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

GTGCAGAACTCTAATATTTGTTGGCCAGAACTCTCAGTTCCATGCTGAGGCTGTTCATATGACCTCAAAGCTTGATGAGAGATATAGTGCTCTCGTAGAGgtgcttatttaactgatagtttgatccaacgaaaaaaaaatatgttctttggtttgaaatgtcaatcttgatgtctttgcag

Basic information

species Oryza sativa
transcript LOC_Os06g36740.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g36740.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G058328_T01 (Zea mays), 5'ss of exon 4
GTGCAGAACTCTAATATTTGTTGGCCAGAACTCTCAGTTCCATGCTGAGGCTGTTCATATGACCTCAAAGCTTGATGAGAGATATAGTGCTCTCGTAGAGgtgcttatttaactgatagtttgatccaacgaaaaaaaaatatgttctttggtttgaaatgtcaatcttgatgtctttgcag
|||||| || ||||| ||||||||  |||| || |||||||||||||| | ||| || |||||  |||||||||||  | ||||||| ||||| || ||||| |  ||||    |  | ||| ||   |||   |    |   ||| |||      | ||  |||  ||| ||||| | |||
GTGCAGGACACTAATTTTTGTTGGTGAGAATTCCCAGTTCCATGCTGAAGTTGTGCACATGACTGCAAAGCTTGATAGGCGATATAGCGCTCTTGTGGAGgtaccaatttgtacgcaaattttattttacgttgatttta-gggtttttt------acataccaagtttggtgtctctacag

upper sequence: LOC_Os06g36740.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G161390_T01 (Zea mays), 5'ss of exon 5
GTGCAGAACTCTAATATTTGTTGGCCAGAACTCTCAGTTCCATGCTGAGGCTGTTCATATGACCTCAAAGCTTGATGAGAGATATAGTGCTCTCGTAGAGgtgcttatttaactgatagtttgatccaacgaaaaaaaaatatgttctttggtttgaaatgtcaatcttgatgtctttgcag
|||||| || || || ||||||||  |||| || |||||||||||||| ||||| || |||||  |||||||||||  | ||||||| ||||| || ||||| |  ||||    |    ||| ||   |||   |    |   ||| |||      | ||  |||  ||| || || | |||
GTGCAGGACACTTATTTTTGTTGGTGAGAATTCCCAGTTCCATGCTGAAGCTGTGCACATGACTGCAAAGCTTGATAGGCGATATAGCGCTCTTGTGGAGgtaccaatttgtacgcagattttattttacgttgatttta-gggtttttt------acataccaagtttggtgactctacag

upper sequence: LOC_Os06g36740.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G142927_T01 (Zea mays), 5'ss of exon 5
GTGCAGAACTCTAATATTTGTTGGCCAGAACTCTCAGTTCCATGCTGAGGCTGTTCATATGACCTCAAAGCTTGATGAGAGATATAGTGCTCTCGTAGAGgtgcttatttaactgatagtttgatccaacgaaaaaaaaatatgttctttggtttgaaatgtcaatcttgatgtctttgcag
|||||| || ||||| ||||||||  |||| || |||||||||||||| | ||| || |||||  |||||||||||  | ||||||| ||||| || ||||| |  ||||    |    ||| ||   |||   |    |   ||| |||      | ||  |||  ||| ||||| | |||
GTGCAGGACACTAATTTTTGTTGGTGAGAATTCCCAGTTCCATGCTGAAGTTGTGCACATGACTGCAAAGCTTGATAGGCGATATAGCGCTCTTGTGGAGgtaccaatttgtacgcagattttattttacgttgatttta-gggtttttt------acataccaagtttggtgtctctacag

upper sequence: LOC_Os06g36740.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G467159_T01 (Zea mays), 5'ss of exon 11
-GTGCAGAACTCTAATATTTGTTGGCCAGAACTCTCAGTTCCATGCTGAGGCTGTTCATATGACCTCAAAGCTTGATGAGAGATATAGTGCTCTCGTAGAGgtgcttatttaactgatagtttgatccaacgaaaaaaaaatatgttctttggtttgaaatgtcaatcttgatgtctttgcag
 |||||| || ||||| ||||||||  |||| || |||||||||||||| |||||||| |||||  |||||||||||  | ||||||| ||||| || ||||| |  ||||    |    ||| ||   ||    |   | | |    |||  ||| | ||  |||  ||| || || | |||
AGTGCAGGACACTAATTTTTGTTGGTGAGAATTCCCAGTTCCATGCTGAAGCTGTTCACATGACTGCAAAGCTTGATAGGCGATATAGCGCTCTTGTGGAggtaccaatttgtacgcagattttattttac----attgattttagggttt--ttttacataccaagtttggtgcctctacag

upper sequence: LOC_Os06g36740.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G383817_T01 (Zea mays), 5'ss of exon 6
GTGCAGAACTCTAATATTTGTTGGCCAGAACTCTCAGTTCCATGCTGAGGCTGTTCATATGACCTCAAAGCTTGATGAGAGATATAGTGCTCTCGTAGAGgtgcttatttaactgatagtttgatccaacgaaaaaaaaatatgttctttggtttgaaatgtcaatcttgatgtctttgcag
|||||| || ||||| ||||||||  |||| || |||||||||||||| ||||| || |||||  |||||||||||  | ||||||| ||||| || ||||| |  ||||    |    ||| ||   |||   |    |   ||| |||      | ||  |||  ||| ||||| | |||
GTGCAGGACACTAATTTTTGTTGGTGAGAATTCCCAGTTCCATGCTGAAGCTGTGCACATGACTGCAAAGCTTGATAGGCGATATAGCGCTCTTGTGGAGgtaccaatttgtacgcagattttattttacgttgatttta-gggtttttt------acataccaagtttggtgtctctacag

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|88963890|gb|CI031223.1|CI031223
EST:     CTGTTCATATGACCTCAAAGCTTGATGAGAGATATAGTGCTCTCGTAGAG                         GTACAAGGATGTGGATCTGTTGTGACAGAGGAGCAACCGCATGCAATGCTT
genomic: CTGTTCATATGACCTCAAAGCTTGATGAGAGATATAGTGCTCTCGTAGAGgtgcttattt ... gtctttgcagGTACAAGGATGTGGATCTGTTGTGACAGAGGAGCAACCGCATGCAATGCTT
EST: gi|87004289|gb|CI296831.1|CI296831
EST:     CTGTTCATATGACCTCAAAGCTTGATGAGAGATATAGTGCTCTCGTAGAG                         GTACAAGGATGTGGATCTGTTGTGACAGAGGAGCAACCGCA
genomic: CTGTTCATATGACCTCAAAGCTTGATGAGAGATATAGTGCTCTCGTAGAGgtgcttattt ... gtctttgcagGTACAAGGATGTGGATCTGTTGTGACAGAGGAGCAACCGCA
EST: gi|86256344|gb|CI012634.1|CI012634
EST:     CTGTTCATATGACCTCAAAGCTTGATGAGAGATATAGTGCTCTCGTAGAG                         GTACAAGGATGTGGATCTGTTGTGACAGAGGAGCAACCGCATGCAATGCTT
genomic: CTGTTCATATGACCTCAAAGCTTGATGAGAGATATAGTGCTCTCGTAGAGgtgcttattt ... gtctttgcagGTACAAGGATGTGGATCTGTTGTGACAGAGGAGCAACCGCATGCAATGCTT

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: 53 (upstream exon), 23 (downstream exon)
Score: 1

GTGCAGAACTCTAATATTTGTTGGCCAGAACTCTCAGTTCCATGCTGAGGCTGTTCATATGACCTCAAAGCTTGATGAGAGATATAGTGCTCTCGTAGAGgtgcttattt ... gtctttgcagGTACAAGGATGTGGATCTGTTGTGACAGAGGAGCAACCGCATGCAATGCTTATGCCGCTGGAGTACTTCCTCATGGGATACGGATTGTACAGACCAAGCC




<











<


<