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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgctctctaaatagaatatattttgctgtaaatatatccttttcacattaatacaatctaaaaatgaccctatgtagGTTGCATTGAAGCTTGAGCATCGAAACAGTAAAGGGTGCAATTATGGTGCCCCCTATGAGTGGCAAGTTTACCA

Basic information

species Oryza sativa
transcript LOC_Os07g07560.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 3
gtttgctctctaaa-tagaatatattttgctgtaaatatatccttttcacattaatacaatctaaaaatgaccctatgtagGTTGCATTGAAGCTTGAGCATCGAAACAGTAAAGGGTGCAATTATGGTGCCCCCTATGAGTGGCAAGTTTACCA
|||||     |||  |   ||  ||||   |      || |     | |||| ||| ||||| ||   | |   | ||||||||||||||||  | |||||||| ||||||||||| |||||||||||  |||| |||||||||||||||||  |
gtttgtcacttaaccttttatgaatttgatt-----catttttcccttacataaatccaatc-aattgtaattttttgtagGTTGCATTGAAATTCGAGCATCGTAACAGTAAAGGATGCAATTATGGCCCCCCATATGAGTGGCAAGTTTATAA

upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G164265_T03 (Zea mays), 3'ss of exon 3
gtttgctctctaaatagaatat-attttgctgtaaatatatccttttcacattaatacaatctaaaaatgaccctatgtagGTTGCATTGAAGCTTGAGCATCGAAACAGTAAAGGGTGCAATTATGGTGCCCCCTATGAGTGGCAAGTTTACCA
|||||     || | |   ||| | |||| || |    | |  |  | |||| ||| || |  |      |   | ||||||| ||||||||  | |||||||||||||||||||| |||||||||||  | || ||||||||||| |||||  |
gtttgtcacttacacattttatgaatttgatgga----ttttttccttacataaatccattaaatggtaaaatttttgtagGTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCTCCATATGAGTGGCAGGTTTATAA

upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 3
-----gtttg---ctctctaaatagaatatattttgctgtaaatatatccttttcacattaatacaatctaaaaatgaccctatg-tagGTTGCATTGAAGCTTGAGCATCGAAACAGTAAAGGGTGCAATTATGGTGCCCCCTATGAGTGGCAAGTTTACCA
      ||      | | |||  | |  | | ||| |     || ||  |  |||| ||  || | || ||||      |  ||   |||| ||||||||| ||||||| || || || ||||| |||||||||||  | || |||||||||||||| ||| |
gtactattcaaatttttttaaccatatcaaagttttccaatgat-tagtcacttcagat--atgctatttaaagggattcgcataacagGTAGCATTGAAGTTTGAGCACCGGAATAGCAAAGGATGCAATTATGGCCCTCCTTATGAGTGGCAAGTCTACAA

upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------gtttgctctctaaatagaatatattttgctgtaaa--tatatccttttcacattaatacaatctaaa-----aatgaccc----tatgtagGTTGCATTGAAGCTTGAGCATCGAAACAGTAAAGGGTGCAATTATGGTGCCCCCTATGAGTGGCAAGTTTACCA
                                              |  || |    | |||   |  || ||||    |     | |  |||| |   |||||   | |  |     | ||| |     | || ||||||| |||||| | |||||||| |  ||||| || |||||||||||| | || ||||||||||| ||||||  
gtattcaatttcttacaatttgttctgctctacttctttcgcagcagcatgtttggaagatactctgcatattgcatcgaggtcttgtgatttttaatgtaataagttttgtattcatattgaactcgtttgtgcagGTTGCGTTGAAGTTCGAGCATCGGAGTAGTAAGGGCTGCAATTATGGTCCTCCTTATGAGTGGCAGGTTTACAC

upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 2
gtttgctctctaaatagaatatattttgctgtaaatatatccttttcacattaatacaatctaaaaatgaccctatgtagGTTGCATTGAAGCTTGAGCATCGAAACAGTAAAGGGTGCAATTATGGTGCCCCCTATGAGTGGCAAGTTTACCA
||   || |   ||    || |  |  | ||   ||     |||||| ||        ||| ||| |||    | |  ||||||| |||||| |||| ||  ||| ||||||||| ||||| |||||  | || ||||||||||||||||||  
gtagactgttcgaa---gatttgctcagttg--gattggctcttttctcagcggc-tgatc-aaagatg---ttgt-cagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACAC

upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 2
gtttgctctctaaatagaatatattttgctgtaaatatatccttttcacattaatacaatctaaaaatgaccctatgtagGTTGCATTGAAGCTTGAGCATCGAAACAGTAAAGGGTGCAATTATGGTGCCCCCTATGAGTGGCAAGTTTACCA
||   || |   || |       |||  | ||     |   |||||| ||        ||| ||| |||    | |  ||||||| |||||| |||| ||  ||| ||||||||| ||||| |||||  | || ||||||||||||||||||  
gtagactgttcgaagat------tttctcagttggattgctcttttctcagcggc-tgatc-aaagatg---ttgt-cagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACAC

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|66915500|gb|CX102348.1|CX102348
EST:     GTAGAAGGGTATCTGGTGGAACTAATCGTACTGGTCCTGATGCATATGAG                         GTTGCATTGAAGCTTGAGCATCGAAACAGTAAAGGGTGCAATTATGGTGCC
genomic: GTAGAAGGGTATCTGGTGGAACTAATCGTACTGGTCCTGATGCATATGAGgtttgctctc ... ccctatgtagGTTGCATTGAAGCTTGAGCATCGAAACAGTAAAGGGTGCAATTATGGTGCC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctgtaaatatatccttttcacattaatacaatctaaaaatgaccctatgtagGTTGCATTGAAGCTTGAGCATCGAAACAGTAAAGGGTGCAATTATGGTGCCCCCTATGAGTGGCAAGTTTACCA
                                 atctaaa  putative branch site (score: 3)
                      acattaatacaatcta  TA-rich tract