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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatcaattaaccacttcccgtattcctccagacaatcttttcataacttttataatccacactttttatcttaacagATTGTCGAAGCATTGAGTAATGCATATTTTGGACCTGATTACTCTCAG

Basic information

species Oryza sativa
transcript LOC_Os07g22400.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g22400.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G130351_T01 (Zea mays), 3'ss of exon 10
gtgagt-atcaattaaccacttcccgta--ttcctccagacaatcttttcataacttttataatccacactttttatcttaacagATTGTCGAAGCATTGAGTAATGCATATTTTGGACCTGATTACTCTCAG
|||||| |||| |  ||| ||||||     ||| | |||| |   |||| ||| | | | | || |  | |||| ||  | |||||||||||||||||| || ||||| ||||||||||| |||||||| |||
gtgagttatcagtgtaccgcttcccaccctttctttcaga-accttttttatatcctctgtgatgcctaatttt-attatgacagATTGTCGAAGCATTAAGCAATGCTTATTTTGGACCCGATTACTCCCAG

upper sequence: LOC_Os07g22400.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G044317_T03 (Zea mays), 3'ss of exon 10
gtgagtatcaattaaccacttcccgtattcctccagacaatcttttcataacttttataatccacactttttatcttaacagATTGTCGAAGCATTGAGTAATGCATATTTTGGACCTGATTACTCTCAG
||||||| ||    ||| |||| |    |       | || ||||| |||  |  ||| || |  | |||| ||  | ||||||||| |||||||| || ||||| ||||||||||||||||||||||||
gtgagtaccagagtaccgcttctccacctttctttcagaacctttttata--tcctatgatgcctaatttt-attatgacagATTGTTGAAGCATTAAGCAATGCGTATTTTGGACCTGATTACTCTCAG
















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|3766960|gb|AU031070.1|AU031070
EST:     AAAATGGACGGCCACCATTAAGGAACAAGAAAAGGATAGGTTGACTCCT                         ATTGTCGAAGCATTGAGTAATGCATATTTTGGACCTGATTACTCTCAG
genomic: AAAATGGACGGCCACCATTAAGGAACAAGAAAAGGATAGGTTGACTCCTgtgagtatca ... atcttaacagATTGTCGAAGCATTGAGTAATGCATATTTTGGACCTGATTACTCTCAG




















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: 48 (upstream exon), 49 (downstream exon)
Score: 6

AAAATGGACGGCCACCATTAAGGAACAAGAAAAGGATAGGTTGACTCCTgtgagtatca ... atcttaacagATTGTCGAAGCATTGAGTAATGCATATTTTGGACCTGATTACTCTCAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctccagacaatcttttcataacttttataatccacactttttatcttaacagATTGTCGAAGCATTGAGTAATGCATATTTTGGACCTGATTACTCTCAG
                  tcataac  putative branch site (score: 6)
                                       ctttttatctt  putative PPT
           aatcttttcataactt  TA-rich tract