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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagggatacttgaattgtttgttgttcttttgatgtaaattgaattgtttgttctttaggtcttaaggaatgagtttcataaagtatgctttggtctatgcgaaatcactttttttttttgtggacatcattattctgctactgatttgacttgccattttcttacatgcagTGACAATAGCTTAATTCGGGTTGACCGTCTTGAATATCATATCAGAGAAGAGCTTAATAAAACAGCTTCCCGTGCCATGGTTGTGTTGAATCCTCTAAAG

Basic information

species Oryza sativa
transcript LOC_Os01g09000.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g09000.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G048012_T01 (Zea mays), 3'ss of exon 14
gtagggatacttgaattgtttgttgttcttttgatgtaaattgaattgtttgttctttaggtcttaaggaatgagtttcataaagtatgctttggtctatgcgaaatcactttttttttttgtggacatcattattctgctactgatttgacttgccattttcttacatgcagTGACAATAGCTTAATTCGGGTTGACCGTCTTGAATATCATATCAGAGAAGAGCTTAATAAAACAGCTTCCCGTGCCATGGTTGTGTTGAATCCTCTAAAG
                                                                        ||  | ||||    ||| |      ||||        || | |  | |  |   |    || || |  ||   |||||  |||  |||||||   |||||||||||| ||||||||||| ||||| ||||| ||||| || ||||| ||||||||||| ||||||||  | ||  |||||||||| |||  ||||||||||
---------------------------------------------------------------------gtagaaatacatagttgatgttacctgttatgga----tgctctgtcatctattattctgtttttttttcttatgcatttg--ttgt-attttct---atgcagTGACAACAGCTTAATTCGTGTTGATCGTCTAGAATACCACATCAGGGAAGAGCTTAACAAAACAGCCCCTCGAACCATGGTTGTTTTGCGTCCTCTAAAG

upper sequence: LOC_Os01g09000.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G032049_T01 (Zea mays), 3'ss of exon 15
gtagggatacttgaattgtttgttgttcttttgatgtaaattgaattgtttgttctttaggtcttaaggaatgagtttcataaagtatgctttggtctatgcgaaatcactttttttttttgtggacatcattattctgct-actgatttgacttgccattttcttacatgcagTGACAATAGCTTAATTCGGGTTGACCGTCTTGAATATCATATCAGAGAAGAGCTTAATAAAACAGCTTCCCGTGCCATGGTTGTGTTGAATCCTCTAAAG
                                                               |  |   |     ||  |      || | |||   |   | |   |    |  | | |      || ||| | ||  |  ||||| |   ||   |||||||   |||||||||||||||||||||||| ||||| ||||| |||||||| ||||| || |||||||| ||||||||  | ||  |||||||||| |||   |||||||||
--------------------------------------------------------------gtagaaatacatagttactgttacttgttatggaacacttgcatctatacatgctctat-catctattattctgctttttgctgatgtatttttttattttct---atgcagTGACAATAGCTTAATTCGTGTTGATCGTCTAGAATATCACATCAGGGAGGAGCTTAACAAAACAGCCCCTCGAACCATGGTTGTTTTGCGACCTCTAAAG
















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|58675085|gb|CK063772.1|CK063772
EST:     TCATCAACTGCAATTAATTCGTTTATTCGTGGAATTGGAATAACAAGAAG                         TGACAATAGCTTAATTCGGGTTGACCGTCTTGAATATCATATCAGAGAAGA
genomic: TCATCAACTGCAATTAATTCGTTTATTTGTGGAATTGGAATAACAAGAAGgtagggatac ... ttacatgcagTGACAATAGCTTAATTCGGGTTGACCGTCTTGAATATCATATCAGAGAAGA
EST: gi|29660827|gb|CB657102.1|CB657102
EST:     TCATCAACTGCAATTAATTCGTTTATTTGTGGAATTGGAATAACAAGAAG                         TGACAATAGCTTAATTCGGGTTGACCGTCTTGAATATCATATCAGAGAAGA
genomic: TCATCAACTGCAATTAATTCGTTTATTTGTGGAATTGGAATAACAAGAAGgtagggatac ... ttacatgcagTGACAATAGCTTAATTCGGGTTGACCGTCTTGAATATCATATCAGAGAAGA
EST: gi|33677551|gb|CF305790.1|CF305790
EST:     TCATCAACTGCAATTAATTCGTTTATTTGTGGAATTGGAATAACAAGAAG                         TGACAATAGCTTAATTCGGGTTGACCGTCTTGAATATCATATCAGAGAAGA
genomic: TCATCAACTGCAATTAATTCGTTTATTTGTGGAATTGGAATAACAAGAAGgtagggatac ... ttacatgcagTGACAATAGCTTAATTCGGGTTGACCGTCTTGAATATCATATCAGAGAAGA

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: 70 (upstream exon), 73 (downstream exon)
Score: 37

GGGATGACCCTCGTTTGTTGACACTAGCAGGATTGCGGCGACGTGGAGTGTCATCAACTGCAATTAATTCGTTTATTTGTGGAATTGGAATAACAAGAAGgtagggatac ... ttacatgcagTGACAATAGCTTAATTCGGGTTGACCGTCTTGAATATCATATCAGAGAAGAGCTTAATAAAACAGCTTCCCGTGCCATGGTTGTGTTGAATCCTCTAAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtggacatcattattctgctactgatttgacttgccattttcttacatgcagTGACAATAGCTTAATTCGGGTTGACCGTCTTGAATATCATATCAGAGAAGAGCTTAATAAAACAGCTTCCCGTGCCATGGTTGTGTTGAATCCTCTAAAG
                                          ttcttac  putative branch site (score: 37)
                                 cttgccattttctt  CT-rich tract
         atcattatt  TA-rich tract