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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgcttccttttgactttgctaatgccaataaataaaaaaaaatttaacatgccatatttattccagtctagttatttacatttccaagttctgtttcagTGAAGGTATTATTGGTGATGGCACACATGACTACAGTGTTGATCATGAGAAATATGCAAGCATGTATGGGCCTACAACTGGTGACAAGATTAGACTTGGT

Basic information

species Oryza sativa
transcript 13114.m00153
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: 13114.m00153 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G060656_T01 (Zea mays), 3'ss of exon 1
gttgcttccttttgactttgctaatgccaataaataaaaaaaaatttaacatgccatatttattccagtctagttatttacatttccaagttctgtttcagTGAAGGTATTATTGGTGATGGCACACATGACTACAGTGTTGATCATGAGAAATATGCAAGCATGTATGGGCCTACAACTGGTGACAAGATTAGACTTGGT-------------------------------------------------
                                                   |  |  |      |    |||   |  |    |   |||||    | ||| ||||||||||| ||||||||  ||  |||||  | ||||||||||||||| ||||| ||||| ||||| ||||| || ||||| |||||||| ||||||                                                 
-----------------------------------------------gttgtaacgcacgagcactgaccta---aagtgtcctagtaagtttatatgcagggaaggtattatcggtgatggttcatttgactgtactgttgatcatgagAAGTATGCGAGCATTTATGGACCTACCACCGGTGATAAGATTAGGCTTGGTGATACCAATCTTTATGCTGAGATTGAAAAGGACTTCGCCTTTTATGGTG

upper sequence: 13114.m00153 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G465035_T01 (Zea mays), 3'ss of exon 1
gttgcttccttttgactttgctaatgccaataaataaaaaaaaatttaacatgccatatttattccagtctagttatttacatttccaagttctgtttcagTGAAGGTATTATTGGTGATGGCACACATGACTACAGTGTTGATCATGAGAAATATGCAAGCATGTATGGGCCTACAACTGGTGACAAGATTAGACTTGGT-------------------------------------------------
                                                | |||   ||| |      |    |  | | ||  |   |||||    | ||| ||||||||||| ||||||||  ||  |||||  | ||||||||||||||| ||||| ||||| ||||| ||||| || ||||| |||||||| ||||||                                                 
------------------------------------------------atatgat-tatgttgcaacgcacgggcactgac-ctagtaagtttatatgcagggaaggtattatcggtgatggttcatttgactgtactgttgatcatgagAAGTATGCGAGCATTTATGGACCTACCACCGGTGATAAGATTAGGCTTGGTGATACCAATCTTTATGCTGGGATTGAAAAGGACTTCGCCTTTTATGGTG

upper sequence: 13114.m00153 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G461569_T01 (Zea mays), 3'ss of exon 7
gttgcttccttttgactttgctaatgccaataaataaaaaaaaatttaacatgccatatttattccagtctagttatttacatttccaagttctgtttcagTGAAGGTATTATTGGTGATGGCACACATGACTACAGTGTTGATCATGAGAAATATGCAAGCATGTATGGGCCTACAACTGGTGACAAGATTAGACTTGGT
|||| | ||||   | |||  | | | | |   | ||||          | |   || | | ||   | |||   |||||   ||  |||||    | ||| ||||||||||||||||||||  ||  |||||  | ||||||||||||||| ||||| ||||| ||||| ||||| || ||||| |||||||| ||||||
gttgat-ccttcctattttattgacggccaatgacaaaat---------cgttttatttattttttggcctaa--atttat-cttttaagtttatatgcagGGAAGGTATTATTGGTGATGGTTCATTTGACTGTACTGTTGATCATGAGAAGTATGCGAGCATTTATGGACCTACCACCGGTGATAAGATTAGGCTTGGT

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|29616662|gb|CB621674.1|CB621674
EST:     GAAAAGGTTATTGCAAATGGTTTTGGGCATGAAGATTATCCAGATTCAAG                         TGAAGGTATTATTGGTGATGGCACACATGACTACAGTGTTGATCATGAGAA
genomic: GAAAAGGTTATTGCAAATGGTTTTGGGCATGAAGATTATCCAGATTCAAGgttgcttcct ... tctgtttcagTGAAGGTATTATTGGTGATGGCACACATGACTACAGTGTTGATCATGAGAA




















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: 32 (upstream exon), 63 (downstream exon)
Score: 5

ATGGAATTGCTGATGGTGCTGTCAACAGATCTCAGCTTAATGAGGTAATGGAAAAGGTTATTGCAAATGGTTTTGGGCATGAAGATTATCCAGATTCAAGgttgcttcct ... tctgtttcagTGAAGGTATTATTGGTGATGGCACACATGACTACAGTGTTGATCATGAGAAATATGCAAGCATGTATGGGCCTACAACTGGTGACAAGATTAGACTTGGT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacatgccatatttattccagtctagttatttacatttccaagttctgtttcagTGAAGGTATTATTGGTGATGGCACACATGACTACAGTGTTGATCATGAGAAATATGCAAGCATGTATGGGCCTACAACTGGTGACAAGATTAGACTTGGT
 atttaac  putative branch site (score: 5)
                                            ttctgtttc  putative PPT
                        tagttatttacattt  TA-rich tract