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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGATTCGCTCAGAATCAGCTCACTTTGTGGAAGTACCCGTCAATGGTTAAGATGGCTGAACTCACTGGCCATACCTCTCGTGTCCTTTTCACGGCTCAGgttatcttttgctccttgtacctgccgtttaaattgacaaatattgctctgaacagattgctgattacttgtcttgtggtaatcttgcag

Basic information

species Oryza sativa
transcript LOC_Os04g51110.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g51110.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA01G43980.1 (Glycine max), 5'ss of exon 4
TGGATTCGCTCAGAATCAGCTCACTTTGTGGAAGTACCCGTCAATGGTTAAGATGGCTGAACTCACTGGCCATACCTCTCGTGTCCTTTTCACGGCTCAGgttatcttttgctccttgtacctgccgtttaaattgac-aaatattgctctgaacagattgctgattacttgtcttgtggtaatcttgcag----
||| ||  | ||||||||| | ||  | ||||| ||||| |||||||| ||||||||||| |||||||| ||||||||  | || ||||||| ||| ||||| || | ||  |   | |   ||      ||  |||  | ||  |    |     | ||  |  | | | ||    ||  || ||| |      
TGGTTTTACCCAGAATCAGTTAACACTTTGGAAATACCCCTCAATGGTGAAGATGGCTGAGCTCACTGGTCATACCTCCAGAGTTCTTTTCATGGCCCAGgtaatttatttttggattttgttgagcagaaacctgattagattgtctattttgaggcttttttctgattagtgcaatgccaaacttcctttcag

upper sequence: LOC_Os04g51110.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA11G01450.1 (Glycine max), 5'ss of exon 3
TGGATTCGCTCAGAATCAGCTCACTTTGTGGAAGTACCCGTCAATGGTTAAGATGGCTGAACTCACTGGCCATACCTCTCGTGTCCTTTTCACGGCTCAGgttatcttttgctccttgtacctgcc-gtttaaattgacaaatattgctctgaacagattgctgattacttgtcttgtggtaatcttgcag
||| ||  | ||||||||| | ||  | ||||| ||||| |||||||| ||||||||||| |||| ||||||||| ||  | || ||||||| ||| ||||| || ||||    |  | ||   || | || | ||||    | ||  | |||     || ||||||| | ||  |||     || | |||
TGGTTTTACCCAGAATCAGTTAACACTTTGGAAATACCCCTCAATGGTGAAGATGGCTGAGCTCAATGGCCATACTTCAAGAGTTCTTTTCATGGCCCAGgtaatttttt--ctcgagcacaaacctgattgatttgattg-tcttattatgaggcttttcctgattagt-gtgatgtcaacttccttcag

upper sequence: LOC_Os04g51110.2 (Oryza sativa), 5'ss of exon 4
lower sequence: AT4G33270.1 (Arabidopsis thaliana), 5'ss of exon 4
TGGATTCGCTCAGAATCAGCTCACTTTGTGGAAGTACCCGTCAATGGTTAAGATGGCTGAACTCACTGGCCATACCTCTCGTGTCCTTTTCACGGCTCAGgt---------tatcttttgctccttgtacctgccgtttaaattgacaaatatt----gctctgaac---agattgctgattacttgtcttgtggtaatcttgcag
 || ||  | ||||||||||||||  | |||||||| || || ||||| || |||||||| |||||||| ||||| ||  | || || |  | ||| |||||          | ||    |   || || |||  |     | |   | || ||    |   | |     | |       ||  |||| ||||  |  |||| |||
CGGGTTTACACAGAATCAGCTCACACTTTGGAAGTATCCATCCATGGTGAAAATGGCTGAGCTCACTGGTCATACATCAAGAGTTCTATATATGGCCCAGgtaaaggaaaacaactaaatcaatttttaactgttgaaagtagttggagatgtttgaggtctttagtcctaaaacttgtgttgtttgtgttgtatt--tcttacag

upper sequence: LOC_Os04g51110.2 (Oryza sativa), 5'ss of exon 4
lower sequence: AT4G33260.2 (Arabidopsis thaliana), 5'ss of exon 4
TGGATTCGCTCAGAATCAGCTCACTTTGTGGAAGTACCCGTCAATGGTTAAGATGGCTGAACTCACTGGCCATACCTCTCGTGTCCTTTTCACGGCTCAGgtta--tcttttgctccttgtacctgccgtttaaattgacaaatattgctctgaacagattgctgattacttgtc--ttgtggtaatct-tgcag
||| ||  | ||||||||||| ||  | ||||||||||| || ||||| || |||||||| |||||||| ||||| ||  | || || |  | ||| ||||| |  || |    | |||  |   |     ||  ||||      |||   | |     |   | |     |||   |||| ||  | | | |||
TGGGTTTACACAGAATCAGCTTACACTTTGGAAGTACCCATCCATGGTGAAAATGGCTGAGCTCACTGGTCATACATCAAGAGTTCTATATATGGCCCAGgtaacgtcatcaatttctttaagtggtgaagtagtttga--gtctttgaggtcattcagtccttaaacttgtgttgtttgttgtgttttctacag

upper sequence: LOC_Os04g51110.2 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv16s0039g02510.t01 (Vitis vinifera), 5'ss of exon 4
TGGATTCGCTCAGAATCAGCTCACTTTGTGGAAGTACCCGTCAATGGTTAAGATGGCTGAACTCACTGGCCATACCTCTCGTGTCCTTTTCACGGCTCAGgttatcttttgctccttg---tacctgccgtttaa-attgacaaatattgctctgaacagattgctgattacttgtcttgtggtaatcttgcag------
||| ||  | |||||||| || ||| ||||||||||||| |||||||| |||||  |||| || ||||| ||||| ||  | || ||||||| |||||||||  |  | ||   |||    ||      ||||     | |||||| ||  |    |    | | |         | |    ||||      ||      
TGGCTTTTCACAGAATCAACTTACTCTGTGGAAGTACCCATCAATGGTGAAGATTACTGAGCTTACTGGTCATACATCCAGAGTTCTTTTCATGGCTCAGgtactaatatggatcttagtttagtgaatgtttctcggtaacaaatctttatggctatgtttggttcccagaaaatttaagagtaaatgcaaagaaaaga

upper sequence: LOC_Os04g51110.2 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv15s0107g00320.t01 (Vitis vinifera), 5'ss of exon 4
TGGATTCGCTCAGAATCAGCTCACTTTGTGGAAGTACCCGTCAATGGTTAAGATGGCTGAACTCACTGGCCATACCTCTCGTGTCCTTTTCACGGCTCAGgttatcttttgctccttgtacctgccgtttaaattgacaaatattgctctgaacagattgctgattac----ttgtcttgtggtaatcttgcag
 || ||  | |||||||| |||||| ||||||||||||| || ||||| || ||||| || || ||||| ||||| || || |||||||||| |||||||||  |  | |     ||          ||    |||   | | | |   |   ||   ||| | ||      ||  |||||  |  | |  |||
CGGTTTTACACAGAATCAACTCACTCTGTGGAAGTACCCATCGATGGTGAAAATGGCAGAGCTTACTGGTCATACATCCCGAGTCCTTTTCATGGCTCAGgtactaatataaaaattcccttctatcttcttgttggtgattttcgtagtagccaatctgcgggttctgatttttccttgttctcttttaccag

upper sequence: LOC_Os04g51110.2 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S27_42V6.1 (Physcomitrella patens), 5'ss of exon 8
TGGATTCGCTCAGAATCAGCTCACTTTGTGGAAGTACCCGTCAATGGTTAAGATGGCTGAACTCACTGGCCATACCTCTCGTGTCCTTTTCACGGCTCAGgttatcttttgctcctt------gtacctgccgtttaaattgacaaatattgctctgaacagattgctgattacttgtcttgtggtaatcttgcag
||||||    || ||||||||   | |||||||||| ||||| ||||| ||| ||||||| |||||||||||||||||  | ||| |      ||| ||||| | ||| ||   |||       ||   | |  | || |   |   |  ||     |||  || | |  | ||||||    |  |  ||| ||||
TGGATTTAGCCAAAATCAGCTATGTCTGTGGAAGTATCCGTCTATGGTGAAGCTGGCTGAGCTCACTGGCCATACCTCAAGAGTCTTGCATCTGGCACAGgtaaccttctgggtctttaggagatagtggtctctcaattccgc---tggtgtatccaacctat-gtttgtaacttgtgcaatattc-tctggcag

upper sequence: LOC_Os04g51110.2 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ31840 (Selaginella moellendorffii), 5'ss of exon 3
TGGATTCGCTCAGAATCAGCTCACTTTGTGGAAGTACCCGTCAATGGTTAAGATGGCTGAACTCACTGGCCATACCTCTCGTGTCCTTTTCACGGCTCAGgttatcttttgctccttgtacctgccgtttaaattgacaaatattgctctgaacagattgctgattacttgtcttgtggtaatcttgcag
|||||||   ||||| ||| | |  ||||||||||||||||| ||||| |||||||| ||||| || || || || ||  | ||| |   |  ||| |||||     ||    | | ||  |   |   |    |  | ||    ||| ||  |   |||| |                           
TGGATTCAGCCAGAACCAGTTGATCTTGTGGAAGTACCCGTCTATGGTGAAGATGGCGGAACTTACCGGTCACACATCCAGAGTCTTGCACTTGGCGCAGgtagatgttcttgcttggtttccatcagctgg--tatctaaccacgctgtgttcg--ttgcag---------------------------

upper sequence: LOC_Os04g51110.2 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ38024 (Selaginella moellendorffii), 5'ss of exon 3
TGGATTCGCTCAGAATCAGCTCACTTTGTGGAAGTACCCGTCAATGGTTAAGATGGCTGAACTCACTGGCCATACCTCTCGTGTCCTTTTCACGGCTCAGgttatcttttgctccttgtacctgccgtttaaattgacaaata-ttgctctgaacagattgctgattacttgtcttgtggtaatcttgcag
|||||||   ||||| ||| | |  ||||||||||||||||| ||||| |||||||| ||||| || || || || ||  | ||| |   |  ||| |||||     ||    | | ||   | || | | |  ||  |  ||    | |||      |||| |                           
TGGATTCAGCCAGAACCAGTTGATCTTGTGGAAGTACCCGTCTATGGTGAAGATGGCGGAACTTACCGGTCACACGTCCAGAGTCTTGCACTTGGCGCAGgtagatgttcttgcttggt---ttccatgtcagctggtatctaaccacgctgtgttcgttgcag---------------------------

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|58606176|gb|CK034209.1|CK034209
EST:     AGATGGCTGAACTCACTGGCCATACCTCTCGTGTCCTTTTCACGGCTCAG                         AGCCCTGATGGTCTCACAGTAGCATCTGCTGCAGCAGATGAGACCCTGAGA
genomic: AGATGGCTGAACTCACTGGCCATACCTCTCGTGTCCTTTTCACGGCTCAGgttatctttt ... aatcttgcagAGCCCTGATGGTCTCACAGTAGCATCTGCTGCAGCAGATGAGACCCTGAGA
EST: gi|87009881|gb|CI277382.1|CI277382
EST:     AGATGGCTGAACTCACTGGCCATACCTCTCGTGTCCTTTTCACGGCTCAG                         AGCCCTGATGGTCTCACAGTAGCATCTGCTGCAGCAGATGAGACCCTGAGA
genomic: AGATGGCTGAACTCACTGGCCATACCTCTCGTGTCCTTTTCACGGCTCAGgttatctttt ... aatcttgcagAGCCCTGATGGTCTCACAGTAGCATCTGCTGCAGCAGATGAGACCCTGAGA

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: 73 (upstream exon), 56 (downstream exon)
Score: 6

TGGATTCGCTCAGAATCAGCTCACTTTGTGGAAGTACCCGTCAATGGTTAAGATGGCTGAACTCACTGGCCATACCTCTCGTGTCCTTTTCACGGCTCAGgttatctttt ... aatcttgcagAGCCCTGATGGTCTCACAGTAGCATCTGCTGCAGCAGATGAGACCCTGAGATTCTGGAACGTATTTGGGGCTCCTGAAGCACCCAAGACTGCAACCAAGG




<











<


<