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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGAAGTCGATGTGCTGACGGGAGAAACCACCATCCTGAGGAGCGACCTCGTGTACGACTGTGGGCAGAGCCTGAATCCTGCTGTGGACTTGGGCCAGgtcagtcaatctactaaattaccttcaaaatatcagttgcatctgcaattctgcgcgttgcaaaatcattgcaagaatgagatgtaaattatatgtgatctgaatgtgcaatcgttgttttttgtgatcag

Basic information

species Oryza sativa
transcript LOC_Os03g57690.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g57680.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G141535_T01 (Zea mays), 5'ss of exon 8
GTGGAAGTCGATGTGCTGACGGGAGAAACCACCATCCTGAGGAGCGACCTCGTGTACGACTGTGGGCAGAGCCTGAATCCTGCTGTGGACTTGGGCCAGgtcagtcaatctactaaattaccttcaaaatatcagttgcatctgcaattctgcgcgttgcaaaatcattgcaagaatgagatgtaaattatatgtgatctgaatgtgcaatcgttgttttttgtgatcag
|||||||| ||| | || || |||| |||||| || ||| | |||||||| ||||| ||||| ||||||||||| || |||||||| |||||||||||||||||  | |  | | ||     ||||      |  ||| |||  |||   || ||    |     |  |  ||  |       | | ||||                                       
GTGGAAGTTGATATCCTAACAGGAGCAACCACAATTCTGCGAAGCGACCTGGTGTATGACTGCGGGCAGAGCCTAAACCCTGCTGTAGACTTGGGCCAGgtcagcta-taaaatgaacacagttcacgcagaccattgtatcaacaaaaatgtgctcctc-----ctctaaaaacactgttcatcatttatccag-----------------------------------

upper sequence: LOC_Os03g57680.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G141473_T01 (Zea mays), 5'ss of exon 8
GTGGAAGTCGATGTGCTGACGGGAGAAACCACCATCCTGAGGAGCGACCTCGTGTACGACTGTGGGCAGAGCCTGAATCCTGCTGTGGACTTGGGCCAGgtcagtcaatctactaaattaccttcaaaatatcagttgcatctgcaattctgcgcgttgcaaaatcattgcaagaatgagatgtaaattatatgtgatctgaatgtgcaatcgttgttttttgtgatcag
|||||| | ||||||||||| |||| ||| || || || ||||| ||||| || ||||| || ||||| ||| |||| |||||||| ||||||||||||||||  |     |  |||    || ||    | || || ||||   ||        |||||        |  ||  || |    | | | | |                                      
GTGGAAATTGATGTGCTGACAGGAGCAACAACAATTCTAAGGAGTGACCTTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCCAGgtcaacctgaaaataaaaaccgctccagctgaccactt-catca--aaggaaatatgttgc-----tcctctaaacattattcttcattaacacag-----------------------------------

upper sequence: LOC_Os03g57680.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G019799_T01 (Zea mays), 5'ss of exon 8
GTGGAAGTCGATGTGCTGACGGGAGAAACCACCATCCTGAGGAGCGACCTCGTGTACGACTGTGGGCAGAGCCTGAATCCTGCTGTGGACTTGGGCCAGgtcagtcaatctactaaattaccttcaaaatatcagttgcatctgcaattctgcgcgttgcaaaatcattgcaagaatgagatgtaaattatatgtgatctgaatgtgcaatcgttgttttttgtgatcag
|||||||| ||||| ||||| |||| |||||| |||||  ||||||||||| |  | ||||| |||||||||||||| ||||| || ||| | |||||||| || |        || ||         | | |  ||||      || | |||  | |   ||  || ||| |       |   |                                             
GTGGAAGTTGATGTACTGACAGGAGCAACCACGATCCTACGGAGCGACCTCATTCATGACTGCGGGCAGAGCCTGAACCCTGCAGTAGACCTTGGCCAGgttagcctcaaacaaaacttgatgctgttagaccgtttgccaacagaaatatgc-tgctctgaa--cactgctattgattcactcag--------------------------------------------

upper sequence: LOC_Os03g57680.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G124175_T01 (Zea mays), 5'ss of exon 3
GTGGAAGTCGATGTGCTGACGGGAGAAACCACCATCCTGAGGAGCGACCTCGTGTACGACTGTGGGCAGAGCCTGAATCCTGCTGTGGACTTGGGCCAGgtcagtcaatctactaaa--ttaccttcaaaatatcagttgcatctgcaattctgcgcgttgcaaaatcattgcaagaatgagatgtaaattatatgtgatctgaatgtgcaatcgttgttttttgtgatcag
|||||| | ||||| ||||| |||| ||| || || || ||||| ||||| || ||||| || ||||| ||| |||| |||||||| || |||||||||||||| |     || |||  |     |     |||   |  | ||  |||      |   | |        |  ||  || |    | | | | |                                      
GTGGAAATTGATGTCCTGACAGGAGCAACAACAATTCTAAGGAGTGACCTTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGATTTGGGCCAGgtcagccccaaaacaaaagctggtgctggtcctattgatcacttcatcaa----aggaaatacgctgctcctctaaacattattcttcattaacacag-----------------------------------

upper sequence: LOC_Os03g57680.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G141535_T02 (Zea mays), 5'ss of exon 1
-GTGGAAGTCGATGTGCTGACGGGAGAAACCACCATCCTGAGGAGCGACCTCGTGTACGACTGTGGGCAGAGCCTGAATCCTGCTGTGGACTTGGGCCAGgtcagtcaatctactaaattaccttcaaaatatcagttgcatctgcaattctgcgcgttgcaaaatcattgcaagaatgagatgtaaattatatgtgatctgaatgtgcaatcgttgttttttgtgatcag
 |||||||| ||| | || || |||| |||||| || ||| | |||||||| ||||| ||||| ||||||||||| || |||||||| |||||||||||||||||  | |  | | ||     ||||      |  ||| |||  |||   || ||    |     |  |  ||  |       | | ||||                                       
GGTGGAAGTTGATATCCTAACAGGAGCAACCACAATTCTGCGAAGCGACCTGGTGTATGACTGCGGGCAGAGCCTAAACCCTGCTGTAGACTTGGGCCAGgtcagcta-taaaatgaacacagttcacgcagaccattgtatcaacaaaaatgtgctcctc-----ctctaaaaacactgttcatcatttatccag-----------------------------------

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|38480128|gb|CF964217.1|CF964217
EST:     TCGTGTATGACTGTGGGCAGAGCCTGAATCCTGCTGTGGACTTGGGCCAG                         GTGGAAGGCGCATTCGTGCAAGGGATCGGCTTCTTCACGAACGAGGAGTAC
genomic: TCGTGTACGACTGTGGGCAGAGCCTGAATCCTGCTGTGGACTTGGGCCAGgtcagtcaat ... ttgtgatcagGTGGAAGGCGCATTCGTGCAAGGGATCGGCTTCTTCACGAACGAGGAGTAC
EST: gi|38475485|gb|CF959618.1|CF959618
EST:     TCGTGTATGACTGTGGGCAGAGCCTGAATCCTGCTGTGGACTTGGGCCAG                         GTGGAAGGCGCATTCGTGCAAGGGATCGGCTTCTTCACGAACGAGGAGTAC
genomic: TCGTGTACGACTGTGGGCAGAGCCTGAATCCTGCTGTGGACTTGGGCCAGgtcagtcaat ... ttgtgatcagGTGGAAGGCGCATTCGTGCAAGGGATCGGCTTCTTCACGAACGAGGAGTAC
EST: gi|55410620|gb|CV722996.1|CV722996
EST:     TCGTGTACGACTGTGGGCAGAGCCTGAATCCTGCTGTGGACTTGGGCCAG                         GTGGAAGGCGCATTCGTGCAAGGGATCGGCTTCTTCACGAACGAGGAGTAC
genomic: TCGTGTACGACTGTGGGCAGAGCCTGAATCCTGCTGTGGACTTGGGCCAGgtcagtcaat ... ttgtgatcagGTGGAAGGCGCATTCGTGCAAGGGATCGGCTTCTTCACGAACGAGGAGTAC
EST: gi|58612529|gb|CK040241.1|CK040241
EST:     TCGTGTATGACTGTGGGCAGAGCCTGAATCCTGCTGTGGACTTGGGCCAG                         GTGGAAGGCGCATTCGTGCAAGGG
genomic: TCGTGTACGACTGTGGGCAGAGCCTGAATCCTGCTGTGGACTTGGGCCAGgtcagtcaat ... ttgtgatcagGTGGAAGGCGCATTCGTGCAAGGG
EST: gi|218480362|gb|FG968520.1|FG968520
EST:     TCGTGTATGACTGTGGGCAGAGCCTGAATCCTGCTGTGGACTTGGGCCAG                         GTGGAAGGCGCATTCGTGCAAGGGATCGGCTTCTTCACGAACGAGGAGTAC
genomic: TCGTGTACGACTGTGGGCAGAGCCTGAATCCTGCTGTGGACTTGGGCCAGgtcagtcaat ... ttgtgatcagGTGGAAGGCGCATTCGTGCAAGGGATCGGCTTCTTCACGAACGAGGAGTAC
EST: gi|218505497|gb|FG958276.1|FG958276
EST:     TCGTGTATGACTGTGGGCAGAGCCTGAATCCTGCTGTGGACTTGGGCCAN                         GTGGAAGGCGCATTCGTGCAAGGGATCGGCTTCTTCACGAACGAAGAGTAC
genomic: TCGTGTACGACTGTGGGCAGAGCCTGAATCCTGCTGTGGACTTGGGCCAGgtcagtcaat ... ttgtgatcagGTGGAAGGCGCATTCGTGCAAGGGATCGGCTTCTTCACGAACGAGGAGTAC

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), 72 (downstream exon)
Score: 31

GTGGAAGTCGATGTGCTGACGGGAGAAACCACCATCCTGAGGAGCGACCTCGTGTACGACTGTGGGCAGAGCCTGAATCCTGCTGTGGACTTGGGCCAGgtcagtcaat ... ttgtgatcagGTGGAAGGCGCATTCGTGCAAGGGATCGGCTTCTTCACGAACGAGGAGTACACGACCAACTCCGATGGGCTGGTCATCAACGACGGCACGTGGACGTACA




<











<


<