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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatactttaatgagagtatgagacttaggcgattaaccaccatggcttttagaacattgtttggtttgtaacaccacatctatttccttatggatgcagATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATGGTTAATTTGCTAAGACAGCTTCAGACTACATTGCCTCCTTCAGTACTGG

Basic information

species Oryza sativa
transcript LOC_Os03g49420.2
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g49420.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G033619_T01 (Zea mays), 3'ss of exon 18
--------------------------------------------------------------------------------------------------ttatact-ttaatgagagtatgagacttaggcgattaa-ccaccatggcttttagaacattgtttggtttgtaacaccacatctatttccttatggatgcagATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATGGTTAATTTGCTAAGACAGCTTCAGACTACATTGCCTCCTTCAGTACTGG
                                                                                                  ||  ||  || |  |||  || |     |||  | | | | | |   |      || |||| |||  ||   |||   |  |   |||  |   | |||||||||||||||||||| || ||||| ||||||||||| |||   || | |||||||||| | ||||| || |||||| | |||||||||||||||||| | |
gtacctttagccttttcttattttcctcaatcttgttttctttatattatcccccttctgtttcccaaggtctatggaatatggataaactgcaactcttgaaccgtttaaaagaccatcatttggaggaaactgagctatccaagtgacaggagcattatttactt---aacttgatctgccttttgtatggaatgcagATATTATGTGCGGGCAAAGATCTAGCAACAGAACAGACTGCCAGCAGGATGGTTAATCTACTAAGGCAACTTCAGGCAACATTGCCTCCTTCAGTATTAG

upper sequence: LOC_Os03g49420.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA19G29010.1 (Glycine max), 3'ss of exon 19
ttatacttt-aatgagagtatgagacttaggcgattaaccaccatggcttttagaacattgtttggtt-tgtaacaccacatctatttccttatggatgcagATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATGGTTAATTTGCTAAGACAGCTTCAGACTACATTGCCTCCTTCAGTACTGG
   |||||| ||||  |||      |||||    |   |   || |  | |     || | ||   || |  ||       | |   ||      |||| |||| ||||||||||| || |||||||| || ||||| ||| |||||| |||| |||||||  | || ||||||||    || || || |||||    || |
--gtactttcaatgctagttct---cttagttact--gctgtca-gattctggatccacttttcccttataaaatgtttgttttgcatcgactatgatgtagATTTTATGTGCGGGAAATGATCTGGCTACCGAACAGACTGTTAGTAGGATGATTAATTTATTGAGGCAGCTTCAACAGACTTTACCACCTTCTACCCTTG

upper sequence: LOC_Os03g49420.4 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 19
----ttatactt-taatgagagtatgagacttaggcgattaaccaccatggcttttagaacattgtttggtttgtaacaccacatctatttccttatggatgcagATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATGGTTAATTTGCTAAGACAGCTTCAGACTACATTGCCTCCTTCAGTACTGG
    |   | |   | ||  | |||      | |    ||       |   ||  | ||| | | |||  ||| |      | ||     || | ||  ||| || |  ||||||||||||||||||| |||||||| |||||  | ||   |||| | || ||||| ||||| ||||||   ||  | || |||||     |||
aatttagcagtcacattgccattatacagtatggtactttttatgttacaactgatggaaaaatctttcctttattgatgaaaat-----tcatcattaatgtagGTTCTATGTGCGGGTAAGGATCTTGCAACAGAGCAAACCATAAGCCGGATGATAAACTTGCTGAGACAACTTCAGCAGACGCTACCACCTTCCACCTTGG

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|29681491|gb|CB677766.1|CB677766
EST:     TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTTTATTTTTGCGGAG                         ATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
genomic: TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAGgtacctattt ... atggatgcagATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
EST: gi|29679232|gb|CB675507.1|CB675507
EST:     TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAG                         ATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
genomic: TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAGgtacctattt ... atggatgcagATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
EST: gi|29629241|gb|CB634252.1|CB634252
EST:     TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAG                         ATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
genomic: TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAGgtacctattt ... atggatgcagATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
EST: gi|88849788|gb|CI001494.1|CI001494
EST:     TGGGTCATAACAACCAGTATCTTCCCAAGATTGTCTCTATTTTTGCGGAG                         ATATTATGTGCGGGTAAGGATCTGGCCACAGAACAAACTTTTAGTAAGATG
genomic: TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAGgtacctattt ... atggatgcagATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
EST: gi|27576974|gb|CA999668.1|CA999668
EST:     TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAG                         ATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
genomic: TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAGgtacctattt ... atggatgcagATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
EST: gi|29629841|gb|CB634850.1|CB634850
EST:     TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAG                         ATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
genomic: TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAGgtacctattt ... atggatgcagATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttttagaacattgtttggtttgtaacaccacatctatttccttatggatgcagATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATGGTTAATTTGCTAAGACAGCTTCAGACTACATTGCCTCCTTCAGTACTGG
                     ttgtaac  putative branch site (score: 2)
                                      tttccttat  putative PPT
                                 atctattt  TA-rich tract