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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttctaacatagagcaattacatcacgattagcatgttcccttcacatttatctgcctcataaaccaatatgggttttttcctatatctaatgtctttcttgaccgatgcctggtacctgattctgcaattctgttcattcgaattatttgaaatatgcatgacattag

Basic information

species Oryza sativa
transcript LOC_Os01g62420.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62420.5 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G146206_T02 (Zea mays), 5'ss of exon 6
AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttctaacata-gagcaattacatcacgattagcatgttcccttcacatttatctgcctcataaaccaatatgggttttttcctatatctaatgtctttcttgaccgatgcct-ggtacctgattctgcaattctgttcattcgaattatttgaaatatgcatgacattag--
| || ||||| |||||||| ||| |||| ||||||||||||||||||||||| ||||| |||||||| |||||||| ||||||||||||||||||||||  ||||| |   | ||||||| ||  || ||||      ||   | |||||          | || |    ||   | ||     | | |||   |   |||||||   |    | | || |    |    ||||||| |  |  | || |||||| || ||||||  |||    
AAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGGCTATTGGTACCGGCAAAGTTGCAACTCCTGCTCAGGCTCAGGAGgtatagcttcttatgcacgagcaataactgcatgatt------ttttttccacat----------cgtaga----tagttgcttccatttgtgtctcccggtattcttgatttacatatcgatatcaatgttcttaattctgctt-tgtgtatcatttgagatgtgcatggtattgtag

upper sequence: LOC_Os01g62420.5 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA15G04290.1 (Glycine max), 5'ss of exon 6
AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttctaacatagagcaattacatcacgattagcatgttcccttcacatttatctgcctcataaaccaatatgggttttttcctatatctaatgtctttcttgaccgatgcctggtacctgattctgcaattctgttcattcgaattatttgaaatatgcatgacattag
  || |||||  |||||  |||||| |||||||| || || |||||||||||||||||||| || |||||||| || |||||||||||||| ||||||| | | |  | ||   |  |  |||  || |||    || |      | | ||   |||| | ||  |   | |   ||| |   |  || | ||   | ||                                                                      
CTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTACGAGCCAGTTTGGGCCATTGGAACAGGAAAGGTTGCTACTCCTGCTCAGGCTCAAGAGgtatgcttgcctatattttgtta--acagtacaattgttttggt----gaaaacttgcttgccac-tatgctgttttttttttgtgtgtgaattttattgttctcac--------------------------------------------------------------------

upper sequence: LOC_Os01g62420.5 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA13G41120.1 (Glycine max), 5'ss of exon 6
AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttctaacatagagcaattacatcacgattagcatgttcccttcacatttatctgcctcataaaccaatatgggttttttcctatatctaatgtctttcttgaccgatgcctggtacctgattctgcaattctgttcattcgaattatttgaaatatgcatgacattag
  || |||||  |||||  |||||| |||||||| ||||| |||||||||||||||||||| || ||||||||||| |||||||||||||| ||||||| | |    | ||   |  |  |||  || |||    || |     |    |   |    |  | |    || |  |  ||||  | | ||| |  | ||                                                                        
CTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGGCCATTGGAACAGGAAAGGTTGCAACTCCTGCTCAGGCTCAAGAGgtatgcttgtctatattttgtta--acagtactattgttttggtgaaaacttgctcgccattatggtgattatatttttgaattttattgt-tctcacatatt------------------------------------------------------------------------

upper sequence: LOC_Os01g62420.5 (Oryza sativa), 5'ss of exon 5
lower sequence: AT3G55440.1 (Arabidopsis thaliana), 5'ss of exon 6
AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttctaacatagagcaattacatcacgattagcatgttccct-tcacatttatctgcctcataaaccaatatgggttttttc-ctatatctaatgtctttcttgaccgatgcctggtacctgattctgcaattctgttcattcgaattatttgaaatatgcatgacattag
|   | |  |  | ||| | ||||||||  | || ||||||||||| ||||||||||||||||| ||||| || | ||| || || ||||| || |||     |     || | ||| || ||       || | |||| | | |     | || |       ||||||||   | |||  |  | | | ||  | || ||  ||| |                                                                
ATCGGGTGACAAACTGGTCAAATGTTGTCATAGCCTATGAACCAGTGTGGGCCATTGGAACCGGAAAGGTCGCTAGCCCAGCCCAAGCTCAAGAAgtaagtggttctcgat-gcgcagttgcactg----taacgtgttgcatatggtcatgatttaataggaaaaccaatgctgttttccttacgagagcttgtttcgtttatgaacag--------------------------------------------------------------

upper sequence: LOC_Os01g62420.5 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv06s0004g04800.t01 (Vitis vinifera), 5'ss of exon 6
AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttctaacatagagcaattacatcacgattagcatgttccctt-cacatttatctgcctcataaaccaat-atgggttttttcctatatctaatgtctttcttgaccgatgcctggtacctgattctgcaattctgttcattcgaattatttgaaatatgcatgacattag
| ||  | ||    |||   ||| |||||||||| |||||||| |||||||||||||| || || ||||||||||||||||||||||| ||||| |||   ||       ||  | | ||        |||| || |   | ||   |    |      | |||   || | || | |        || ||||||                                                                             
AAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAAgtaagtctgggttgttattgaatttgtcatttcattaacaaggatctttatgctggaaagcatgttatagttcagttattgttaaaccggaatctctaat-----------------------------------------------------------------------------

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|29669431|gb|CB665706.1|CB665706
EST:     TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG                         GTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
genomic: TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttc ... atgacattagGTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
EST: gi|27576926|gb|CA999620.1|CA999620
EST:     TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG                         GTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
genomic: TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttc ... atgacattagGTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
EST: gi|58679577|gb|CK068264.1|CK068264
EST:     TTTGGGCCATTGGAACCGGCCAGGTTGCAACCCCTGCTCAGGCTCAGGAG                         GTTCATGATGGTCTGAGAAAGTGGC
genomic: TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttc ... atgacattagGTTCATGATGGTCTGAGAAAGTGGC
EST: gi|58597190|gb|CK007718.1|CK007718
EST:     TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG                         GTTCATGATGGTCTGAGAAAGTGGCTTGTG
genomic: TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttc ... atgacattagGTTCATGATGGTCTGAGAAAGTGGCTTGTG
EST: gi|163928335|gb|EG712603.1|EG712603
EST:     TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG                         GTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
genomic: TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttc ... atgacattagGTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
EST: gi|33691551|gb|CF319790.1|CF319790
EST:     TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG                         GTTCATGATGGTTTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
genomic: TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttc ... atgacattagGTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
EST: gi|27576424|gb|CA999118.1|CA999118
EST:     TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG                         GTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
genomic: TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttc ... atgacattagGTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
EST: gi|58674808|gb|CK063495.1|CK063495
EST:     TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG                         GATCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
genomic: TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttc ... atgacattagGTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
EST: gi|33690114|gb|CF318353.1|CF318353
EST:     TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG                         GTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
genomic: TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttc ... atgacattagGTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT

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), 73 (downstream exon)
Score: 23

AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttc ... atgacattagGTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTTGCTGAATCAACCAGGATTATTTACAGAG




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