Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGCCATTGCTTCAACAAATGCAATTGTTTCTGCTGCATGTGCGTTGGAAGCTCTTAAGCTTATCTCTGGGTGCAGCAAAACTGTGTCGAATTATCTCACgtgagttcactacttttctgagtcttattttaaattttggtttcgacttggaatatttatttatccccaagattgtttaactataattaacaagcacatctgaagcgattgatttcttgaccaggttagaaacacttaacatggttctgtttgaagtgcattatttttctttgactatctgcag

Basic information

species Oryza sativa
transcript LOC_Os01g16540.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g16540.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G007915_T02 (Zea mays), 5'ss of exon 7
CAGCCATTGCTTCAACAAATGCAATTGTTTCTGCTGCATGTGCGTTGGAAGCTCTTAAGCTTATCTCTGGGTGCAGCAAAACTGTGTCGAATTATCTCACgtgagttcactacttttctgagtc----ttattttaaattttggtttcgacttggaatatttatttatccccaagattgtttaactataattaacaagcacatctgaagcgattgatttcttgaccaggttagaaacacttaacatggttctgtttgaagtgcattatttttctttgactatctgcag
|||||||||| ||||| ||||||||| | || ||||| ||||| ||||||||  | |||||||| |||||||||||||||| |||||| || ||||||||||||||||  |  |||| | |  |    ||| | ||||  ||||||||  |    |||     | |||   | | || | |||| ||| | |      ||||| | |                                                                                 
CAGCCATTGCATCAACGAATGCAATTATATCGGCTGCTTGTGCATTGGAAGCCTTAAAGCTTATTTCTGGGTGCAGCAAAAGTGTGTCAAACTATCTCACgtgagttccattgttttataacccatagttactgtaaaagttggtttcctc----aat-----tgtatggactaaatgggttaaatattagtc-tgcacacatttaagct------------------------------------------------------------------------------

upper sequence: LOC_Os01g16540.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv05s0020g02820.t01 (Vitis vinifera), 5'ss of exon 7
CAGCCATTGCTTCAACAAATGCAATTGTTTCTGCTGCATGTGCGTTGGAAGCTCTTAAGCTTATCTCTGGGTGCAGCAAAACTGTGTCGAATTATCTCACgtgagtt-cactacttttctgagtcttattttaaattttggtttcgacttggaatatt-tatttatccccaagattgtttaactataattaacaagcacatctgaagcgattgatttcttgaccaggttagaaacacttaacatggttctgtttgaagtgcattatttttctttgactatctgcag
| |||||||| || |||||||||||| |||| |||||||||||  ||||| |  | ||| || | || || |||||||||||| | || || ||||| ||||| |    ||| | | |   | | ||| || | |||    ||    |    | | || |  || |      |||  ||| | || || |||     |  |                                                                                     
CGGCCATTGCATCCACAAATGCAATTATTTCAGCTGCATGTGCACTGGAAACCTTGAAGATTGTATCAGGATGCAGCAAAACTTTATCAAACTATCTAACgtgcgccatacttcctcttcaatttttaattaatattcaactt----cacaaagtcttgtccttgttatatggatcattttattagaactaaatgataggttaa----------------------------------------------------------------------------------
















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|6799296|gb|AU082247.1|AU082247
EST:     GCAAAACTGTGTCGANTTATCTCCAC                         GTATNACGGCCTTGATGNAACCCACATTAATGTAACCGAATTTGCAAGAG
genomic: GCAAAACTGTGTCGAATTATCT-CACgtgagttcac ... ctatctgcagGTATAACGGCCTTGATGGAACACACATTAATGTAAGCGAATTTGCAAGAG
EST: gi|6799264|gb|AU082215.1|AU082215
EST:     GCTCTTAAGCTTATCTCTGGGTGCAGCAAAACTGTGTCGAATTATCTCAC                         GTATAACGGCCTTGATGGAACACACATTAATGTAAGCGAATTTGCAAGAGA
genomic: GCTCTTAAGCTTATCTCTGGGTGCAGCAAAACTGTGTCGAATTATCTCACgtgagttcac ... ctatctgcagGTATAACGGCCTTGATGGAACACACATTAATGTAAGCGAATTTGCAAGAGA
EST: gi|58596703|gb|CK007231.1|CK007231
EST:     GCTCTTAAGCTTATCTCTGGGTGCAGCAAAACTGTGTCGAATTATCTCAC                         GTATAACGGCCTTGATGGAACACACATTAATGTAAGCGAATTTGCAAGAGA
genomic: GCTCTTAAGCTTATCTCTGGGTGCAGCAAAACTGTGTCGAATTATCTCACgtgagttcac ... ctatctgcagGTATAACGGCCTTGATGGAACACACATTAATGTAAGCGAATTTGCAAGAGA
EST: gi|86260414|gb|CI066287.1|CI066287
EST:     AGCAAAACTGTGTCGAATTATCTCAC                         GTATAACGGCCTTGATGGAACACACATTAATGTAAGCGAATTTGCAAGAGA
genomic: AGCAAAACTGTGTCGAATTATCTCACgtgagttcac ... ctatctgcagGTATAACGGCCTTGATGGAACACACATTAATGTAAGCGAATTTGCAAGAGA
EST: gi|88844602|gb|CI020449.1|CI020449
EST:     CAAAACTGTGTCGAATTATCTCAC                         GTATAACGGCCTTGATGGAACACACATTAATGTAAGCGAATTTGCAAGAGA
genomic: CAAAACTGTGTCGAATTATCTCACgtgagttcac ... ctatctgcagGTATAACGGCCTTGATGGAACACACATTAATGTAAGCGAATTTGCAAGAGA
EST: gi|86420887|gb|CI056876.1|CI056876
EST:     CTCTTAAGC-TATCTGCTGGGTGCAGCAAAACTGTGTCGAATTATCTCAC                         GTATAACGGCCTTGATGGAACACACATTAATGTAAGCGAATTTGCAAGAGA
genomic: CTCTTAAGCTTATCT-CTGGGTGCAGCAAAACTGTGTCGAATTATCTCACgtgagttcac ... ctatctgcagGTATAACGGCCTTGATGGAACACACATTAATGTAAGCGAATTTGCAAGAGA
EST: gi|89173666|gb|CI041559.1|CI041559
EST:     GAATTATCTCAC                         GTATAACGGCCTTGATGGAACACACATTAATGTAAGCGAATTTGCAAGAGA
genomic: GAATTATCTCACgtgagttcac ... ctatctgcagGTATAACGGCCTTGATGGAACACACATTAATGTAAGCGAATTTGCAAGAGA
EST: gi|86854593|gb|CI258886.1|CI258886
EST:     GCTCTTAAGCTTATCTCTGGGTGCAGCAAAACTGTGTCGAATTATCTCAC                         GTATAACGGCCTTGATGGAACACACATTAATGTAAGCGAATTTGCAAGAGA
genomic: GCTCTTAAGCTTATCTCTGGGTGCAGCAAAACTGTGTCGAATTATCTCACgtgagttcac ... ctatctgcagGTATAACGGCCTTGATGGAACACACATTAATGTAAGCGAATTTGCAAGAGA
EST: gi|86434920|gb|CI106153.1|CI106153
EST:     GCTCTTAAGCTTATCTCTGGGTGCAGCAAAACTGTGTCGAATTATCTCAC                         GTATAACGGCCTTGATGGAACACACATTAATGTAAGCGAATTTGCAAGAGA
genomic: GCTCTTAAGCTTATCTCTGGGTGCAGCAAAACTGTGTCGAATTATCTCACgtgagttcac ... ctatctgcagGTATAACGGCCTTGATGGAACACACATTAATGTAAGCGAATTTGCAAGAGA
EST: gi|86412974|gb|CI067379.1|CI067379
EST:     TCTGGGTGCAGCAAAACTGTGTCGAATTATCTCAC                         GTATAACGGCCTTGATGGAACACACATTAATGTAAGCGAATTTGCAAGAGA
genomic: TCTGGGTGCAGCAAAACTGTGTCGAATTATCTCACgtgagttcac ... ctatctgcagGTATAACGGCCTTGATGGAACACACATTAATGTAAGCGAATTTGCAAGAGA

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), 73 (downstream exon)
Score: 50

CAGCCATTGCTTCAACAAATGCAATTGTTTCTGCTGCATGTGCGTTGGAAGCTCTTAAGCTTATCTCTGGGTGCAGCAAAACTGTGTCGAATTATCTCACgtgagttcac ... ctatctgcagGTATAACGGCCTTGATGGAACACACATTAATGTAAGCGAATTTGCAAGAGAGAAAGACTGCCTTGTATGTGGACCTGGTACCCTTATTGAACTTGGGACA




<











<


<