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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttctaaaatactgcgctgatattcgttagttggaatatgtgattctaaagccttactggagactcattggttgctataaatattcagGTCACATATGGTGCAAGTTTTATTGAATACTTTGCTGAAGAAGCAAAGCGTATATATGGTGATATTATTCCCCCAACTCTATCTGATCGTAGATTATTGG

Basic information

species Oryza sativa
transcript LOC_Os02g07760.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07760.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G128114_T01 (Zea mays), 3'ss of exon 5
gtacttt-ctaaaatactgcgctgatattcgttagttggaatatgtgattctaaagccttactggagactcattggttgcta--taaatattcagGTCACATATGGTGCAAGTTTTATTGAATACTTTGCTGAAGAAGCAAAGCGTATATATGGTGATATTATTCCCCCAACTCTATCTGATCGTAGATTATTGG
||||||   | | ||  | | |||||    ||||||||     ||||||| | | |   |  ||| | || |||||||  ||  |   | |||||||||  |||||||||||||| || ||||| ||||| || ||||||||||| |||||||||||||| ||||| |||||| |||||||||||||||| ||||
gtacttgatttatatcatccactgat----gttagttgatggttgtgattttgaggttcttttggggcctgattggtttgtacttctctgttcagGTCAATTATGGTGCAAGTTTCATAGAATATTTTGCAGAGGAAGCAAAGCGCATATATGGTGATATAATTCCTCCAACTTTATCTGATCGTAGATTGTTGG

upper sequence: LOC_Os02g07760.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G119482_T01 (Zea mays), 3'ss of exon 5
gtacttt-ctaaaatactgcgctgatattcgttagttggaatatgtgattctaaagccttactggagactcattggttgctataaatat--tcagGTCACATATGGTGCAAGTTTTATTGAATACTTTGCTGAAGAAGCAAAGCGTATATATGGTGATATTATTCCCCCAACTCTATCTGATCGTAGATTATTGG
||||||   |   ||  | | |||||    |||||||||    ||||||| | | |   |  ||| | ||||||||||| |     | |  ||||||||  |||||||||||||| || ||||| ||||| || ||||||||||||||||||||||| || |||||||||||| |||||||||| ||||| ||||
gtacttgatttgtatcattcactgat----gttagttggtgcttgtgattttgaggttcttttggggcctcattggttgttgctcctctgatcagGTCAATTATGGTGCAAGTTTCATAGAATATTTTGCAGAGGAAGCAAAGCGTATATATGGTGACATCATTCCCCCAACTTTATCTGATCGCAGATTGTTGG

upper sequence: LOC_Os02g07760.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA15G41690.1 (Glycine max), 3'ss of exon 5
-------gtactttctaaaatactgcg-ctgatattcgttagttggaatatgtgattctaaagccttactggagactcattggttgctataaatatt---cagGTCACATATGGTGCAAGTTTTATTGAATACTTTGCTGAAGAAGCAAAGCGTATATATGGTGATATTATTCCCCCAACTCTATCTGATCGTAGATTATTGG
        |   |    || || ||   ||  | ||  |||  |    |   |  ||  |     ||| ||| |    ||   |    || | ||||   ||| | |  ||||| ||  | |||||||| |     ||||| || ||||| ||||||||||| ||||| |||||  || |||||||||||||  ||||||| |
gtacacaatgggtgaagaattattgtttcttttctttcttatgtatgttccctagttgaatttggttattggtgcagtatatatgtaaatgactattttgcagATAAACTATGGGGCTGGCTTTATTGAGTTTGCAGCTGAGGAGGCAAAACGTATATATGGGGATATAATTCCTGCACCTCTATCTGATCGGCGATTATTTG

upper sequence: LOC_Os02g07760.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G79440.1 (Arabidopsis thaliana), 3'ss of exon 5
-----------------------gtactttctaaaatactgcgctgatattcgttagttggaatatgtgattctaaagccttactggagactcattggttgctataaatattcagGTCACATATGGTGCAAGTTTTATTGAATACTTTGCTGAAGAAGCAAAGCGTATATATGGTGATATTATTCCCCCAACTCTATCTGATCGTAGATTATTGG
                         |   |  ||  | |||    |   |   | |  ||    |   | |||| ||     |     || ||     ||      | | | |||||  ||||||| |||||||||||||| |||| ||| || || ||||| ||| ||||||||||||| ||||| || | ||| ||||||||  || | ||||
gttaatgattcattttttatttgagaacattgaatgtgctgtttaggcttgtctcaactgttgcaatcgtttcttaaatgcaatatatgattctgcaattt-----agtttacagGTAGCATATGGGGCAAGTTTTATTGAGTACTATGCGGAGGAGGCAAAACGTGTATATGGTGATATAATTCCTCCGAATCTGTCTGATCGCCGACTGTTGG

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|218496520|gb|FG947906.1|FG947906
EST:     TTCTCATGACACTGGAGCAAGGGAAACCTATGAAAGAGGCTCTTGTTGAG                         GTCACATATGGTGCAAGTTTTATTGAATACTTTGCTGAAGAAGCAAAGCGT
genomic: TTCTCATGACACTGGAGCAAGGGAAACCTATGAAAGAGGCTCTTGTTGAGgtactttcta ... aaatattcagGTCACATATGGTGCAAGTTTTATTGAATACTTTGCTGAAGAAGCAAAGCGT
EST: gi|7404226|gb|AU062684.2|AU062684
EST:     TTCTCATGACACTGGAGCAAGGGAAACCTATGAAAGAGGCTCTTGTTGAG                         GTCACATATGGTGCAAGTTTTATTGAATACTTTGCTGAAGAAGCAAAGCGN
genomic: TTCTCATGACACTGGAGCAAGGGAAACCTATGAAAGAGGCTCTTGTTGAGgtactttcta ... aaatattcagGTCACATATGGTGCAAGTTTTATTGAATACTTTGCTGAAGAAGCAAAGCGT
EST: gi|33794852|gb|CF323305.1|CF323305
EST:     TTCTCATGACACTGGAGCAAGGGAAACCTATGAAAGAGGCTCTTGTTGAG                         GTCACATATGGTGCAAGTTTTATTGAATACTTTGCTGAAGAAGCAAAGCGT
genomic: TTCTCATGACACTGGAGCAAGGGAAACCTATGAAAGAGGCTCTTGTTGAGgtactttcta ... aaatattcagGTCACATATGGTGCAAGTTTTATTGAATACTTTGCTGAAGAAGCAAAGCGT
EST: gi|218490997|gb|FG945735.1|FG945735
EST:     TTCTCATGACACTGGAGCAAGGGAAACCTATGAAAGAGGCTCTTGTTGAG                         GTCACATATGGTGCAAGTTTTATTGAATACTTTGCTGAAGAAGCAAAGCGT
genomic: TTCTCATGACACTGGAGCAAGGGAAACCTATGAAAGAGGCTCTTGTTGAGgtactttcta ... aaatattcagGTCACATATGGTGCAAGTTTTATTGAATACTTTGCTGAAGAAGCAAAGCGT
EST: gi|218488132|gb|FG951352.1|FG951352
EST:     TTCTCATGACACTGGAGCAAGGGAAACCTATGAAAGAGGCTCTTGTTGAG                         GTCACATATGGTGCAAGTTTTATTGAATACTTTGCTGAAGAAGCAAAGCGT
genomic: TTCTCATGACACTGGAGCAAGGGAAACCTATGAAAGAGGCTCTTGTTGAGgtactttcta ... aaatattcagGTCACATATGGTGCAAGTTTTATTGAATACTTTGCTGAAGAAGCAAAGCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatatgtgattctaaagccttactggagactcattggttgctataaatattcagGTCACATATGGTGCAAGTTTTATTGAATACTTTGCTGAAGAAGCAAAGCGTATATATGGTGATATTATTCCCCCAACTCTATCTGATCGTAGATTATTGG
                                      ttgctataaatatt  TA-rich tract