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'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   		30  
 5'  3'   		31  
 5'  3'   		32  
 5'  3'   		33  
 5'  3'   		34  
 5'  3'   		35  
 5'  3'   		36  
 5'  3'   		37  
 5'  3'   		38  
 5'  3'   		39  
 5'  3'   		40  
 5'  3'   
41  
 5'  3'   		42  
 5'  3'   		43  
 5'  3'   		44  
 5'  3'   		45  
 5'  3'   		46  
 5'  3'   		47  
 5'  3'   		48  
 5'  3'   		49  
 5'  3'   		50  
 5'  3'   		51  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttattggttatgagtttgtttatttcagccagttattataatgtatgtcgcataagctaccttttctattttaattcctgaaacaagaactattttcagGTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAG

Basic information

species Oryza sativa
transcript LOC_Os01g60040.1
intron # 49
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 49
lower sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 32
gttattggttatgagtttgtttatttcagccagttattataa-tgtat-gtcgcataagctaccttttctattttaattcctgaaacaagaactat-tttcagGTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAG
    || | |||   | ||||   | ||       |||  || |||||  ||   | |||   ||||||| |||  | || ||||     | |  | | ||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||||
--ggtttggtattcatatgttctgtgcatatttccattgaaagtgtatcatctactgagcattcttttctgtttctaatc-tgaattgccatcattatctcagGTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAG

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 49
lower sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 50
-------------------------------------------------------------------------gttattggttatgagtttgtttatttcagccagttattataa-tgtat-gtcgcataagctaccttttctattt-taattcctgaaacaagaactattttcagGTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAG
                                                                          ||   | || | |   ||    || ||     | |||  || ||| | ||    | |||   |||| || |||  |||        | |  | ||| | |||||||||||||||||||||||||||||||| |||||||| ||||||||||||||||||||||| |||||||||
gtattattcctagtgtacttccacattaacattcgtattcctttggggaactatttgtaaaatggcggtcttcattgcagattttaatcatgcactttgcatgttttcattgcaagtgttttgtttattgagcattctttcctgtttacaatctgatctgccatcattatct-cagGTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAG

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 49
lower sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 51
gttattggttatgagtttgtttatttcagccagttattataatgtatgtcgcataagctaccttttctattttaattcctgaaacaagaactattttcagGTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAG
|||    ||||  | || | | |  |       || | ||||    |   || |     |  ||| ||  ||| |||   |          |  | | ||||||| ||||||||||||||||| ||||| ||||| |||||| | ||||| || |||||||| || ||||||
gtttcatgttaatatttagataagatgtaaggattttaataaaaccttaagcctgtatcatttttgctcatttgattaaggttctggtgctttatcttagGTTGACATATTTGCTCAGCTTCAAAATGCTAGTGAGGCATTTCGCACCTACATTAGAGATGGTCTTGCTCAG

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 49
lower sequence: GLYMA10G35140.1 (Glycine max), 3'ss of exon 52
gttattggttatgagtttgttta--tttcagccagttattataatgtatgtcgcataagctaccttttctattttaattcctgaaacaagaactattttcagGTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAG
  |    ||||  | || | | |  | | |     | ||| |||    |   || ||    |  ||| ||   || ||    |    |     |  | | ||||||| ||||||||||||||||| ||||| ||||| |||||| | ||||| || |||||||| || ||||||
--ttcatgttaatatttggataagatgtaatgttatgattttaaaaccttaagcctatatcatttttgctcaattgatcaaggttctagtgctttatcttagGTTGACATATTTGCTCAGCTTCAAAATGCTAGTGAGGCATTTCGCACCTACATTAGAGATGGTCTTGCTCAG

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 49
lower sequence: Vv00s0652g00030.t01 (Vitis vinifera), 3'ss of exon 21
---------------------------------------------------------------gttattggttatgagtttgtttatttcagccagttattataatgtat--gtcgcataagctaccttttctattttaattcctgaaacaagaact----attt-----tcagGTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAG
                                                               ||||||||||  |     |   |     || |   |  || || | |   |   ||       | | |||| |  | || |   ||    || |    ||||     |||||||||||||||||| ||||| || ||||| ||||| || ||| | || |||||||| |||||| |||| |||
gtaaactataaattgcatggtatatgtttaaaagaagtttaagtagtgaatagcatgaggtttgttattggttgagctcgggccaaagattgctaac-acaatgatctcttaattagatctatcttcctgtctactgcatttgccagaaagttaatttgtgatttctatttcagGTTGATATATTTGCGCAGCTCCAAAATGCTAGTGAGGCGTTTCGGACTTATATCAGGGATGGGTTAGCCCAG

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|58675157|gb|CK063844.1|CK063844
EST:     GGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAG                         GTGGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGGACCTAT
genomic: GGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAGgtatattatt ... ctattttcagGTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTAT
EST: gi|58658439|gb|CK047119.1|CK047119
EST:     GTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAG                         GTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGGACCTAT
genomic: GTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAGgtatattatt ... ctattttcagGTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTAT
EST: gi|58601380|gb|CK011908.1|CK011908
EST:     GTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAG                         GTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGGACCTAT
genomic: GTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAGgtatattatt ... ctattttcagGTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTAT
EST: gi|29680245|gb|CB676520.1|CB676520
EST:     GTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCCAG                         GTTGATATATTTG
genomic: GTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAGgtatattatt ... ctattttcagGTTGATATATTTG
EST: gi|218497579|gb|FG955134.1|FG955134
EST:     GTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAG                         GTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGGACCTAT
genomic: GTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAGgtatattatt ... ctattttcagGTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTAT
EST: gi|58677253|gb|CK065940.1|CK065940
EST:     GTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAG                         GTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGGACCTAT
genomic: GTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAGgtatattatt ... ctattttcagGTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTAT
EST: gi|58690696|gb|CK079383.1|CK079383
EST:     GTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAG                         GTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGGACCTAT
genomic: GTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAGgtatattatt ... ctattttcagGTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTAT

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: 33

CAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAGgtatattatt ... ctattttcagGTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtcgcataagctaccttttctattttaattcctgaaacaagaactattttcagGTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAG
                        ttttaat  putative branch site (score: 33)
                                             ctattttc  putative PPT
                 ttttctattttaatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttattggttatgagtttgtttatttcagccagttattataatgtatgtcgcataagctaccttttctattttaattcctgaaacaagaactattttcagGTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - -atgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attcctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaaga