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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgactttattttctctataacataatttcccctgtaagattttcatagacttatactgtggtttgcaatttgaagGATTATGTGGCAACAAGGTGGTACCGAGCTCCTGAATTATGTGGTTCTTTTTTCTCCAAA

Basic information

species Oryza sativa
transcript LOC_Os02g04230.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g04230.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G374088_T01 (Zea mays), 3'ss of exon 3
gtacgactttattttctctataacataatt--tcccctgtaagattttcatagactta--tactgtggtttgcaatttgaagGATTATGTGGCAACAAGGTGGTACCGAGCTCCTGAATTATGTGGTTCTTTTTTCTCCAAA
||| ||   | ||   || ||    || |   ||   | |  |    | ||    |||  || ||||  |||||| |||||||||||||| ||||||||||||||||| ||||||||||||||||| || ||||||||||  
gtaagatcct-ttccatcaattttgtattcaatcatttttttgccccttatttcattaactattgtg-cttgcaacttgaagGATTATGTCGCAACAAGGTGGTACCGGGCTCCTGAATTATGTGGCTCCTTTTTCTCCAGT

upper sequence: LOC_Os02g04230.2 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S80_71V6.2 (Physcomitrella patens), 3'ss of exon 3
---------------------------------------------------------------------------gtacgactttattttctctataacataatttccc---ctgtaagattttcatagacttatactgtggtttgcaatttgaagGATTATGTGGCAACAAGGTGGTACCGAGCTCCTGAATTATGTGGTTCTTTTTTCTCCAAA
                                                                           | |||     | |||      |  | || |||     ||||   |  | |||  | |    |||| ||| |  | || | |||||||||||| ||||||||||| |||||||| ||  | |||||||| || || || || 
gtatggtcttccgccattgctggaaattaaaaatattataggttctcggaaaccattgttattaagtccttctaggcacggtcaaactttactgccaggaaaagttctgaagctgtgtaacctgcatgaatt----ctgttgttgggtacttca-gGATTATGTGGCTACAAGGTGGTATCGAGCTCCAGAGCTTTGTGGTTCATTCTTTTCGAAG

upper sequence: LOC_Os02g04230.2 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 3
---------------------------------------------------------------------------gtacgactttattttctctataacataatttcccctgtaagattttcatagacttatactgtg---gtttgcaatt--tga-------agGATTATGTGGCAACAAGGTGGTACCGAGCTCCTGAATTATGTGGTTCTTTTTTCTCCAAA
                                                                            |   ||| ||   |||   | | ||  | ||    |||   |||| |     ||||| | ||    | | | |||  |||       ||||||||||||| ||||||||||| |||||||| ||  |||||||||| || || || || 
gtatggtttaaccctgttaatacaattcgaaatagtacgttcggaaattgtacttctttgcaccgaattaattccttttaactctaaactctgggtcaaattttatcggaggtagagttttaagcttgttataatatgtgtatatcctattgttgagtgcttcagGATTATGTGGCCACAAGGTGGTATCGAGCTCCGGAGCTATGTGGTTCATTCTTTTCTAAG

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|58655691|gb|CK044371.1|CK044371
EST:     GACTTGCACGTGTAGCATTTAATGATTCACCTTCAACAATTTTTGGGACC                         GATTATGTGGCAACAAGGTGGTACCGAGCTCCTGAATTATGTGGTTCTTTT
genomic: GACTTGCACGTGTAGCATTTAATGATTCACCTTCAACAATTTTTTGGACCgtacgacttt ... caatttgaagGATTATGTGGCAACAAGGTGGTACCGAGCTCCTGAATTATGTGGTTCTTTT
EST: gi|33677513|gb|CF305752.1|CF305752
EST:     GACTTGCACGTGTAGCATTTAATGATTCACCTTCAACAATTTTTTGGACC                         GATTATGTGGCAACAAGGTGGTACCGAGCTCCTGAATTATGTGGTTCTTTT
genomic: GACTTGCACGTGTAGCATTTAATGATTCACCTTCAACAATTTTTTGGACCgtacgacttt ... caatttgaagGATTATGTGGCAACAAGGTGGTACCGAGCTCCTGAATTATGTGGTTCTTTT

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: 58 (upstream exon), 70 (downstream exon)
Score: 12

AAAGAACATACTGGCCAATTCAGACTGCAAACTGAAGATTTGTGATTTTGGACTTGCACGTGTAGCATTTAATGATTCACCTTCAACAATTTTTTGGACCgtacgacttt ... caatttgaagGATTATGTGGCAACAAGGTGGTACCGAGCTCCTGAATTATGTGGTTCTTTTTTCTCCAAA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cataatttcccctgtaagattttcatagacttatactgtggtttgcaatttgaagGATTATGTGGCAACAAGGTGGTACCGAGCTCCTGAATTATGTGGTTCTTTTTTCTCCAAA
              taagatttt  TA-rich tract