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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactaacttgactgctgttattctttacctattattcttttacatattcttctctttgattaactgtttggattgttatgtagGTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCACTTGATGCTTTCCCAGCTTTG

Basic information

species Oryza sativa
transcript LOC_Os01g49940.1
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g49940.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G466139_T01 (Zea mays), 3'ss of exon 19
gtactaacttgactgctgttattctttacctattattcttttacatattcttctctttgattaactgtttggattgttatgtagGTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCACTTGATGCTTTCCCAGCTTTG
||||  || | || |||| ||||       |     |||||       | |||   |||  |||     || | |||  || |||||||||   |||||||||| |||||||| |||||||||||||||||||| ||||||||||| || ||||||
gtacatacattaccgctgctattggagttttgcgtgtcttta------ttttcatcttgcctaataagctgaactgtcttgcagGTTGACAGAATACCAATTCCTCTTCTTTTTATGAGAACAGTTATTCAAGCGCTTGATGCTTTTCCTGCTTTG

upper sequence: LOC_Os01g49940.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA04G09480.1 (Glycine max), 3'ss of exon 21
gtactaacttgactgctgttattctttacctattattcttttacatattcttctctttgattaactgtttggattgttatgtagGTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCACTTGATGCTTTCCCAGCTTTG
    |||   || |     ||||    |   ||  |   ||||| |    |  |  | | |  | |||||  ||| |     |||||||  |    ||  | || || ||||||||||||||||||||||| ||| |||||||||| || ||  ||
---gtaaggagattctgtgtattgggcaataatactggatttacttcaaatcttaatggctatattgtttaaattttc----agGTTGATCAAACTCCGCTGCCTCTACTTTTCATGAGAACAGTTATTCAGGCAATTGATGCTTTTCCTGCAATG

upper sequence: LOC_Os01g49940.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA06G09580.1 (Glycine max), 3'ss of exon 20
gtactaacttgactgctgttattctttacctattattcttttacatattcttctctttgattaactgtttggattgttatgtagGTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCACTTGATGCTTTCCCAGCTTTG
    |||   || |      |||    |   ||  |   ||||| |    |  || | | |  | |||||  ||| |     |||||||  |    ||| | || || ||||||||||||||||||||||| ||| |||||||||| || ||  ||
---gtaaggagattcagtgcattggccaataatactggatttacttcaaatcttcatggctctattgtttaaattttc----agGTTGATCAAACTCCACTGCCGCTACTTTTCATGAGAACAGTTATTCAGGCAATTGATGCTTTTCCTGCACTG

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|87004655|gb|CI300977.1|CI300977
EST:     CACTGAATAAATTG                         GTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCA
genomic: CACTGAATAAATTGgtactaactt ... tgttatgtagGTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCA
EST: gi|163925961|gb|EG714989.1|EG714989
EST:     AGCGCACGGTATTTACTCAGCAAGTTTTGGAGAAGTCACTGAATAAATTG                         GTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCA
genomic: AGCGCACGGTATTTACTCAGCAAGTTTTGGAGAAGTCACTGAATAAATTGgtactaactt ... tgttatgtagGTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCA
EST: gi|29644685|gb|CB649692.1|CB649692
EST:     AGCGCACGGTATTTACTCAGCAAGTTTTGGAGAAGTCACTGAATAAATTG                         GTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCA
genomic: AGCGCACGGTATTTACTCAGCAAGTTTTGGAGAAGTCACTGAATAAATTGgtactaactt ... tgttatgtagGTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCA
EST: gi|27577961|gb|CB000656.1|CB000656
EST:     AGCGCACGGTATTTACTCAGCAAGTTTTGGAGAAGTCACTGAATAAATTG                         GTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCA
genomic: AGCGCACGGTATTTACTCAGCAAGTTTTGGAGAAGTCACTGAATAAATTGgtactaactt ... tgttatgtagGTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCA
EST: gi|300215772|gb|HO088398.1|HO088398
EST:     AGCGCACGGTATTTACTCAGCAAGTTTTGGAGAAGTCACTGAATAAATTG                         GTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCA
genomic: AGCGCACGGTATTTACTCAGCAAGTTTTGGAGAAGTCACTGAATAAATTGgtactaactt ... tgttatgtagGTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCA
EST: gi|33794819|gb|CF323289.1|CF323289
EST:     AGCGCACGGTATTTACTCAGCAAGTTTTGGAGAAGTCACTGAATAAATTG                         GTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCA
genomic: AGCGCACGGTATTTACTCAGCAAGTTTTGGAGAAGTCACTGAATAAATTGgtactaactt ... tgttatgtagGTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCA

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: 50 (upstream exon), 74 (downstream exon)
Score: 23

GTCACTGATGCTTGCACAGCTTGCTTTGAACAGCGCACGGTATTTACTCAGCAAGTTTTGGAGAAGTCACTGAATAAATTGgtactaactt ... tgttatgtagGTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCACTTGATGCTTTCCCAGCTTTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctattattcttttacatattcttctctttgattaactgtttggattgttatgtagGTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCACTTGATGCTTTCCCAGCTTTG
                             gattaac  putative branch site (score: 23)
     attcttttacatatt  TA-rich tract