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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtttccttttgtcgtaactaaagctcagtaccaaattagtctaatgcactagtcaatttgtgttctacttgaacttatgggtgtttctgcatatatagGTTACCAGCCAGGAGACTAACCTTGTGGCTAGATGCCGAAGAGTGTATGCCCATGCTCATGATTACCATATTAATTCAATCTCCAATAGCAG

Basic information

species Arabidopsis thaliana
transcript AT1G17720.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 5
---------------------------------------------ttgtttccttttgtcgtaactaaagctcagtaccaaattagtctaatgcactagtcaatttgtgttcta-cttgaacttatgggtgtttctgcatatatagGTTACCAGCCAGGAGACTAACCTTGTGGCTAGATGCCGAAGAGTGTATGCCCATGCTCATGATTACCATATTAATTCAATCTCCAATAGCAG
                                             ||| |  |||   ||    |||   |      |     ||   |||    |  | |||  | || || |     || ||    |  |||||    ||  ||||| | || || ||    |||||||| |||||||| ||| | || ||||| ||||||||||||||||||||||| || || || |  |  ||
gtagttgtacttaacctctatatatcttaatcaacagaagatgacttgatgtcttg-atcagctctagcacatctagctggcatatgataacttgcacggcaacctatgatcaagtccaaaattgactgcatttcttatcatgcagGTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 5
------------------------------------------ttgtttccttttgtcgtaactaaagctcagtaccaaattagtctaatgcactagtcaatttgtgttctactt-gaacttatgggtgtttctgcatatatagGTTACCAGCCAGGAGACTAACCTTGTGGCTAGATGCCGAAGAGTGTATGCCCATGCTCATGATTACCATATTAATTCAATCTCCAATAGCAG
                                          ||| |  |||   ||    |||   |      |     ||   |||    |  | |||  | || || | |   || ||    |  |||||    ||  ||||| | || || ||    |||||||| |||||||| ||| | || ||||| ||||||||||||||||||||||| || || || |  |  ||
gttgtacttaacctctatatatcttaatcaacagaagatgacttgatgtcttg-atcagctctagcacatctagctggcatatgataacttgcacggcaacctatgatcaagtccaaaattgactgcatttcttatcatgcagGTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 5
-------------------------------------------------------------------------------------ttgtttccttttgtcgtaacta-----aagctcagtaccaaattagtctaatgcactagtcaatttgtgttctacttgaacttatgggtgttt-ctgcatatatagGTTACCAGCCAGGAGACTAACCTTGTGGCTAGATGCCGAAGAGTGTATGCCCATGCTCATGATTACCATATTAATTCAATCTCCAATAGCAG
                                                                                       || |||||||| | | | ||     |     | |  |   |||    ||    |   |    ||    | ||   | | ||||     ||| ||   |||  |||| ||  |||| ||    ||||||||  | ||||||||  | || ||| | |||||||||||||||||||||||||| || || ||||  ||
gttgtacttaacccactttattcattatctcatctgtaatcgtgttgttctgtacagcaccaaatctggtgttcacatgtaaaataagtctccttttggcatgaatacttatagatagattttcttcttatggcaaactgcacatatgattacaatatatgagtatttattttcatttactatgtatgcagGTCACTGGCCAAGATTTGAACCTTGTACCAAGATGCCGGCGTGTATATTCACATGCTCATGATTACCATATTAATTCCATTTCAAATAATAG

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G20830.1 (Glycine max), 3'ss of exon 5
ttgtttccttttgtcgt--aactaaagctcagtaccaaattagtctaatgcactagtcaatttgtgttcta-cttgaacttatgggt--gtttctgcatatatagGTTACCAGCCAGGAGACTAACCTTGTGGCTAGATGCCGAAGAGTGTATGCCCATGCTCATGATTACCATATTAATTCAATCTCCAATAGCAG
   |||   | ||| ||  | |||    |||   |   |  | |   |     | |  | |||||  | || |  |  || |   ||   ||     |||| ||||| |||||||| ||||| |   |  ||||| ||||||| ||||| |||||||||||||||||||| ||||||||||| || || |||| |||
--attttagtatgtagtggagctagttttcaagccttgacaatt---acttgtttgaaactttgtagtttagcgagttctaacacgttgattgtaaaatatgtagGTAACCAGCCATGAGACCAGTTTGATGGCTCGATGCCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 5
ttgtttccttttgtcgtaactaaagctcagtaccaaattagtctaatgcactagtcaatttgtgttctactt-gaacttatgggt--gtttctgcatatatagGTTACCAGCCAGGAGACTAACCTTGTGGCTAGATGCCGAAGAGTGTATGCCCATGCTCATGATTACCATATTAATTCAATCTCCAATAGCAG
 | |||   | |   | | |||    |||   |   |  | |   |     | |  | |||||  | || |  |  || |    |   ||     |||| ||||| |||||||| ||||| |   | |||||| |||| || ||||| |||||||||||||||||||| ||||||||||| || || |||| |||
atttttgtatgtagtggagctagttttcaagccttgacaatt---acttgtttgaaactttgtagtttagtgagtgctaacacattgattgtaaaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 5
-ttgtttccttttgtcgtaactaaagctcagtaccaaattagtctaatgcactagtcaatttgtgttctacttgaacttatgggtgtttctgcatatatagGTTACCAGCCAGGAGACTAACCTTGTGGCTAGATGCCGAAGAGTGTATGCCCATGCTCATGATTACCATATTAATTCAATCTCCAATAGCAG
   |      || |  ||   | ||| ||  | |    | |  ||    || | |    |||| |   |  | | ||| |   ||||||    |||| ||||| |  ||||| || || | | | || ||  ||||||| ||||||||||| |||||||||||||| || || ||||| || || |||| |||
gaagaaagaattggaagtggttgaagttcttt-ctttttcaaactttgacaattgcttttttgagaatttgtagtactaacctgtgttttaaaatatgtagGTAAGTAGCCATGAAACCAGCTTAGTTGCCCGATGCCGTAGAGTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAG

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|116478423|gb|EG521015.1|EG521015
EST:     ACTTTTCTTTCCCGCCAGGAGGCATTCCATCTCTGCGTTTGCCTGTGGTA                         GTTACCAGCCAGGAGACTAACCTTGTGGCTAGATGCCGAAGAGTGTATGCC
genomic: ACTTTTCTTTCCCGCCAGGAGGCATTCCATCTCTGCGTTTGCCTGTGGTAgttgtactcg ... gcatatatagGTTACCAGCCAGGAGACTAACCTTGTGGCTAGATGCCGAAGAGTGTATGCC
EST: gi|116411283|gb|EG453875.1|EG453875
EST:     ACTTTTCTTTCCCGCCAGGAGGCATTCCATCTCTGCGTTTGCCTGTGGTA                         GTTACCAGCCAGGAG
genomic: ACTTTTCTTTCCCGCCAGGAGGCATTCCATCTCTGCGTTTGCCTGTGGTAgttgtactcg ... gcatatatagGTTACCAGCCAGGAG
EST: gi|116432328|gb|EG474920.1|EG474920
EST:     ACTTTTCTTTCCCGCCAGGAGGCATTCCATCTCTGCGTTTGCCTGTGGTA                         GTTACCAGCCAGGAGACTAACCTTGTGGCTAGATGCCGAAGAGTGTATGCC
genomic: ACTTTTCTTTCCCGCCAGGAGGCATTCCATCTCTGCGTTTGCCTGTGGTAgttgtactcg ... gcatatatagGTTACCAGCCAGGAGACTAACCTTGTGGCTAGATGCCGAAGAGTGTATGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcactagtcaatttgtgttctacttgaacttatgggtgtttctgcatatatagGTTACCAGCCAGGAGACTAACCTTGTGGCTAGATGCCGAAGAGTGTATGCCCATGCTCATGATTACCATATTAATTCAATCTCCAATAGCAG
 gtctaat  putative branch site (score: 3)
                                        tttctgc  putative PPT
                                               atatata  TA-rich tract