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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacttcctcctctcagatcttcttcttcttcttcttcgcctcaagagtcagatctcatgtactagtattgtcgtgtgcttgttaatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGTCCACCGCAGCCTCGGCG

Basic information

species Oryza sativa
transcript LOC_Os03g63710.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63710.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G176612_T01 (Zea mays), 3'ss of exon 1
gtaacttcctcctctcagatcttcttcttcttcttcttcgcctcaagagtcagatctcatgtactag----tattgtcgtgtgcttgttaatttcc--cagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGTCCACCGCAGCCTCGGCG
                     | | | ||   || |   |||       |  |  ||| ||  |       || ||||     | |      | ||  ||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||| |
----------------gtgcgtgcgtattgccctgcgctgccatggatctagggcctcctgctccgccggctactgtctctcacatcacgtctccctgcagATGTGCTTCGACTGCAACGCCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGCCCACCGCAGCCTCGGGG

upper sequence: LOC_Os03g63710.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G083546_T01 (Zea mays), 3'ss of exon 1
gtaacttcctcctctcagatcttcttcttcttcttcttcgcctcaagagtcagatctcatgtacta--gtattgtcgtgtgcttgttaatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGTCCACCGCAGCCTCGGCG
              |  |  ||| ||   || | |    |||    ||   ||  ||| ||       | ||  ||   |      |    |  ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||| || |
-------------gtacgtgcttattggcctgcctgcctgccctg-gatctaggcctcctgcttcgccggatcctcagatcacatctctccttgcagATGTGCTTCGACTGCAACGCCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCGGCCGTCCACCGCAGCCTTGGGG

upper sequence: LOC_Os03g63710.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA08G36700.2 (Glycine max), 3'ss of exon 1
----------------------------------------------------------------------------------------------gtaacttcctcctctc-agatcttcttcttcttcttcttcgcct-----caagagtcagatctcatgtactagtattgtcgtgtgcttgttaatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGTCCACCGCAGCCTCGGCG
                                                                                              ||   |||    |  | ||||||  ||     ||| |    |||        | ||  ||| |  || | | |||| ||  | |  |||||  |||  |||||||| ||||| ||||  || |||||||| |||||||| |||||||| || || ||||| |||||| |||| ||||||||||| |||||||| |||||||
gtttggtttttgtaattttgaatttcgaatttcaatttgagtgcataatcgttggttccgtgatttcgttttatacagtttgaaattttcgtttgtggtttctgatttacgagatctggtttcagatctgcaatacctgtgcttgtgcgtttgatttt-tgaattggtatggtttttttgttgtttttttttcagATGTGTTTCGATTGCAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTTCTCTGCATCGATTGCTCCGCCGTACACCGCAGTCTCGGCG

upper sequence: LOC_Os03g63710.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA01G12340.2 (Glycine max), 3'ss of exon 1
---------------------------------------------------------------------------------------gtaacttcctcctctc-agatcttcttcttcttcttcttcgcc-----tcaagagtcagatctcatgtactagtattgtcgtgtgcttgttaatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGTCCACCGCAGCCTCGGCG
                                                                                       ||   |||    |  | ||||||  ||     |||      ||     |   | ||  ||| |  || | | |||| |   | |  || ||    |  |||||||| ||||| ||||  || |||||||| |||||||| |||||||| || || |||||||||||| |||| ||||||||||| |||||||| |||||||
gttttttgtttataattttgaatttcaatttgagtgcataatcgttggttccgtgatttcgtttaatatagtctgaacttttcgtttgtggtttctgatttacgagatctggtttcagatctgtgatacccgtggtagtgtgtttgatttt-tgaatttgtatggcttttttttttttttaatttcagATGTGTTTCGATTGCAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCG

upper sequence: LOC_Os03g63710.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv02s0012g01330.t01 (Vitis vinifera), 3'ss of exon 1
-------------------------------------------------gtaact-tcctcctctcagatcttcttcttct----tcttcttcgcctcaagag---tca-gatctcatgtactagtattgtcgtgtgcttgttaatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGTCCACCGCAGCCTCGGCG
                                                 ||   | |  |  | |  | | ||||  |  |    |||  |||   ||  |||   ||  |||   || |     | || |  |||   | ||   ||   ||||||| || || || |  || |||||||| || ||||| |||||||| || || |||||||||||| |||||||||||||||| ||  | || || || |
gtctgttctttactgaatttcttcgcggtatttttaaatgttttcttttgtttttattttggtttttggttttctgttcttgagatctggttcagatctggaggtttcgcgattggatctcggttttttattttgtttctttttggtttttagATGTGTTTTGATTGTAATGCGAAGAACCCGACTTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGACTGCTCCGCCGTGCATAGGAGTCTTGGGG

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|88739668|gb|CI763176.1|CI763176
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|88364273|gb|CI612222.1|CI612222
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGGAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|88302091|gb|CI667937.1|CI667937
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|88826434|gb|CI776999.1|CI776999
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|88361014|gb|CI604581.1|CI604581
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|428827|gb|D24983.1|D24983
EST:     CCGACAAGAACGCCGTNTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|58658150|gb|CK046830.1|CK046830
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCCAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|58664331|gb|CK053017.1|CK053017
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|66916299|gb|CX103147.1|CX103147
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|88721612|gb|CI744911.1|CI744911
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|88341494|gb|CI635692.1|CI635692
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|29645173|gb|CB650180.1|CB650180
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|58680319|gb|CK069006.1|CK069006
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|58677850|gb|CK066537.1|CK066537
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|87006728|gb|CI285762.1|CI285762
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCCAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|29677839|gb|CB674114.1|CB674114
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|29635513|gb|CB640522.1|CB640522
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|88288415|gb|CI661620.1|CI661620
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|88723709|gb|CI747219.1|CI747219
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|88351379|gb|CI627395.1|CI627395
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAT                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|11443001|gb|BF430888.1|BF430888
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|29679055|gb|CB675330.1|CB675330
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|33654274|gb|CF276888.1|CF276888
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctcaagagtcagatctcatgtactagtattgtcgtgtgcttgttaatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGTCCACCGCAGCCTCGGCG
                                         tgttaat  putative branch site (score: 3)
                                               tttccc  CT-rich tract
                                        ttgttaattt  TA-rich tract