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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catcagtacaagcgttgaaagtagaaaattgtacctggctattagatggacataaacattcctgagattaattactgacacagcattttagtaataacagATAACTTCAACAGCTGGTGGTGGCACTTTGACACTGGAATTTGGTGTCCTGAGTCGTTTGACTAATGATAGCG

Basic information

species Oryza sativa
transcript LOC_Os01g56670.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G173868_T02 (Zea mays), 3'ss of exon 6
catcagtacaagcgttgaaagtagaaaattgtacctggctattagatggacataaaca-ttcctgagattaattactgaca--cagcattttagtaataacagATAACTTCAACAGCTGGTGGTGGCACTTTGACACTGGAATTTGGTGTCCTGAGTCGTTTGACTAATGATAGCG
 | ||  ||    ||  |    |   | ||     | |   | | |||| ||||| || ||  |||| || | | |||| |     || | || || |  |||||||| ||||| ||||||||||| ||||||||||||||||||||  |  ||||||| ||||||||| |||  |
-aacatcaccc-tgtcaatctcacctagtttccattcgtgctcaaatgggcataagcagtttttgagtttgactgctgagagctgacactatattattc-cagATAACATCAACGGCTGGTGGTGGTACTTTGACACTGGAATTTGGCATATTGAGTCGCTTGACTAATAATACTG

upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA10G32320.1 (Glycine max), 3'ss of exon 5
catcagtacaagcgttgaaagtag----aaaattgtacctggctattagatggacataaacattcctgagattaat----tactgaca--cagcattttagtaataacagATAACTTCAACAGCTGGTGGTGGCACTTTGACACTGGAATTTGGTGTCCTGAGTCGTTTGACTAATGATAGCG
       | |     ||| |  ||     |  ||||   ||  ||| | ||      ||  |||  |    || ||    |  | | |   || | ||| ||  |   ||||||||||||||||||||||||| || ||||| || |||||||| || || || || ||||| ||||||    
-------atattttctgagatcagttctgatcttgt-tttgtttatcatatttcttcaactattttttgtgtttatattgtgttaaaagttagtacttttgtgct--tagATAACTTCAACAGCTGGTGGTGGGACCTTGACTCTTGAATTTGGAGTTCTAAGCCGATTGACAAATGATCCTA

upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv05s0020g04650.t01 (Vitis vinifera), 3'ss of exon 7
catcagtacaagcgttgaaagtagaaaattgtacctggctattagatggacataaacattcctgagattaattactgac-acagcattttagtaataacagATAACTTCAACAGCTGGTGGTGGCACTTTGACACTGGAATTTGGTGTCCTGAGTCGTTTGACTAATGATAGCG
                                                              | ||||  ||| ||||       ||||   |  |   |||||||||||||||| |||||||| ||||||||  |||||||||| || || || || || |||||||||  | 
------------------------------------------------------------gttcagatacatttctgattgtctgatttgtctttttttagATAACTTCAACAGCAGGTGGTGGGACTTTGACCTTGGAATTTGGGGTGCTTAGCCGCTTAACTAATGATCCCA

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|29678673|gb|CB674948.1|CB674948
EST:     CATTTGGATCAGTAAATTTATTGTATGGAGTCGATGAAAATGAAAGCAAG                         ATAACTTCAACAGCTGGTGGTGGCACTTTGACACTGGAATTTGGTGTCCTG
genomic: CATTTGGATCAGTAAATTTATTGTATGGAGTCGATGAAAATGAAAGCAAGgcaagcttat ... gtaataacagATAACTTCAACAGCTGGTGGTGGCACTTTGACACTGGAATTTGGTGTCCTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggacataaacattcctgagattaattactgacacagcattttagtaataacagATAACTTCAACAGCTGGTGGTGGCACTTTGACACTGGAATTTGGTGTCCTGAGTCGTTTGACTAATGATAGCG
                           tactgac  putative branch site (score: 1)
                                       attttagtaataaca  TA-rich tract