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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGATATGTGGTCAGTTGGTTGTATCTTTGCAGAAATGGTGAACCAGAAACCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattatcgtactgagattacctttttttgttctgttatttgtgtttttgccaactctctgatttatgtggtgtgttctggttacttttgaag

Basic information

species Oryza sativa
transcript LOC_Os03g01850.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01850.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G143213_T02 (Zea mays), 5'ss of exon 6
TTGATATGTGGTCAGTTGGTTGTATCTTTGCAGAAATGGTGAACCAGAAACCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattatcgtactgagattacctttttttgttctgttatttgtgtttttgccaactctctgatttatgtggtgtgttctggttacttttgaag
                 || ||||||||||| |||||||||||||| || ||||| |||||||||||||||||||| || ||| | || ||||||||||||||||||  | || |||   |||  ||| ||   |||  ||||||    |||      | |||||||    | || |  | |||| ||| ||||||
-----------------GGCTGTATCTTTGCGGAAATGGTGAACCAAAAGCCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtttgtgctggcgttagatttctta--tcttgtatttgcacattttaggtttatctgattctgtttgtat-ctatggtcactgttgaag

upper sequence: LOC_Os03g01850.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G008327_T01 (Zea mays), 5'ss of exon 5
TTGATATGTGGTCAGTTGGTTGTATCTTTGCAGAAATGGTGAACCAGAAACCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattatcgtactgagattacctttttttgttctgttatttgtgtttttgccaactctctgatttatgtggtgtgttctggttacttttgaag
||||| ||||||| || || ||||||||||| |||||||||||||| || ||||| |||||||| ||||||||||| || ||| | ||||||||||||||||||||| || || |||  ||||  ||| ||  |||||| ||||| || |||   | || ||||| || |||  |||||  | |  |||  |||||
TTGATGTGTGGTCTGTGGGCTGTATCTTTGCGGAAATGGTGAACCAAAAGCCACTATTCCCTGGCGATTCTGAGATCGACGAACTTTTTAAGATATTCAGgttctatgattgtgctggcattaaatttctt-attctgt-atttgcgtattttagacctgtctgactt-tgtt-tgtgtcattgccactgctgaag

upper sequence: LOC_Os03g01850.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G143213_T01 (Zea mays), 5'ss of exon 5
TTGATATGTGGTCAGT-TGGTTGTATCTTTGCAGAAATGGTGAACCAGAAACCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattatcgtactgagattacctttttttgttctgttatttgtgtttttgccaactctctgatttatgtggtgtgttctggttacttttgaag
 |||  | ||||| || ||| ||||||||||| |||||||||||||| || ||||| |||||||||||||||||||| || ||| | || ||||||||||||||||||  | || |||   |||  ||| ||   |||  ||||||    |||      | |||||||    | || |  | |||| ||| ||||||
-TGACGTATGGTCTGTGTGGCTGTATCTTTGCGGAAATGGTGAACCAAAAGCCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtttgtgctggcgttagatttctta--tcttgtatttgcacattttaggtttatctgattctgtttgtat-ctatggtcactgttgaag

upper sequence: LOC_Os03g01850.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA15G14390.1 (Glycine max), 5'ss of exon 5
TTGATATGTGGTCAGTTGGTTGTATCTTTGCAGAAATGGTGAACCAGAAACCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttc-tattatcgtactgagattacctttttttgttctgttatttgtgtttttgccaactctctgatttatgtggtgtgt-tctggttacttttgaag-----
||||| | |||||||| || ||||| |||||||| ||||| ||||    ||| || |||||||| || ||||||||||||||||||||||| ||||||||||   |||     | ||||  |       |||||   |  |   |   | ||    || ||| | || ||||   | ||| ||| |  |||||| ||      
TTGATGTTTGGTCAGTGGGATGTATATTTGCAGAGATGGTAAACCGACGACCTCTATTCCCTGGGGACTCTGAGATTGATGAATTATTTAAAATATTCAGgtaaatatctatttcctgatttccataaattttgcatttcttggtaaatcttaataaaatctatcatctatg-aatatgtctctag--acttttaaatgtcat

upper sequence: LOC_Os03g01850.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA09G03470.1 (Glycine max), 5'ss of exon 5
TTGATATGTGGTCAGTTGGTTGTATCTTTGCAGAAATGGTGAACCAGAAACCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttc-tattatcgtactgagattacctttttttgttctgttatttgtgtttttgccaactctctgatttatgtggtgtgt-tctggttacttttgaag-----
||||| | |||||||| || || || |||||||| ||||| |||     ||| || |||||||| || ||||||||||||||||||||||| ||||||||||   |||     | ||||  |       |||||   |  |   |   | ||    |  | | | || ||||   | ||| ||| |  |||||| ||      
TTGATGTTTGGTCAGTGGGATGCATATTTGCAGAGATGGTAAACAGACGACCTCTATTCCCTGGGGACTCTGAGATTGATGAATTATTTAAAATATTCAGgtgaatatctatttcctgatttccatgaattttgcatttctgggtaaatcttaataatatttatcatctatg-aatatgtctctag--acttttaaatgccat

upper sequence: LOC_Os03g01850.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA05G25320.1 (Glycine max), 5'ss of exon 4
TTGATATGTGGTCAGTTGGTTGTATCTTTGCAGAAATGGTGAACCAGAAACCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgt------tctattatcgtactgagattacctttttttgttctgt-tatttgtgttttt--gccaactctctgatttatgtggtgtgttctggttacttttgaag
||||||| |||||||| || || || |||||||| ||||| || ||   |||||| |||||||| || ||||||||||||||||| ||||| ||||||||||       || || |   |       ||   || ||||    |  ||||    | | |  ||  |     |||   |    |  ||  |   || |  |     
TTGATATTTGGTCAGTGGGATGCATATTTGCAGAGATGGTAAATCAACGACCACTTTTCCCTGGGGACTCTGAGATTGATGAATTGTTTAAAATATTCAGgtgaatagcctttttttccataatttctattgttctttgggaagcatattaaaatctgttggctgaaaacttgacaaagaatgcctgcccaaattcccct-----

upper sequence: LOC_Os03g01850.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA08G08330.1 (Glycine max), 5'ss of exon 5
TTGATATGTGGTCAGTTGGTTGTATCTTTGCAGAAATGGTGAACCAGAAACCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattatcgtactgagattacctttttt-tgttctgttatttgtgtttttgccaactctctga----tttatgtggtgtgttctggttacttttgaag-
||||||| |||||||| || || || |||||||| ||||| || ||   ||| || |||||||| || ||||||||||||||||| ||||| ||||||||||   ||   | |  |   || |  | | || |  | ||  | |  | ||     |   |  ||||    || |    |  ||  |||   |  ||  ||  
TTGATATTTGGTCAGTGGGATGCATATTTGCAGAGATGGTAAATCAACGACCTCTTTTCCCTGGGGACTCTGAGATTGATGAATTGTTTAAAATATTCAGgtga-atagccttttttccatgatttctattgttctttgggagtcatattaaaatctcttggctgaaaacttgacaaagaatgc-ctgcccaaattcaaatt

upper sequence: LOC_Os03g01850.2 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv15s0045g00310.t01 (Vitis vinifera), 5'ss of exon 6
TTGATATGTGGTCAGTTGGTTGTATCTTTGCAGAAATGGTGAACCAGAAACCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattatcgtactgagattacctttttttgttctgttatttgtgtttttgccaactctctgatttatgtggtgtgttctggttacttttgaag----
||||| ||||||| || || ||||| ||||| || ||||||||||||  |||| |||| ||||| || || |||||||||||||| || ||||| |||||||  ||     ||  |    ||   ||| ||| |   |    |||  |    |   |    |     | | |      ||   ||    |||||||    
TTGATGTGTGGTCTGTGGGCTGTATATTTGCTGAGATGGTGAACCAGCGACCATTGTTTCCTGGGGACTCGGAGATTGATGAATTGTTCAAGATCTTCAGgtgttaaccatgttgtacttttttttttctttctatagcctcttgattagaagttgaaaagccatgctctttataaattttcagtagactttgaagtttg

upper sequence: LOC_Os03g01850.2 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S281_23V6.1 (Physcomitrella patens), 5'ss of exon 6
TTGATATGTGGTCAGTTGGTTGTATCTTTGCAGAAATGGTGAACCAGAAACCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattatcgtactgagattacctttttttgttctgttatttgtgtttttgccaactctctgatt-tatgt-ggtgtgttctggttactt--ttgaag--
| ||  | ||||| ||||| || || || || ||||||||||  || |  || ||||||||||||||||| ||||||||||| ||||| |  ||||||||||  || | | | |    |  ||  |      | |  | ||  || |  || || || |   || |  ||| |  ||||   |    ||  |   ||| |  
TAGACGTCTGGTCCGTTGGATGCATATTCGCTGAAATGGTGACTCAAAGGCCTCTGTTCCCTGGTGATTCAGAGATTGATGAGTTATTCAGAATATTCAGgta-tactctagaatcctggatat-tcacggagattcgctaactgggaattggcaaagtgcttgttaatatctcagtgtcaaccatatagctacctgatgaa

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|33803869|gb|CF327809.1|CF327809
EST:     GGTGATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: GGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|29662032|gb|CB658307.1|CB658307
EST:     CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|88253212|gb|CI351838.1|CI351838
EST:     CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAAATGAACAAAAGTTGGCCAGGAGTTAGCTCATTA
genomic: CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCC-AAATGAAC-AAAGTTGGCCAGGAGTTAGCTCATTA
EST: gi|88978284|gb|CI384727.1|CI384727
EST:     ATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: ATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|86885548|gb|CI318699.1|CI318699
EST:     CCACTGTTCCCTGGTGATTCTGACATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|88509819|gb|CI437325.1|CI437325
EST:     AGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: AGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|38482398|gb|CF966438.1|CF966438
EST:     CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|88522726|gb|CI450366.1|CI450366
EST:     GATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: GATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC

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: 55 (upstream exon), 73 (downstream exon)
Score: 68

TTGATATGTGGTCAGTTGGTTGTATCTTTGCAGAAATGGTGAACCAGAAACCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG




<











<


<