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'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGCCTGTAGAAAAGAGGCTGAGAAAGTTGATTATTCCGTTAGCAGGCATCCTGAATTTCGCTACAAAACTGAGTTTCAAAGCCATGAACCAGAGgtatattgtacaagactaactgcttagtgaagtacctgtaatttctgttgtttaactaatttgtcttgtcatgcgattag

Basic information

species Oryza sativa
transcript LOC_Os01g41630.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g41630.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G142334_T02 (Zea mays), 5'ss of exon 3
AATGCCTGTAGAAAAGAGGCTGAGAAAGTTGATTATTCCGTTAGCAGGCATCCTGAATTTCGCTACAAAACTGAGTTTCAAAGCCATGAACCAGAGgtatattgtacaagactaactgcttagtga-agtacctgt------aatttct-gttgtttaactaatttgtcttgtcatgcgattag
 |||||| ||||||||| |||||||||| |||||||||  | |||||||||||||| |||||||||||||||||||||||||||||||| ||||||||||||| |   |  |  | || ||||||  | ||  |||      |||| || |   ||| || || |  | || | ||  || |||
CATGCCTCTAGAAAAGATGCTGAGAAAGCTGATTATTCTATCAGCAGGCATCCTGAGTTTCGCTACAAAACTGAGTTTCAAAGCCATGAGCCAGAGgtatattctcgcaagc--attgtttagtggtattatttgtcttatgaattacttgaaatttgacaaagtgatgttattat-tgaatag

upper sequence: LOC_Os01g41630.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G164185_T02 (Zea mays), 5'ss of exon 3
AATGCCTGTAGAAAAGAGGCTGAGAAAGTTGATTATTCCGTTAGCAGGCATCCTGAATTTCGCTACAAAACTGAGTTTCAAAGCCATGAACCAGAGgtatattgtacaagactaactgcttagtga-agtacctgt------aatttct-gttgtttaactaatttgtcttgtcatgcgattag
 |||| ||||||||||| |||||||||| |||| ||||  | |||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||| |   | ||  | || | ||||  | ||  |||      |||| || |   ||| |  || |  | |||| |||  || ||
CATGCTTGTAGAAAAGATGCTGAGAAAGCTGATCATTCTATCAGCAGGCATCCTGAATTTCGCTACAAAACTGAGTTTCAAAGCCACGAACCAGAGgtatattctcacaaac--attgttaagtggtattatttgtcttctgaattacttgaaatttgataaagtgatgttgttatggaatcag

upper sequence: LOC_Os01g41630.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA15G02640.1 (Glycine max), 5'ss of exon 3
---AATGCCTGTAGAAAAGAGGCTGAGAAAGTTGATTATTCCGTTAGCAGGCATCCTGAATTTCGCTACAAAACTGAGTTTCAAAGCCATGAACCAGAGgtatattgtacaagactaac--tgcttagtgaagtacctgtaatttctgttgtttaac--taatt--tgtcttgtcatgcgattag
     ||  |  ||||  ||    ||||   | || |||||  || | ||||||||||| || || |||||||| |||||||| || ||||| |||||||||      |   |   |    || |     ||   ||| |   |        | ||   | ||   ||| |  ||||    | ||
CATGGTGGATCAAGAAGGGATTTGGAGAGGATGGACTATTCTATTGGTAGGCATCCTGAGTTCCGTTACAAAACAGAGTTTCAGAGTCATGAGCCAGAGgtaatcatcatttggtcagtaatgttgcaccaacatcctatgggtcagaagagtcaatatttataaatgtatgatcattgtttcag

upper sequence: LOC_Os01g41630.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA13G42800.1 (Glycine max), 5'ss of exon 3
---AATGCCTGTAGAAAAGAGGCTGAGAAAGTTGATTATTCCGTTAGCAGGCATCCTGAATTTCGCTACAAAACTGAGTTTCAAAGCCATGAACCAGAGgtatattgtacaagactaac--tgcttagtgaagtacctgtaatttctgttgtttaac---taatttgtcttgtcatgcgattag
     ||  |  || |  ||    ||||  || || |||||  || | ||||||||||| || || |||||||| |||||||| || || ||||||||||||      |   |   |    || |     ||   ||| |   |        | ||    ||   ||| |  ||||    | ||
CATGGTGGATCAAGTAGGGATTTGGAGAGGGTGGACTATTCTATTGGTAGGCATCCTGAGTTCCGTTACAAAACAGAGTTTCAGAGTCACGAACCAGAGgtaatcatcatttggtcagtaatgttgcaccaacatcctatgggtcagaagagtcaatatttataatgtatgatcattgtttcag

upper sequence: LOC_Os01g41630.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 5'ss of exon 3
---AATGCCTGTAGAAAAGAGGCTGAGAAAGTTGATTATTCCGTTAGCAGGCATCCTGAATTTCGCTACAAAACTGAGTTTCAAAGCCATGAACCAGAGgtatattgtacaagactaactgctt--agtga--agtacctgtaatttctg--ttgtttaactaatttgtcttgtcatgcgattag-
      |  |  || || ||   |||| |    |||||  | |||||   ||||||||| ||||| || ||||| || ||||| || ||||||||||||||| |||  |    |  | | | ||  | | |  ||||  |||  |   ||   |  | ||  |  |||  ||   ||  | ||   
CATGGAGGGTCCAGGAAGGATCTTGAGCAGACGGATTACCCAGTTAG---GCATCCTGAGTTTCGATATAAAACAGAATTTCAGAGTCATGAACCAGAGgtacattaaaacttatcaccagatttcacttacgagtaattgtgttccttgagctactcaataagcttgcttttcaatctgtttcag

upper sequence: LOC_Os01g41630.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 5'ss of exon 3
---AATGCCTGTAGAAAAGAGGCTGAGAAAGTTGATTATTCCGTTAGCAGGCATCCTGAATTTCGCTACAAAACTGAGTTTCAAAGCCATGAACCAGAGgtatattgtacaagactaactgcttagtgaagtacctgtaatttctgttgtttaactaatttgtcttgtcatgcgattag-----------------------------------------
     ||    | ||| |||    ||||  |  ||||||||    |||||||||||||| || | ||| ||||| |||||||| ||||||||||||||||| |  | ||  |   |   | ||  ||     |    ||   | |  | |||| ||  | ||||||        | | |                                         
CATGGTGGGAATCGAAGAGATTTAGAGATGGCGGATTATTCACCAAGCAGGCATCCTGAGTTCCACTATAAAACCGAGTTTCAGAGCCATGAACCAGAGgtgtcctttaagaatttcgtttctgggttgctgatgattaccatatcct-tttatcttgtctgtcttccatccttactggactctggaatttaattctgcatttaatatgtttgaattcag

upper sequence: LOC_Os01g41630.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 5'ss of exon 3
---AATGCCTGTAGAAAAGAGGCTGAGAAAGTTGATTATTCCGTTAGCAGGCATCCTGAATTTCGCTACAAAACTGAGTTTCAAAGCCATGAACCAGAGgtatattgtacaagactaactgcttagtgaagt--acctgtaatttctgttgtttaactaatttgtcttgtcatgcgattag----------------------------
      |  |  ||||  ||   |||||   | || ||  |  ||||   |||||| |||||||| || |||||||||||||| ||||||||||| ||||||| |  | ||  | | ||| ||   ||||||     || |    |  ||| | | |||   | |    |  |   |||                              
CATGGAGGATCAAGAAGGGATCTTGAGAGGATGGACTACCCAATTAG---GCATCCCGAATTTCGTTATAAAACTGAGTTTCAGAGCCATGAACCTGAGgtatttctttcatcagttactcctgcctgaagtttgtttgcaccaccctttgctca-ctaggctctgaaatgttttaattgatgccacattgcttattctctgtgctcag

upper sequence: LOC_Os01g41630.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S167_51V6.1 (Physcomitrella patens), 5'ss of exon 3
-AATGCCTGTAGAAAAGAGGCTGAGAAAGTTGATTATTCCGTTAGCAGGCATCCTGAATTTCGCTACAAAACTGAGTTTCAAAGCCATGAACCAGAGgtatattgtacaagactaac-tgcttagtg--aagtacctgtaatttctgttgtttaactaatttg--tcttgtca-tgcgattag-----------------------------------------------------------------------------------------------------
 || |      || | |||   || | || ||||| | | |    |||||||||||||| ||| |||   || ||||||||||| |||||||||||||||   |   |||  ||||  ||  | |||  || |       ||| |       ||  |   | |  | |||  | |    |||                                                                                                      
CAAAGGACACGGAGA-GAGTTGGAAAGAGCTGATTCTGCGGGGTCCAGGCATCCTGAATATCGATACTCTACCGAGTTTCAAAGTCATGAACCAGAGgtaatgttagcaacgctaaggtgagtcgtggtaatttttcaagattgcgcccacatagttttctagaatattgatagtttccttaaaatcattatatcaacttctctttttcatatttactaagtttgcaagttatctttatcatattgaccgtgttcggtttacgatactgtatttctttctgcag

upper sequence: LOC_Os01g41630.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S425_2V6.1 (Physcomitrella patens), 5'ss of exon 3
-AATGCCTGTAGAAAAGAGGCTGAGAAAGTTGATTATTCCGTTAGC-AGGCATCCTGAATTTCGCTACAAAACTGAGTTTCAAAGCCATGAACCAGAGgtatattgtacaagactaa--ctgcttagtgaagta-cctgt-------aatttctgttgtttaacta-atttgtcttgtcatgcgattag---------
 || |     |  || |  | ||  ||||   | || |  | || | ||||||||||||| ||| |||  ||||||||||||||| ||||| || |||||| ||   | || |  ||  ||||  ||   |||| || ||       ||||||    ||||    |   |||  ||  |||    | |          
CAAAGG--ACACGAAGGGAGTTGGAAAAGGCTAATACTGTGGTATCGAGGCATCCTGAATATCGATACTCAACTGAGTTTCAAAGTCATGAGCCGGAGgtaaatctaataatatcaatgctgcccagatcagtaaccagtttctgagaatttccagcgttttgtgacgattgcgttcacatatagtaactgtatatag

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|29628542|gb|CB633553.1|CB633553
EST:     GGCATCCTGAATTTCGCTACAAAACTGAGTTTCAAAGCCATGAACCAGAG                         TTTGATTATCTGAAGAGCTTGGAAATTGAAGAGAAGATTAACAAGATAAAG
genomic: GGCATCCTGAATTTCGCTACAAAACTGAGTTTCAAAGCCATGAACCAGAGgtatattgta ... atgcgattagTTTGATTATCTGAAGAGCTTGGAAATTGAAGAGAAGATTAACAAGATAAAG
EST: gi|33796366|gb|CF324050.1|CF324050
EST:     GGCATCCTGAATTTCGCTACAAAACTGAGTTTCAAAGCCATGAACCAGAG                         TTTGATTATCTGAAGAGCTTGGAAATTGAAGAGAAGATTAACAAGATAAAG
genomic: GGCATCCTGAATTTCGCTACAAAACTGAGTTTCAAAGCCATGAACCAGAGgtatattgta ... atgcgattagTTTGATTATCTGAAGAGCTTGGAAATTGAAGAGAAGATTAACAAGATAAAG

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: 75 (upstream exon), 74 (downstream exon)
Score: 31

AATGCCTGTAGAAAAGAGGCTGAGAAAGTTGATTATTCCGTTAGCAGGCATCCTGAATTTCGCTACAAAACTGAGTTTCAAAGCCATGAACCAGAGgtatattgta ... atgcgattagTTTGATTATCTGAAGAGCTTGGAAATTGAAGAGAAGATTAACAAGATAAAGTGGTGCCAAACAGCAAATGGAGCATTGTTTCTTCTGTCCACAAATGATA




<











<


<