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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcagcttttgaaatcttgtttcttcgtgaatcttgggattatattaattgttggaagcagatactgaaaattactcgtctcttttcagGTGGGATGATGATGTTGTATTCAAAAACCAGGCACGTGGTGAAATGAAAGCTCCTAAGCGCTTCATCAATGATACAATCAGGAATGACTTCCACAGAAAA

Basic information

species Arabidopsis thaliana
transcript AT3G13200.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G13200.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os06g01700.1 (Oryza sativa), 3'ss of exon 6
gttagcagcttttgaaatcttgtttcttcgtgaatcttgggattatattaattgttgg-aagcagatactgaaaattactcgtctcttttcagGTGGGATGATGATGTTGTATTCAAAAACCAGGCACGTGGTGAAATGAAAGCTCCTAAGCGCTTCATCAATGATACAATCAGGAATGACTTCCACAGAAAA
|||  || |       ||| || |   |        | |  | |||    |   |||   | |  ||    |   |   |  | | | | ||||||||||||||||||||||||||| |||||||| ||||| || |  ||  | || || || |||||||| || || ||||| | ||| |||||| | || 
gtttaca-cacagctcatcgtgctgtattacatgcttcgctaatattagcacacttgatgaacttatttctatcctattttttttttctgcagGTGGGATGATGATGTTGTATTCAAGAACCAGGCTCGTGGAGAGACCAAGACACCGAAACGTTTCATCAACGACACTATCAGAAGTGATTTCCACCGTAAG

upper sequence: AT3G13200.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G04620.1 (Glycine max), 3'ss of exon 6
--------------------------gttagcagcttttgaaatcttgtttcttc-gtgaatcttg--ggatta---tattaatt--gttggaagcagatactgaaaattactcgtctcttttcagGTGGGATGATGATGTTGTATTCAAAAACCAGGCACGTGGTGAAATGAAAGCTCCTAAGCGCTTCATCAATGATACAATCAGGAATGACTTCCACAGAAAA
                          | | ||        ||    ||||| | | || || | ||  || ||    | | |||    ||       | |  || |    ||| || |  ||| ||||||||||||||||| || || || |||||| | ||||||||||  ||| |  ||||||| ||||||||||| || ||||||||||| ||||| ||||||
gtttgactttagatatttttcaaactgctcgctaaaccaaaatgactgtttttcctgttaaccctgttggtttgctgtctcaatctcattttttttcggttttgcatgc-acttgttttgttt-agGTGGGATGATGATGTGGTGTTTAAGAACCAGTCCCGTGGTGAAACCAAAACAGCTAAGCGATTCATCAATGACACCATCAGGAATGATTTCCATAGAAAA

upper sequence: AT3G13200.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA17G15050.2 (Glycine max), 3'ss of exon 5
-------------------gttagcagcttttgaaatct---tgtttcttcgtgaatcttgggattatattaattg-----ttggaagcagatactgaaaattactcgt-------ctcttttcagGTGGGATGATGATGTTGTATTCAAAAACCAGGCACGTGGTGAAATGAAAGCTCCTAAGCGCTTCATCAATGATACAATCAGGAATGACTTCCACAGAAAA
                      | | ||||   ||| |    |||   ||  |   |||    | | |||| |||       | ||     ||  |     ||   | |        | | || ||||||||||||||||| || || || ||||| || ||||||||||  ||| |  ||||||| ||||| ||||| || ||||||||||| ||||| ||||||
gtttgactctagatacttttcaaactgcttgccaaaccaaaatgtcagttttttcttctgttaactctattgatttactgtctcgatctcaattttttgggttttgcatgcacttgttttgtttagGTGGGATGATGATGTGGTGTTTAAGAACCAAGCCCGTGGTGAAACCAAAACAGCTAAGCGATTCATTAATGACACCATCAGGAATGATTTCCATAGAAAA

upper sequence: AT3G13200.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv19s0015g00980.t01 (Vitis vinifera), 3'ss of exon 6
gttagcagcttttgaa----atcttgtttcttcgtgaatcttgggattata-ttaattgttgga---agca------------gatactgaaaattact---cgtctctt--ttcagGTGGGATGATGATGTTGTATTCAAAAACCAGGCACGTGGTGAAATGAAAGCTCCTAAGCGCTTCATCAATGATACAATCAGGAATGACTTCCACAGAAAA
||| |  || |    |    |  |    ||| |  |  |     |||| || || |||| ||      | |            ||| |  |   || ||   | |   ||  |||||||||||||||||||| ||||| || |||||||| |||||||||   ||  |||| |||||||| |||||||| |||||||| |||||||| ||||| || 
gtttgtggcctgaagatccaacttcccctctactcgggtagatagattttagtttattgatgagtctggtatggtcctgtcctgattccaatgttttctatgcattgtttggttcagGTGGGATGATGATGTGGTATTTAAGAACCAGGCCCGTGGTGAAGCTAAGACTCCCAAGCGCTTTATCAATGACACAATCAGAAATGACTTTCACAGGAAG

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|124730121|gb|EH821523.1|EH821523
EST:     AAAGGAAACCCATTGCTTAATACTCCAACGTCTTTTAGCGTCAAAAGGAG                         GTGGGATGATGATGTTGTATTCAAAAACCAGGCACGTGGTGAAA
genomic: AAAGGAAACCCATTGCTTAATACTCCAACGTCTTTTAGCGTCAAAAGGAGgttagcagct ... ctcttttcagGTGGGATGATGATGTTGTATTCAAAAACCAGGCACGTGGTGAAA
EST: gi|86077837|gb|DR373594.1|DR373594
EST:     AAAGGAAACCCATTGCTTAATACTCCAACGTCTTTTAGCGTCAAAAGGAG                         GTGGGATGATGATGTTGTATTCAAAAACCAGGCACGTGGTGAAATGAAAGC
genomic: AAAGGAAACCCATTGCTTAATACTCCAACGTCTTTTAGCGTCAAAAGGAGgttagcagct ... ctcttttcagGTGGGATGATGATGTTGTATTCAAAAACCAGGCACGTGGTGAAATGAAAGC
EST: gi|164120115|gb|ES069837.1|ES069837
EST:     AATACTCCAACGTCTTTTAGCGTCAAAAGGAG                         GTGGGATGATGATGTTGTATTCAAAA-CCAGGCACGTGGTGAAATGTAAGC
genomic: AATACTCCAACGTCTTTTAGCGTCAAAAGGAGgttagcagct ... ctcttttcagGTGGGATGATGATGTTGTATTCAAAAACCAGGCACGTGGTGAAATGAAAGC
EST: gi|164196466|gb|ES096302.1|ES096302
EST:     CGTCAAAAGGAG                         GTGGGATGATGATGTTGTATTCAAAAACCAGGCACGTGGTGAAATGAAAGC
genomic: CGTCAAAAGGAGgttagcagct ... ctcttttcagGTGGGATGATGATGTTGTATTCAAAAACCAGGCACGTGGTGAAATGAAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgggattatattaattgttggaagcagatactgaaaattactcgtctcttttcagGTGGGATGATGATGTTGTATTCAAAAACCAGGCACGTGGTGAAATGAAAGCTCCTAAGCGCTTCATCAATGATACAATCAGGAATGACTTCCACAGAAAA
        tattaat  putative branch site (score: 2)
                                     ttactcgtctcttttc  putative PPT
     ttatattaattgtt  TA-rich tract