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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCGgtatggaccagttcaccattttttggttatttatatgccacatcatatgcattttcacactcttcttttttgcacgaattgaaatag

Basic information

species Oryza sativa
transcript LOC_Os01g06600.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g06600.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM5G862219_T01 (Zea mays), 5'ss of exon 1
-----------------------GTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCGgtatggaccagttcaccattttttggttatttatatgccacatcatatgcattttcacactcttcttttttgcacgaattgaaatag-------------------------
                       || || || ||||||||  | |||||||||||||||||| |||| |||||||||||||| || ||  | ||||| ||||| |     |  |   |  || ||    ||  |    ||||    || | ||  | | | | | || |||   |   |  |||                            
CTATTCTCACTGTGTGCAAGCAGGTGCTCGCCATTTCACGCATTATGGTGGCATGGCAACCGGTTGGCATATCAATGGGGGTCTTCGACATGTGCCACCGgtacg---tggcgccatacgttctgacacttctttcatcacaggcaatcctttcaccccccccttttcttttgtcatgtaaaaaacaaaaaaacaaaaaccgatcgaaacag

upper sequence: LOC_Os01g06600.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM5G862219_T02 (Zea mays), 5'ss of exon 10
GTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCGgtatggaccagttcaccattttttggttatttatatgccacatcatatgcattttcacactcttcttttttgcacgaattgaaatag-------------------------
|| || || ||||||||  | |||||||||||||||||| |||| |||||||||||||| || ||  | ||||| ||||| |     |  |   |  || ||    ||  |    ||||    || | ||  | | | | | || |||   |   |  |||                            
GTGCTCGCCATTTCACGCATTATGGTGGCATGGCAACCGGTTGGCATATCAATGGGGGTCTTCGACATGTGCCACCGgtacg---tggcgccatacgttctgacacttctttcatcacaggcaatcctttcaccccccccttttcttttgtcatgtaaaaaacaaaaaaacaaaaaccgatcgaaacag

upper sequence: LOC_Os01g06600.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA03G07540.1 (Glycine max), 5'ss of exon 10
GTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCGgtatggaccagttcaccattttttggttatttatatgccacatcatatgcattttcacactcttcttttttgcacgaattgaaatag
|| |||||| ||||||| || ||||| || |||||||| ||||||||||| |||||  | |  ||| | || ||  ||||| |   | || |  || || |  | | ||| ||    ||    |   ||||    ||   | ||  |     |           
GTACTTGCTGTTTCACGCGTAATGGTTGCTTGGCAACCCATTGGTATATCGATGGGCATCTACGATATGTGTCACAGgtattgcttaatt-agaatgttatcat-acttacat-tttcactgcaaatatttctgaacctgtattgatcaatag-----------

upper sequence: LOC_Os01g06600.2 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv08s0105g00460.t01 (Vitis vinifera), 5'ss of exon 10
GTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCGgtatggac-cagttcaccattttttggttatt-tatatgccacatcatatgcatttt---cacactcttc--ttttttgcac---gaattgaaatag------
|| |||||| |||||||||||||||| || |||||||| || || || |||||||| |  | |||| | || ||  |||||  |     |  |  || | |  | | || | | |  |  ||||     |||||     ||  ||||  | | |||||    || || || | |      
GTGCTTGCTGTTTCACGTGTCATGGTTGCCTGGCAACCTATAGGCATTTCAATGGGAGCCTATGATATGTGTCACAGgtattaatgtgataaatgatatgtatgctgttctctttatctgatcaccactattttgtcttcagccttcagtatgttgcattctgattttaagtggttgaag

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|29658082|gb|CB654357.1|CB654357
EST:     CGATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCG                         GTATC-GAAAGAAAGGAAACAGTTTGGAGTTCCTCTAGTAGCTTTTCAGCT
genomic: CGATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCGgtatggacca ... attgaaatagGTATCTGAAAGAAAGGAAACAGTTTGGAGTTCCTCTAGTAGCTTTTCAGCT
EST: gi|88344179|gb|CI654609.1|CI654609
EST:     GCATGGCAACCGATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCG                         GTATCTGAAAGAAAGGAAACAGTTTGGAGTTCCTCTAGTAGCTTTTCAGCT
genomic: GCATGGCAACCGATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCGgtatggacca ... attgaaatagGTATCTGAAAGAAAGGAAACAGTTTGGAGTTCCTCTAGTAGCTTTTCAGCT
EST: gi|56157778|gb|C26441.2|C26441
EST:     CATGGCAACCGATTGGTATATCAATGGGGGGTGTTTGATGTCTGCCATCG                         -TATCTGAAAGAAAGG
genomic: CATGGCAACCGATTGGTATATCAATGGGGG-TGTTTGATGTCTGCCATCGgtatggacca ... attgaaatagGTATCTGAAAGAAAGG
EST: gi|29668419|gb|CB664694.1|CB664694
EST:     GATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCG                         GTATCTGAAAGAAAGGAAACAGTTTGGAGTTCCTCTAGTAGCTTTTCAGCT
genomic: GATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCGgtatggacca ... attgaaatagGTATCTGAAAGAAAGGAAACAGTTTGGAGTTCCTCTAGTAGCTTTTCAGCT
EST: gi|29660291|gb|CB656566.1|CB656566
EST:     GCATGGCAACCGATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCG                         GTATCTGAAAGAAAGGAAACAGTTTGGAGTTCCTCTAGTAGCTTTTCAGCT
genomic: GCATGGCAACCGATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCGgtatggacca ... attgaaatagGTATCTGAAAGAAAGGAAACAGTTTGGAGTTCCTCTAGTAGCTTTTCAGCT

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: 73 (upstream exon), 75 (downstream exon)
Score: 22

GTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCGgtatggacca ... attgaaatagGTATCTGAAAGAAAGGAAACAGTTTGGAGTTCCTCTAGTAGCTTTTCAGCTGAACCAAGAAAAACTTGTGCGAATGCTTGGTAACATCCAAGCGATGCTT




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