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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattataaagtttctaaatatgccaaccatgatttcttctttttttactatcacttatggttgtttattgtatttcgtatttgtgttaagATTGTTAATGGACCTCGAGGAGCAGTTCAATCTCCAGAGGAGGAATTTGAAGTGTTCTACATCGATTATGGAAACCAAGAAATAGTTCCGTACAGCGCAA

Basic information

species Arabidopsis thaliana
transcript AT5G61780.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G61780.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: LOC_Os02g32350.1 (Oryza sativa), 3'ss of exon 14
------gtaaattataaagtttctaaatatgccaaccatgatttcttctttttttactatcacttatggttgtttattgtat---ttcgtatttgtgttaagATTGTTAATGGACCTCGAGGAGCAGTTCAATCTCCAGAGGAGGAATTTGAAGTGTTCTACATCGATTATGGAAACCAAGAAATAGTTCCGTACAG-CGCAA
       | | |  |  | ||  ||| |    ||  |  |  ||  |  ||| |   | |||   ||  ||    | | |||   ||   | |  | |  ||||||| ||||||||||||||||| ||   ||||| ||| ||  | |||||||| |||||||| || ||||| ||||||||| | ||||| ||||| |||| 
aaccattttagtcctggacttgttaagttgaacattcccg--tttctagtttctggttttcaaaaataattaggaagtatatccattttaactgatctgcagATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAAGTATTCTACATTGACTATGGCAACCAAGAAGTCGTTCCTTACAGTCGCA-

upper sequence: AT5G61780.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA08G00910.1 (Glycine max), 3'ss of exon 15
-----gtaaattataaa-gtttctaaatatgccaaccatgatttcttctttttttactat-cacttatggttgtttattgtatttcgtatttgtgtta-agATTGTTAATGGACCTCGAGGAGCAGTTCAATCTCCAGAGGAGGAATTTGAAGTGTTCTACATCGATTATGGAAACCAAGAAATAGTTCCGTACAGCGCAA-
     | | ||  ||   ||    | || |  ||    |  ||| | |    |   || | || | |   || |||||   ||    |     ||||  || | || ||||||||||||||| | ||| ||||| || | ||    |||||||| |||||||| ||||||||||| |||||| |||| || |||  | ||  
tttgtgcacatgctatttgtcaacacattttgcacttgtactttgtaccacctagtctgttcagtcaaacttctttatgaaatggtatggg-atgttgtagGTAGTCAATGGACCTCGAGGACCTGTTGAATCTTCAAATGACATGTTTGAAGTATTCTACATTGATTATGGAAATCAAGAAGTAGTACCTTACT-CTCAGC

upper sequence: AT5G61780.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv00s0283g00020.t01 (Vitis vinifera), 3'ss of exon 15
----gtaaattataaagtttctaaatatgccaaccatgatttcttctttttttactatcacttatggttgtttattgtatttcgtatttg---tgttaagATTGTTAATGGACCTCGAGGAGCAGTTCAATCTCCAGAGGAGGAATTTGAAGTGTTCTACATCGATTATGGAAACCAAGAAATAGTTCCGTACAGCGCAA-
    | ||    | |  | |||||  ||  |||  |   | | |   || | |  | |  ||  |  ||  ||    | ||||  |||||   |||  |||||||||||| |||||| || || ||| |||| ||| | ||  ||||||||||||||||||| || |||||||| ||||||||  |||| |||||  ||  
agaagcaataacttatttctctaataattacaagaagtctatttcagttatattgtgttcctgtttcttagtttgaatctttctcatttgacatgtacagATTGTTAATGCACCTCGGGGGGCTGTTGAATCCCCAAAAGACAAATTTGAAGTGTTCTACATTGACTATGGAAATCAAGAAATTATTCCTTACAGT-CAGT

upper sequence: AT5G61780.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv14s0068g00720.t01 (Vitis vinifera), 3'ss of exon 14
------gtaaattataaagtttctaaatatgccaa-ccatgatttcttctttttttactatcacttatggttgtttattgtatttcgtatttgtgttaagATTGTTAATGGACCTCGAGGAGCAGTTCAATCTCCAGAGGAGGAATTTGAAGTGTTCTACATCGATTATGGAAACCAAGAAATAGTTCCGTACAGCGCAA
           | | ||    | ||    |  ||  |||  |  | || |||||||  |    ||| || |  |||    | |||  |   ||| | |||||||| |||| ||  |||||||| || ||||| ||| | || ||||||||||| |||||||| || ||||| || |||||| ||||||| ||        
tctcccactgttcaaaagagatgtagtagtttcagtccaaaacatttttttttttttttggtccttgtgctaattttgactgtttgtttgatgtatcaagATTGTCAATGCACAACGAGGAGCTGTCCAATCCCCAAAAGATGAATTTGAAGTTTTCTACATTGACTATGGGAATCAAGAAGTAGTTCCTTATGATCGGT

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|86047622|gb|DR343377.1|DR343377
EST:     ACATCGTCCTTGCACAATTTAGCCTCGATAACTCCTGGAACCGCGCAATG                         ATTGTTAATGGACCTCGAGGAGCAGTTCAATCTCC
genomic: ACATCGTCCTTGCACAATTTAGCCTCGATAACTCCTGGAACCGCGCAATGgtaaattata ... ttgtgttaagATTGTTAATGGACCTCGAGGAGCAGTTCAATCTCC
EST: gi|86047626|gb|DR343381.1|DR343381
EST:     ACATCGTCCTTGCACAATTTAGCCTCGATAACTCCTGGAACCGCGCAATG                         ATTGTTAATGGACCTCGAGGAGCAGTTCAATCTCCAGAGGAGGA
genomic: ACATCGTCCTTGCACAATTTAGCCTCGATAACTCCTGGAACCGCGCAATGgtaaattata ... ttgtgttaagATTGTTAATGGACCTCGAGGAGCAGTTCAATCTCCAGAGGAGGA
EST: gi|86047625|gb|DR343380.1|DR343380
EST:     ACATCGTCCTTGCACAATTTAGCCTCGATAACTCCTGGAACCGCGCAATG                         ATTGTTAATGGACCTCGAGGAGCAGTTCA
genomic: ACATCGTCCTTGCACAATTTAGCCTCGATAACTCCTGGAACCGCGCAATGgtaaattata ... ttgtgttaagATTGTTAATGGACCTCGAGGAGCAGTTCA
EST: gi|86047623|gb|DR343378.1|DR343378
EST:     ACATCGTCCTTGCACAATTTAGCCTCGATAACTCCTGGAACCGCGCAATG                         ATTGTTAATGGACCTCGAGGAGCAGTTCAATCTCCAGAGGAGGAATTTGAA
genomic: ACATCGTCCTTGCACAATTTAGCCTCGATAACTCCTGGAACCGCGCAATGgtaaattata ... ttgtgttaagATTGTTAATGGACCTCGAGGAGCAGTTCAATCTCCAGAGGAGGAATTTGAA
EST: gi|164048103|gb|ES005715.1|ES005715
EST:     CCTGGAACCGCGCAATG                         ATTGTTAATGGACCTCGAGGAGCAGTTCAATCTCCAGAGGAGGAATT-GAA
genomic: CCTGGAACCGCGCAATGgtaaattata ... ttgtgttaagATTGTTAATGGACCTCGAGGAGCAGTTCAATCTCCAGAGGAGGAATTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctttttttactatcacttatggttgtttattgtatttcgtatttgtgttaagATTGTTAATGGACCTCGAGGAGCAGTTCAATCTCCAGAGGAGGAATTTGAAGTGTTCTACATCGATTATGGAAACCAAGAAATAGTTCCGTACAGCGCAA
                         ttgtttattgtattt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattataaagtttctaaatatgccaaccatgatttcttctttttttactatcacttatggttgtttattgtatttcgtatttgtgttaagATTGTTAATGGACCTCGAGGAGCAGTTCAATCTCCAGAGGAGGAATTTGAAGTGTTCTACATCGATTATGGAAACCAAGAAATAGTTCCGTACAGCGCAA

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