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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattatgaataccatcatcccatgttgttagttgccatccttgtttaatgaactatgtttaaacacaatgaaatcataaatttaaacacaatgaagaatgaactatgcttatttgtttcaacatgcatagagacctgggaattaacaagtttatgcaatttcagGGTTCCAATAGGGCAAGGGTATGGTCTTACTGAGACATGTGCTGGAGGAACATTTTCTGAGTATGATGACCCATCTGTTGGTCGCGTTGGTGCTCCACTA

Basic information

species Oryza sativa
transcript LOC_Os12g07110.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g07110.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G118286_T01 (Zea mays), 3'ss of exon 7
gtaagattatgaataccatcatcccatgttgttagttgccatccttgtttaatgaactatgtttaaacacaatgaaatcataaatttaaacacaatgaagaatgaactatgcttatttgtttcaacatgcatagagacctgggaattaacaagtttatgcaatttcagGGTTCCAATAGGGCAAGGGTATGGTCTTACTGAGACATGTGCTGGAGGAACATTTTCTGAGTATGATGACCCATCTGTTGGTCGCGTTGGTGCTCCACTA
||||||||||| || || ||||  | ||||||| | || ||    |  || |    |||||||    | ||  |    |||  ||||||     | ||  |||    ||||   | ||   |||   ||  |  ||  |||  | | |  | |||||||||||||||||| ||||||||||||||| |||||||| ||||| || ||||||||||| |||||||| |||||||||||| ||||||| ||||| |||||||||||||||
gtaagattatgtatgcc-tcatttc-tgttgtttgatggcaattat-cttgaaatcctatgtt----cccatcg----catgcatttaat----acgataaatatgttatg---actt-cctcactgtgtttgcag-tctgacattgataaggtttatgcaatttcagGGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGACATTTTCAGAGTATGATGACACATCTGTCGGTCGTGTTGGTGCTCCACTA

upper sequence: LOC_Os12g07110.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA13G03280.1 (Glycine max), 3'ss of exon 6
gtaagattatgaataccatcatcccatgttgttagttgccatccttgtttaatgaactatgtttaaacacaatgaaatcataaatttaaacacaatgaagaatgaactatgcttatttgtttcaacatgcatagagacctgggaattaacaagtttatg--caatttcagGGTTCCAATAGGGCAAGGGTATGGTCTTACTGAGACATGTGCTGGAGGAACATTTTCTGAGTATGATGACCCATCTGTTGGTCGCGTTGGTGCTCCACTA
                                                                    |  |   | |  ||  ||| |    | ||     |    | ||||| ||||  |   | |   ||        |  ||| | || ||||||  ||  ||||| | |||||| || ||||| ||||||||||| ||||| |||||||| || ||||| |||||   ||||||  ||||||| || || |||||  | || || 
--------------------------------------------------------------------aggaaatatttctagcttttactgtagtgctttttcttttttgctt-tttgcgtttcctttattattcttgctgtcatttataa-tttatggtcatattcagTGCTCCAATCGGTCAAGGATATGGTCTTACAGAGACTTGTGCTGGTGGGACATTCTCTGATGTTGATGATACATCTGTCGGCCGTGTTGGACCACCTCTT

upper sequence: LOC_Os12g07110.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT1G77590.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaagattatgaataccatcatcccatgttgttagttgccatccttgtttaatgaactatgtttaaacacaatgaaatcataaatttaaacacaatgaagaatgaactatgcttatttgtttcaacatgcatagagacctgggaattaacaagtttatgcaatttcagGGTTCCAATAGGGCAAGGGTATGGTCTTACTGAGACATGTGCTGGAGGAACATTTTCTGAGTATGATGACCCATCTGTTGGTCGCGTTGGTGCTCCACTA
                                                                    | || |||  | | ||| |   |   | |     |   ||    | || | |||         |  |   ||  ||  |||||    ||| |    |||||| |||||| || || || ||||| || || ||||| |||||||| ||||| || || |||| ||| ||| |||| ||||| || |||||||||||||| 
------------------------------------------------------------------gta-aacgaatccctgaatatctccttgaggcttgctactctccaat-atatcttttcgtccctttccatttctatgatctaacactgatattc---ctcagGGCTCCAATCGGTCAGGGATATGGGCTCACAGAGACTTGTGCTGGTGGAACCTTCTCGGAGTTTGAGGACACATCCGTTGGCCGTGTTGGTGCTCCACTT

upper sequence: LOC_Os12g07110.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv18s0001g02810.t01 (Vitis vinifera), 3'ss of exon 8
gtaagattatgaataccatcatcccatgttgttagttgccatccttgtttaatgaactatgtttaaacacaatgaaatcataaatttaaaca-caatgaagaatgaactatgcttatttgtttcaacatgcatagagacctgggaattaacaagtttatgcaatttcagGGTTCCAATAGGGCAAGGGTATGGTCTTACTGAGACATGTGCTGGAGGAACATTTTCTGAGTATGATGACCCATCTGTTGGTCGCGTTGGTGCTCCACTA
                                                          || |    | ||| | |  |   ||  |   |||   ||| || ||| | |||  |  ||  | |     |   |      ||   | | |||     | | || |||||| | ||||||||  ||||||||||| || || ||||  |||||||| || |||||||| |||||||||||  ||||||||||||| |||||||||||||| 
----------------------------------------------------------atttaaggaaacacttagctggcaatgtcctacaatcatgcagtatgcaatattatccttcctcttgttgtaattg-----ctctaagtgaac-----tgt-cattttcagTGCTCCAATAGTTCAAGGGTATGGCCTGACAGAGAGTTGTGCTGGTGGTACATTTTCCGAGTATGATGATACATCTGTTGGTCGTGTTGGTGCTCCACTT

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|29669841|gb|CB666116.1|CB666116
EST:     GGAGCACCTCTATCAGGAGATACCCAGAGATTTATCAATATATGCCTTGG                         GGTTCCAATAGGGCAAGGGTATGGTCTTACTGAGACATGTGCTGGAGGAAC
genomic: GGAGCACCTCTATCAGGAGATACCCAGAGATTTATCAATATATGCCTTGGgtaagattat ... gcaatttcagGGTTCCAATAGGGCAAGGGTATGGTCTTACTGAGACATGTGCTGGAGGAAC
EST: gi|29614988|gb|CB620001.1|CB620001
EST:     GGAGCACCTCTATCAGGAGATACCCAGAGATTTATCAATATATGCCTTGG                         GGTTCCAATAGGGCAAGGGTATGGTCTTACTGAGACATGTGCTGGAGGAAC
genomic: GGAGCACCTCTATCAGGAGATACCCAGAGATTTATCAATATATGCCTTGGgtaagattat ... gcaatttcagGGTTCCAATAGGGCAAGGGTATGGTCTTACTGAGACATGTGCTGGAGGAAC
EST: gi|29675500|gb|CB671775.1|CB671775
EST:     GGAGCACCTCTATCAGGAGATACCCAGAGATTTATCAATATATGCCTTGG                         GGTTCCAATAGGGCAAGGGTATGGTCTTACTGAGACATGTGCTGGAGGAAC
genomic: GGAGCACCTCTATCAGGAGATACCCAGAGATTTATCAATATATGCCTTGGgtaagattat ... gcaatttcagGGTTCCAATAGGGCAAGGGTATGGTCTTACTGAGACATGTGCTGGAGGAAC
EST: gi|58030548|gb|CX728091.1|CX728091
EST:     GGAGCACCTCTATCAGGAGATACCCAGAGATTTATCAATATATGCCTTGG                         GGTTCCAATAGGGCAAGGGTATGGTCTTACTGAGACATGTGCTGGAGGAAC
genomic: GGAGCACCTCTATCAGGAGATACCCAGAGATTTATCAATATATGCCTTGGgtaagattat ... gcaatttcagGGTTCCAATAGGGCAAGGGTATGGTCTTACTGAGACATGTGCTGGAGGAAC
EST: gi|29672201|gb|CB668476.1|CB668476
EST:     GGAGCACCTCTATCAGGAGATACCCAGAGATTTATCAATATATGCCTTGG                         GGTTCCAATAGGGCAAGGGTATGGTCTTACTGAGACATGTGCGGGAGGAAC
genomic: GGAGCACCTCTATCAGGAGATACCCAGAGATTTATCAATATATGCCTTGGgtaagattat ... gcaatttcagGGTTCCAATAGGGCAAGGGTATGGTCTTACTGAGACATGTGCTGGAGGAAC
EST: gi|29614945|gb|CB619958.1|CB619958
EST:     GGAGCACCTCTATCAGGAGATACCCAGAGATTTATCAATATATGCCTTGG                         GGTTCCAATAGGGCAAGGGTATGGTCTTACTGAGACATGTGCTGGAGGAAC
genomic: GGAGCACCTCTATCAGGAGATACCCAGAGATTTATCAATATATGCCTTGGgtaagattat ... gcaatttcagGGTTCCAATAGGGCAAGGGTATGGTCTTACTGAGACATGTGCTGGAGGAAC
EST: gi|13420751|gb|AU174841.1|AU174841
EST:     GGAGCACCTCTATCAGGAGATACCCAGAGATTTATCAATATATGCCTTGG                         GGTTCCAATAGGGCAAGGGTATGGTCTTACTGAGACATGTGCTGGAGGAAC
genomic: GGAGCACCTCTATCAGGAGATACCCAGAGATTTATCAATATATGCCTTGGgtaagattat ... gcaatttcagGGTTCCAATAGGGCAAGGGTATGGTCTTACTGAGACATGTGCTGGAGGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttgtttcaacatgcatagagacctgggaattaacaagtttatgcaatttcagGGTTCCAATAGGGCAAGGGTATGGTCTTACTGAGACATGTGCTGGAGGAACATTTTCTGAGTATGATGACCCATCTGTTGGTCGCGTTGGTGCTCCACTA
                              aattaac  putative branch site (score: 2)
                              aattaacaagtttat  TA-rich tract