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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatggagcagccctattcttttcctctttcacagctcatattgtctcgagaacagttactgatagcacacgatgctgcagAACCTTGAGGCAAAGAAGATAAACGATGAAAAGAAAGCAGCACTTGCAGCCCAATTTGCAGCAGAGGCTACACTTCGAAGGGTTCATGCAGCACAGAAGG

Basic information

species Oryza sativa
transcript LOC_Os12g44340.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g44340.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 3
gtaatggagcagccctattcttttcctctttcacagctcatatt----gtctcgagaacagttactgatagcacacgatgct----gcagAACCTTGAGGCAAAGAAGATAAACGATGAAAAGAAAGCAGCACTTGCAGCCCAATTTGCAGCAGAGGCTACACTTCGAAGGGTTCATGCAGCACAGAAGG
||||||    |  ||| |      | |       ||   || |     ||  || |    |||  |  ||  ||  |||  |    |||||| |||||   |||||| || || ||||||||||||||| |  | ||||| || |||||||| || || || ||||||||||| ||||| || |||||||
gtaatgcttgaagcctctatcaagcttagcgaggagtaaatttctgaggttacgtggtgtgtttttactaa-actggatatttcttgcagAATCTTGAAATAAAGAAAATTAATGATGAAAAGAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG

upper sequence: LOC_Os12g44340.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 3
gtaatggagcagccctattcttttcctctttcacagctcatattgtctcg------agaacagttactgatagcacacgatgctg-cagAACCTTGAGGCAAAGAAGATAAACGATGAAAAGAAAGCAGCACTTGCAGCCCAATTTGCAGCAGAGGCTACACTTCGAAGGGTTCATGCAGCACAGAAGG
||| || |  |  ||| |        |     | || |||| ||  |  |       | |   || |||| | |  |   | ||| ||||| |||||    || || || |||||||||||||||||| || | ||||| || |||||||| || || || ||| ||||||| ||||| || ||||| |
gtattgcatgaagcctctatcaactttaggaaatag-tcattttcccaggttaggtggtatgttttctga-atcgaatatttctggcagAATCTTGAAATTAAAAAAATCAACGATGAAAAGAAAGCATCAATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTAGAAGGGTCCATGCTGCCCAGAAAG

upper sequence: LOC_Os12g44340.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 3
gtaatggagcagccctattcttttcctctttcacagctcatat-tgtctcgagaacagttac-tgatagcacacgatgct-gcagAACCTTGAGGCAAAGAAGATAAACGATGAAAAGAAAGCAGCACTTGCAGCCCAATTTGCAGCAGAGGCTACACTTCGAAGGGTTCATGCAGCACAGAAGG
||| || |  |  ||  | | |||    ||  |    |  | | ||| |      |||||   |  || ||   | |  | |||||| || |||   ||||| || || ||||||||||| ||  |  | || || |||||||||||||| || || ||| ||||||||||||| || |||||||
gtattgcatgaaacccttccatttttctttataagttttgtgtgtgtgtgttttgcagttttgtcctaacaattgttttttgcagAATCTCGAGATCAAGAAAATCAATGATGAAAAGAAGGCCTCCATGGCTGCTCAATTTGCAGCAGAAGCCACTCTTAGAAGGGTTCATGCTGCGCAGAAGG

upper sequence: LOC_Os12g44340.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S136_188V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------gtaatggagcagccctattcttttcctctttcacagctcatattgtctcgagaacagttactgata----gcacacgatgctgcagAACCTTGAGGCAAAGAAGATAAACGATGAAAAGAAAGCAGCACTTGCAGCCCAATTTGCAGCAGAGGCTACACTTCGAAGGGTTCATGCAGCACAGAAGG
                ||  |       |    ||  |||   ||   | |  | |  |||| ||      | |||    ||    |     | |  |||||||||||||    |||||| | || || || ||||||||||| || || ||||| |||||||| ||||| || || |||||||| |||||||| ||||| |
gattctcgcattttttgtcttatgtggacgtcgtttctttgtgcta--aaattttaagttgtttctttgttacttatcagtatttggggggtgtttttgcagAACCTTGAATTGAAGAAGCTCAATGACGAGAAGAAAGCAGCTCTGGCCGCCCAGTTTGCAGCGGAGGCAACTCTGCGAAGGGTGCATGCAGCTCAGAAAG

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|88412909|gb|CI578760.1|CI578760
EST:     CAAAGGTGGATGGGAAGCTGAAGCTTACAGAGTCTCTCCTCGAAAGCAAG                         AACCTTGAGGCAAAGAAGATAAACGATGAAAACAAAGCAGCACTTGCAGC
genomic: CAAAGGTGGATGGGAAGCTGAAGCTTACAGAGTCTCTCCTCGAAAGCAAGgtaatggagc ... gatgctgcagAACCTTGAGGCAAAGAAGATAAACGATGAAAAGAAAGCAGCACTTGCAGC




















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: 66 (upstream exon), 51 (downstream exon)
Score: 15

CTTACGGAAGAATTGACAAAGGTGGATGGGAAGCTGAAGCTTACAGAGTCTCTCCTCGAAAGCAAGgtaatggagc ... gatgctgcagAACCTTGAGGCAAAGAAGATAAACGATGAAAAGAAAGCAGCACTTGCAGCCCAATTTGCAGCAGAGGCTACACTTCGAAGGGTTCATGCAGCACAGAAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttcacagctcatattgtctcgagaacagttactgatagcacacgatgctgcagAACCTTGAGGCAAAGAAGATAAACGATGAAAAGAAAGCAGCACTTGCAGCCCAATTTGCAGCAGAGGCTACACTTCGAAGGGTTCATGCAGCACAGAAGG
                               tactgat  putative branch site (score: 15)
          tcatatt  TA-rich tract