAAGCTCTTGAGGATGCTTTAGCTGTCCTTGACAAAATTGCAA
EST: gi|58665405|gb|CK054091.1|CK054091
EST:     TGCAGAAGCATTCATTGATAAGCACTACCACCCAACTGTTATTTGCCGAG                         CATACACCAAAGCTCTTGAGGATGCTTTAGCTGTCCTTGACAAAATTGCAA
genomic: TGCAGAAGCATTCATTGATAAGCACTACCACCCAACTGTTATTTGCCGAGgtattgcttg ... tcattttcagCATACACCAAAGCTCTTGAGGATGCTTTAGCTGTCCTTGACAAAATTGCAA
EST: gi|58672695|gb|CK061381.1|CK061381
EST:     TGCAGAAGCATTCATTGATAAGCACTACCACCCAACTGTTATTTGCCGAG                         CATACACCAAAGCTCTTGAGGATGCTTTAGCTGTCCTTGACAAAATTGCAA
genomic: TGCAGAAGCATTCATTGATAAGCACTACCACCCAACTGTTATTTGCCGAGgtattgcttg ... tcattttcagCATACACCAAAGCTCTTGAGGATGCTTTAGCTGTCCTTGACAAAATTGCAA

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: 69 (upstream exon), 72 (downstream exon)
Score: 20

CTGGTGAGATGCTCCATGTTGCAGAAGCATTCATTGATAAGCACTACCACCCAACTGTTATTTGCCGAGgtattgcttg ... tcattttcagCATACACCAAAGCTCTTGAGGATGCTTTAGCTGTCCTTGACAAAATTGCAATGCATGTTGACGTGAATGACC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctttgttgattttttagtctgttctgaaacatttagtgtctctcattttcagCATACACCAAAGCTCTTGAGGATGCTTTAGCTGTCCTTGACAAAATTGCAATGCATGTTGACGTGAATGACC
      tgttgat  putative branch site (score: 20)
                                       tgtctctcattttc  putative PPT
     ttgttgatttttta  TA-rich tract