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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcttttttgaggaacaatttgttcttccaaccaaaattaattgatgaagcctcctattaaatagtttagggttacctcctaccgattaacttatttttggttctggtcttgttgtgtagGGAGCTCTTAATATCCTTCAGGAAGGCCACTGGGCAAAAGCCATTGAGAATAATTTTCTACAG

Basic information

species Oryza sativa
transcript LOC_Os06g39640.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 15
lower sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 14
gtcttttttgaggaacaatttgttcttccaaccaaaattaattgatgaagcctcctattaaatagtttagggttacctcctaccgattaacttatttttggttctggtcttgttgtgtagGGAGCTCTTAATATCCTTCAGGAAGGCCACTGGGCAAAAGCCATTGAGAATAATTTTCTACAG
|| ||| |  | || |||| || | | |     ||    |||  || |       || |||| |  ||  ||||   |        | ||||||||||  ||  || | || | ||| |||||||| ||||||||||||||||||||||||||||| ||||||||||||||||| ||||||||
gtttttatctatgagcaatgtgatatcctg---aagtgcaatgcataatttaatatagtaaaaatatt--ggttgatt--------tgaacttattttctgtgatg-ttttctcgtgcagGGAGCTGTTAATATCCTTCAGGAAGGCCACTGGGCAGAAGCCATTGAGAATAATATTCTACAG

upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 15
gtcttttttgaggaacaatttgttcttccaaccaaaattaattgatgaagcctcctattaaatagtttagggttacctcctaccgattaacttatttttggttctggtcttgttgtgtagGGAGCTCTTAATATCCTTCAGGAAGGCCACTGGGCAAAAGCCATTGAGAATAATTTTCTACAG
|| ||| |  | || |||| ||   | |     ||    |||  |  |      |||||||| |  ||  ||||   |        | ||||||||||  ||  ||   |||||||||||||||||||||||||||||||||||||||||||| || ||||||||||||||||| ||||||||
gtttttatctacgagcaatgtgaaatcctg---aagtgcaatatacaatttaatctattaaaaatatt--ggttgatt--------tgaacttattttctgtgatg--tttgttgtgtagGGAGCTCTTAATATCCTTCAGGAAGGCCACTGGACAGAAGCCATTGAGAATAATATTCTACAG

upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 15
gtcttttttgaggaacaatttgttcttccaaccaaaattaattgatgaa-gcctcctattaaatagtttagggttacctcctaccgattaacttatttttggttctggtcttgttgtgtagGGAGCTCTTAATATCCTTCAGGAAGGCCACTGGGCAAAAGCCATTGAGAATAATTTTCTACAG
                       | |   || || |||   ||  | |     |  ||||  || |||        | || | |  | ||  | ||||     | ||   |     || |||||||| ||| |||| || | |||||| ||||| ||||| |||||||||||||| || |||||
-----------------gaccactatggaaatcataatggcttttttagcatttattatttgat-gttaccaacgtcttcattcttactagttcatttactaatttg---tgaaactgcagGGAGCTTTTACTATCATTTAAGAAGGCAACTGGACAAAAACCATTGAGAATAATCTTTTACAG

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|58613128|gb|CK040840.1|CK040840
EST:     AAGACATGGCATGATCCTCAAAGAGGCACCGTAACAGGAGGCATGATCAG                         GGAGCTCTTAATATCCT
genomic: AAGACATGGCATGATCCTCAAAGAGGCACCGTAACAGGAGGCATGATCAGgtcttttttg ... tgttgtgtagGGAGCTCTTAATATCCT




















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: 60 (upstream exon), 63 (downstream exon)
Score: 10

GATTGGTGTGTGCTCAGGCTCATCGGCAAGAGCTCATTCAAGATCTTTACAAGACATGGCATGATCCTCAAAGAGGCACCGTAACAGGAGGCATGATCAGgtcttttttg ... tgttgtgtagGGAGCTCTTAATATCCTTCAGGAAGGCCACTGGGCAAAAGCCATTGAGAATAATTTTCTACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagggttacctcctaccgattaacttatttttggttctggtcttgttgtgtagGGAGCTCTTAATATCCTTCAGGAAGGCCACTGGGCAAAAGCCATTGAGAATAATTTTCTACAG
                   gattaac  putative branch site (score: 10)
                                          tcttgtt  putative PPT
                    attaacttattttt  TA-rich tract