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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgttgtgttcattttgtttcgtttgtaatgtttgtgctgcatgctgtatgatggcgtatgtttgaattactgatgcttgattgttaattctatttcatagACGCTGGATTATGTGAAGCAATGCGAAGCAGATATTGTCAACATGTCATTGATGCAACGCCCATCCTTCGCGAATGAACCAACAGCGGATAAGCTTTACA

Basic information

species Oryza sativa
transcript LOC_Os07g06820.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G035098_T01 (Zea mays), 3'ss of exon 12
cgttgtgttcatttt-gtttcgtt--tgtaatgtttgtgctgcatgctgtatgatggcgtatgtttgaattactgatgcttgattgttaattctatttcatagACGCTGGATTATGTGAAGCAATGCGAAGCAGATATTGTCAACATGTCATTGATGCAACGCCCATCCTTCGCGAATGAACCAACAGCGGATAAGCTTTACA
  ||     ||   | |||||     ||     ||| |  ||     | |||  || |  || |    | || || |  |  | || |  |  |     ||||||| |||| || ||||||||||| || ||||||||||||||||||||| | ||||||||  ||||||  |   |||| ||||| || |||||||||||  
--tttctcccacactagtttcaacgatgcgtattttattttgttctttttattgtgtcaaatatcatgagtaatgctaatgtaatgatt-tcttggcatatagACGTTGGACTACGTGAAGCAATGTGAGGCAGATATTGTCAACATGTCAATAATGCAACGTTCATCCTCTGGCTATGAGCCAACCGCAGATAAGCTTTATG

upper sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G120329_T01 (Zea mays), 3'ss of exon 10
cgttgtgttcatttt-gtttcgtt--tgtaatgtttgtgctgcatgctgtatgatggcgtatgtttgaattactgatgcttgattgttaattctatttcatagACGCTGGATTATGTGAAGCAATGCGAAGCAGATATTGTCAACATGTCATTGATGCAACGCCCATCCTTCGCGAATGAACCAACAGCGGATAAGCTTTACA
  ||     ||   | |||||     ||     ||| |  ||     | |||  |  |  ||      || | | || ||    |  | |||   || |||||||| |||| || ||||||||||| || ||||||||||||||||||||| | ||||||||  ||||||  |   |||| ||||| || |||||||||||  
gatttctcccacactagtttcaacgatgcgtattttattttgttctttttattgtatcaaatacc---atgagtaatactaatgtaatgatttctttgcatagACGTTGGACTACGTGAAGCAATGTGAGGCAGATATTGTCAACATGTCAATAATGCAACGTTCATCCTCTGGCTATGAGCCAACCGCAGATAAGCTTTATG
















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|428791|gb|D24947.1|D24947
EST:     GAGATATGGTTGCAAACGACGATGAAATCACCCCAACAGTCTTGGTTCAG                         ACGCTGGATTATGTGAAGCAATGCGAAG-AGANTATTGTCAACATGTCATT
genomic: GAGATATGGTTGCAAACGACGATGAAATCACCCCAACAGTCTTGGTTCAGgtaagataat ... tatttcatagACGCTGGATTATGTGAAGCAATGCGAAGCAGA-TATTGTCAACATGTCATT




















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: 71 (upstream exon), 72 (downstream exon)
Score: 32

ATTCAGCAAAAGATGTTGGAAAATGGAGATATGGTTGCAAACGACGATGAAATCACCCCAACAGTCTTGGTTCAGgtaagataat ... tatttcatagACGCTGGATTATGTGAAGCAATGCGAAGCAGATATTGTCAACATGTCATTGATGCAACGCCCATCCTTCGCGAATGAACCAACAGCGGATAAGCTTTACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatgatggcgtatgtttgaattactgatgcttgattgttaattctatttcatagACGCTGGATTATGTGAAGCAATGCGAAGCAGATATTGTCAACATGTCATTGATGCAACGCCCATCCTTCGCGAATGAACCAACAGCGGATAAGCTTTACA
                                          ttctatttc  CT-rich tract
                                  attgttaattctattt  TA-rich tract