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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaattttgattgattttatgacttttttgttgctacatgcactaatttcgttttgtaattcatgaatgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCAGAATCTTTATGTGGCATTGGTCCACCACCATTTCGTCAATTTGTTGAGT

Basic information

species Oryza sativa
transcript LOC_Os01g10150.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 9
--------------------gttaa--ttttgattgattttatgacttttttgttgctacatg------cactaatttcgt-tttgtaattcatgaatgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCAGAATCTTTATGTGGCATTGGTCCACCACCATTTCGTCAATTTGTTGAGT
                    | | |  ||||  ||  |  ||    |||||||||  ||  |       ||| |||||  | | ||| |||| | ||| || |||||||||||| |||||||||||||| ||||||||||||||||| || ||||| || ||| | ||||| ||  |||||| ||| || ||  | ||||||||||
gttagtgtagttgatgttctgctcacctttttcttactcctactctttttttgtttttatttaaatactcacaaattttttatctgttattcttcaatcaatttagGGAGAGAACAAAGGTTTTCTTGTCTGCAAGAAAAAGATGGCGACATCTCCGGAGTCTCTGTGTGGAATCTGTCCACAACCTTTCCGGAATTTTGTTGAGT

upper sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 9
gttaattttgattgattttatgacttttttgttgcta-catgcactaatttcgtt-ttgtaattcatgaatgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCAGAATCTTTATGTGGCATTGGTCCACCACCATTTCGTCAATTTGTTGAGT
|||| | ||  || |  |  | | |||  |  |  |   |      ||| |  || || | |||  |   |      ||||||| |||||||| |||||||| ||||||||||||||||| || ||||||||| |||| ||| || || |||| | ||||||||| ||||||||||| |
gttattattccttcaaatagtcattttagtactaatggtaaatgaaaatatgattcttatgatttttt--ttgttacagGGAGAAAATAAAGGGTTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCAGAAACTTTGTGTTGCTTTTGTCCTCAACCATTTCGACAATTTGTTGAAT

upper sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 9
gttaattttgattgattttatgacttttttgttg-ctacatgcactaatttcgttttgtaattcatgaatgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCAGAATCTTTATGTGGCATTGGTCCACCACCATTTCGTCAATTTGTTGAGT
|||| | ||| || |  |  | | |||  |  |   |  |      ||| |   | | ||    |    |      ||||||| |||||||| |||||||| ||||||||||||||||| || ||||||||| |||| ||| || || |||| | ||||||||| |||||||| || |
gttattattgtttcaaatagtcattttagtactaattgtaaatgaaaatatgactct-tatgaaactttttgttacagGGAGAAAATAAAGGGTTTCTTGTCTGCAAGAAAAAGATGGCCACGTCTCCAGAAACTTTGTGTTGCTTTTGTCCCCAACCATTTCGGCAATTTGTGGAAT

upper sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 9
gttaattttgattgattttatgacttttttgttgcta-catgcactaatttcgttttgtaattcatgaatgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCAGAATCTTTATGTGGCATTGGTCCACCACCATTTCGTCAATTTGTTGAGT
|||| | |||  | |  |  | | ||   |  |  |   | |    || |  | ||  ||    ||   |      ||||||| |||||||| |||||||| ||||||||||||||||| || ||||| ||| |||| ||| || |  |||| | ||||||||| ||||||||||| |
gttattattgtctcaaatagtcatttgagtactaatggtaagtcaaaaatatgattcttatgagattttttgttacagGGAGAAAATAAAGGATTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCTGAAACTTTGTGTTGCTTGTGTCCTCAACCATTTCGGCAATTTGTTGAAT

upper sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 9
gttaattttgattgattttatgacttttttgttgctacatgcactaatttcgttttgtaattcatgaatgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCAGAATCTTTATGTGGCATTGGTCCACCACCATTTCGTCAATTTGTTGAGT------
||||  |||| || ||||  || |   |||  |  | ||  || ||| || || |    |||  |         ||||||||||| |||||||| |||||||||||||| |||||||| || || |||||| || | ||  || |  |||| | ||| |||||||| ||||| ||||      
gtta--tttgttttatttcctggcaactttccttgt-caatcattaacttggtct----atttgt---------tagggagagAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGTATGTGG

upper sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT2G25760.1 (Arabidopsis thaliana), 3'ss of exon 9
gttaattttgattgattttatgacttttttgttgctacatgcactaatttcgttttgtaattcatgaatgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCAGAATCTTTATGTGGCATTGGTCCACCACCATTTCGTCAATTTGTTGAGT
|||       | | |  ||||   |||| | |     ||        | ||  |   ||| |           |||||||||||| |||||||| |||||||||||||| |||||||| || || |||||| || | ||  || |  |||| | ||| |||||||| ||||| ||||
gttggggac-actaaagttatttgttttatttcctggcaactttccttgtcaatcattaacttggtctatttgttagGGAGAGAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGT

upper sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 9
------------------------------------------------gttaattttgattgattttatgacttttttgttgctacatgcactaatttcgttttgtaattcatgaa----tgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCAGAATCTTTATGTGGCATTGGTCCACCACCATTTCGTCAATTTGTTGAGT
                                                   | ||  |||  | ||| |  ||| | |     |  |     | | ||  |||| |  ||| | ||       |  ||||||||||| || || || |||||||||||||| ||||||||||| ||||| ||| || | ||| || |  |||||   || ||  | || |||||||| |
gttggctccattcgaagttccgataaaatttgttccttctcttcaatttgaagttccgataaaatttgttccttgtcttcctttcaagtttttgacttgatttttttgttcttaaaatcccatatatagGGAGAGAACAAGGGGTTCCTTGTTTGCAAGAAGAAGATGGCAACATCTCCGGAAGCTCTGTGTTGCTTCTGTCCAATGCCTTTCAGACAGTTTGTTGAAT

upper sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 9
gttaattttgattgattttatgacttttttgttgctacatgcactaatttcgttttgtaattcatgaatgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCAGAATCTTTATGTGGCATTGGTCCACCACCATTTCGTCAATTTGTTGAGT
||| |   |     |  |||       |||  |  ||  ||      |      || | |  ||  |      |||||||||||||||||| |  ||||||||||| || ||||||||||| ||||||||| |||| ||| || || |||| |  || ||||| || |||||||| |
gttgacagtttccaaacttaaataggattttcttttatgtgattctgtacatcattctgaaccaacagcttctttagGGAGAGAATAAAGGGTACCTTGTTTGCAAAAAGAAGATGGCAACATCTCCAGAAGCTTTGTGTTGCTTTTGTCCTCAGCCTTTTCGGCAGTTTGTTGAAT

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|58696276|gb|CK084963.1|CK084963
EST:     CACACTTATTTTCCTTCTCCGTGGCCGCCTGCCTTGTGCAAGGATTCCAG                         TGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCA
genomic: CACACTTATTTTCCTTCTCCGTGGCCGCCTGCCTTG-GCAAGGATTCCAGgttaattttg ... atgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCA
EST: gi|88573975|gb|CI665744.1|CI665744
EST:     ACACACTTATTTTCCTTCTCCGTGGCCGCCTGCCTTGGCAAGGATTCCAG                         GGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTC
genomic: ACACACTTATTTTCCTTCTCCGTGGCCGCCTGCCTTGGCAAGGATTCCAGgttaattttg ... atgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTC
EST: gi|29645031|gb|CB650038.1|CB650038
EST:     ACACACTTATTTTCCTTCTCCGTGGCCGCCTGCCTTGGCAAGGATTCCAG                         GGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCA
genomic: ACACACTTATTTTCCTTCTCCGTGGCCGCCTGCCTTGGCAAGGATTCCAGgttaattttg ... atgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCA
EST: gi|29670785|gb|CB667060.1|CB667060
EST:     ACACACTTATTTTCCTTCTCCGTGGCCGCCTGCCTTGGCAAGGATTCCAG                         GGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCA
genomic: ACACACTTATTTTCCTTCTCCGTGGCCGCCTGCCTTGGCAAGGATTCCAGgttaattttg ... atgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCA

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: 37

CCACTTGGGAAGAACTGGATGCAGGAGAGATGACCTTGAATCCCTTGCATACACACTTATTTTCCTTCTCCGTGGCCGCCTGCCTTGGCAAGGATTCCAGgttaattttg ... atgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCAGAATCTTTATGTGGCATTGGTCCACCACCATTTCGTCAATTTGTTGAGT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttttttgttgctacatgcactaatttcgttttgtaattcatgaatgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCAGAATCTTTATGTGGCATTGGTCCACCACCATTTCGTCAATTTGTTGAGT
                   cactaat  putative branch site (score: 37)
                              ttttgtaatt  TA-rich tract