Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCTTCCTTCAGAAGACCGATGAGCTCTTCCAGTGTGGACAGTTCTGTGCCGTTTTCATCAACCCTTGCTACTTCCACACTGGTCTTTTCGTGCTCCAGgtacgatgatgcaattcctgtactttgtacagtattttctagtctgtaccacctgttctgtaactcaacctagaataggatgtgatctaacctaatacaa...

Basic information

species Oryza sativa
transcript LOC_Os10g40640.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g40640.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G114772_T01 (Zea mays), 5'ss of exon 2
CATCTTCCTTCAGAAGACCGATGAGCTCTTCCAGTGTGGACAGTTCTGTGCCGTTTTCATCAACCCTTGCTACTTCCACACTGGTCTTTTCGTGCTCCAGgtacgatgatgcaattcc--tgtactttgtacagtattttctagtctgtaccacctgttctgtaactcaacctagaataggatgtgatc--taacctaatacaa
||||||||| ||||| || || ||||| ||||| ||||||||||||||||| |||||||||||||| |||||||||||||| ||||||||||||||||||||| | |  || | || |  ||| |    |      | | |   |    ||||     | ||| | |   | |  ||| |   | | |   | || ||      
CATCTTCCTCCAGAACACAGACGAGCTATTCCAATGTGGACAGTTCTGTGCTGTTTTCATCAACCCGTGCTACTTCCACACCGGTCTTTTCGTGCTCCAGgtatg-tactgaactttcgttgttccacttgtgacctgtcccgataca-accaaaatctgtgtcattttgcttgaaatcgtgagagcttgttgacttagcta--

upper sequence: LOC_Os10g40640.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G026889_T01 (Zea mays), 5'ss of exon 2
CATCTTCCTTCAGAAGACCGATGAGCTCTTCCAGTGTGGACAGTTCTGTGCCGTTTTCATCAACCCTTGCTACTTCCACACTGGTCTTTTCGTGCTCCAGgtacgatgatgcaattcctgtactttgtacagtattttctagtctgtaccacct--gttctgtaactcaacctagaataggatgtgatctaacctaatacaa
||||||||| ||||| || || ||||| ||||||||||||||||||||||| || ||||||||||| |||||||||||||||||||||||||||||||||||| | |     | ||    |    |  |   | |  | | |  || |        |   |||      ||||||   |    |   ||  ||  ||     
CATCTTCCTCCAGAACACAGACGAGCTATTCCAGTGTGGACAGTTCTGTGCTGTGTTCATCAACCCGTGCTACTTCCACACTGGTCTTTTCGTGCTCCAGgtatg-tcccaaacttttattgtgatacaacctgtcattttgcttgaaatcgtgaggacttgttgactgacctagg-cacctagccgtcatacaaaacctct

upper sequence: LOC_Os10g40640.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ38373 (Selaginella moellendorffii), 5'ss of exon 2
CATCTTCCTTCAGAAGACCGATGAGCTCTTCCAGTGTGGACAGTTCTGTGCCGTTTTCATCAACCCTTGCTACTTCCACACTGGTCTTTTCGTGCTCCAGgtacgatgatgcaattcc---tgtactttgtacagta---ttttctagtctgtaccacctgttctgtaactcaacctagaataggatgtgat--ctaacctaatacaa
||| ||| | || || || || |||||||||||||| ||  |||| || ||    |||||||| || |||||||||||||| || |||||||| ||| |||||||     || ||      ||   |     ||||    ||| ||  |  |  |    |||| |||   |    ||      |  | ||||   |   ||    || 
CATGTTCTTGCACAACACGGACGAGCTCTTCCAGTGCGGGGAGTTTTGCGCGTGCTTCATCAATCCCTGCTACTTCCACACGGGCCTTTTCGTTCTCAAGgtacgcaagcgcgatcataaatgcgttggaggcagtgaagtttgcttcttagatctctttgttttgtgtgtgtgtctgtgtctgtgtctgatagtttcgctttggcag

upper sequence: LOC_Os10g40640.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ14850 (Selaginella moellendorffii), 5'ss of exon 2
CATCTTCCTTCAGAAGACCGATGAGCTCTTCCAGTGTGGACAGTTCTGTGCCGTTTTCATCAACCCTTGCTACTTCCACACTGGTCTTTTCGTGCTCCAGgtacgatgatgcaattcc---tgtactttgtacagta---ttttctagtctgtaccacctgttctgtaactcaacctagaataggatgtgatctaacctaatacaa
||| ||  | || || || || |||||||||||||| ||  |||| || ||    |||||||| || |||||||||||||| || |||||||| ||| |||||||     || ||      ||         ||||    ||| ||  |  |  |    |||| |||   |    || |  |  |||  | |      |   |   
CATGTTTTTGCACAACACGGACGAGCTCTTCCAGTGCGGGGAGTTTTGCGCGTGCTTCATCAATCCCTGCTACTTCCACACGGGCCTTTTCGTTCTCAAGgtacgcaagcgcgatcataaatgcgtaggaggcagtgaagtttgcttcttagatctctttgttttgtgtgtgtgtct-gtgtctgata-gtttcgctttggcag--

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|300216231|gb|HO088016.1|HO088016
EST:     TTCGTGCTCCAG                         CCTTCTATGGATGTCTTCAAAGGCATGCTTCATGACCTAGAGATTGGCCGT
genomic: TTCGTGCTCCAGgtacgatgat ... ccatttacagCCTTCTATGGATGTCTTCAAAGGCATGCTTCATGACCTAGAGATTGGCCGT
EST: gi|38478210|gb|CF962343.1|CF962343
EST:     CCGTTTTCATCAACCCTTGCTACTTCCACACTGGTCTTTTCGTGCTCCAG                         CCTTCTATGGATGTCTTCAAAGGCATGCTTCATGACCTAGAGATTGGCCGT
genomic: CCGTTTTCATCAACCCTTGCTACTTCCACACTGGTCTTTTCGTGCTCCAGgtacgatgat ... ccatttacagCCTTCTATGGATGTCTTCAAAGGCATGCTTCATGACCTAGAGATTGGCCGT

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: 60 (upstream exon), 73 (downstream exon)
Score: 8

CATCTTCCTTCAGAAGACCGATGAGCTCTTCCAGTGTGGACAGTTCTGTGCCGTTTTCATCAACCCTTGCTACTTCCACACTGGTCTTTTCGTGCTCCAGgtacgatgat ... ccatttacagCCTTCTATGGATGTCTTCAAAGGCATGCTTCATGACCTAGAGATTGGCCGTGCCAACTCTGATGGTGCTGACCAAGGGTTTCTTGTCGGCTGCTACCCAG




<











<


<