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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAAGAATCCAACATGGGCTTCTGTTCCTTATGGGATCTTCCTATGCATCGATTGTTCTGCTGTTCATCGAAGTCTAGGTGTTCATATCAGCTTCGTCAGgtaaaactttgaatcttgaggaacacaaatttgaactctttaggcttaatttttagcttcatggacttgtagcaatgtttcaccttctggctagggttta...

Basic information

species Arabidopsis thaliana
transcript AT5G46750.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G46750.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA01G12340.2 (Glycine max), 5'ss of exon 2
-----CGAAGAATCCAACATGGGCTTCTGTTCCTTATGGGATCTTCCTATGCATCGATTGTTCTGCTGTTCATCGAAGTCTAGGTGTTCATATCAGCTTCGTCAGgtaaaactttg--aatcttgaggaacacaaatttgaactctttaggcttaatttttagcttcatggacttgtagcaatgtttcaccttctggctagggttta
     ||||||| || || ||||| || ||  | |||||||||||||| ||||||||||| || || ||||| || ||||| || || || ||||||||||| ||| ||   ||||   || |||         |||    | ||| |  | | | ||||||  | |    | ||||| |  | |   |  |  | |   || |   
CAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTCgtgaggcaagtttttgctgattttg-----tttgaatggtgaatctgtttgttgattttttatgtgcggaaatttgtatcggtttgcaatatgattgtgtggctg--

upper sequence: AT5G46750.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA01G12340.1 (Glycine max), 5'ss of exon 2
CGAAGAATCCAACATGGGCTTCTGTTCCTTATGGGATCTTCCTATGCATCGATTGTTCTGCTGTTCATCGAAGTCTAGGTGTTCATATCAGCTTCGTCAGgtaaaactttg--aatcttgaggaacacaaatttgaactctttaggcttaatttttagcttcatggacttgtagcaatgtttcaccttctggctagggttta----
||||||| || || ||||| || ||  | |||||||||||||| ||||||||||| || || ||||| || ||||| || || || ||||||||||| ||| ||   ||||   || |||         |||    | ||| |  | | | ||||||  | |    | ||||| |  | |   |  |  | | |  || | |    
CGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTCGTGAGgcaagtttttgctgattttg-----tttgaatggtgaatctgtttgttgattttttatgtgcggaaatttgtatcggtttgcaatatgattg-tgtggctgattct

upper sequence: AT5G46750.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv02s0012g01330.t01 (Vitis vinifera), 5'ss of exon 2
CGAAGAATCCAACATGGGCTTCTGTTCCTTATGGGATCTTCCTATGCATCGATTGTTCTGCTGTTCATCGAAGTCTAGGTGTTCATATCAGCTTCGTCAGgtaaaactttgaatcttgaggaacacaaatttgaactctttaggcttaatttttagcttcatggacttgtagc--aatgtttcaccttctggctagggttta----
||||||| || || ||||| || ||  | |||||||||||||| |||||||| || || || || ||| | ||||| || ||||| |||||||||||||||| |   ||| ||| |||||         |||||  ||  |    |    |||| ||         | ||      || ||||  ||   || |  | ||||    
CGAAGAACCCGACTTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAGgtga---tttcaattttgagttttggtggtttga--tccatgatttagggttttggcagttcaatttggtgatttgatatttcgactag-ggttttgatttaagat

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|124790254|gb|EH879933.1|EH879933
EST:     GATTGTTCTGCTGTTCATCGAAGTCTAGGTGTTCATATCAGCTTCGTCAG                         GTCAACGAACTTAGACTCGTGGAGTCCTGAGCAGCTAA
genomic: GATTGTTCTGCTGTTCATCGAAGTCTAGGTGTTCATATCAGCTTCGTCAGgtaaaacttt ... ttttgtgcagGTCAACGAACTTAGACTCGTGGAGTCCTGAGCAGCTAA
EST: gi|125209787|gb|EL224741.1|EL224741
EST:     TGTTCATATCAGCTTCGTCAG                         GTCAACGAACTTAGACTCGTGGAGTCCTGAGCAGCTAAGAACAATAGATGT
genomic: TGTTCATATCAGCTTCGTCAGgtaaaacttt ... ttttgtgcagGTCAACGAACTTAGACTCGTGGAGTCCTGAGCAGCTAAGAACAAT-GATGT
EST: gi|125074113|gb|EL138190.1|EL138190
EST:     GATTGTTCTGCTGTTCATCGAAGTCTAGGTGTTCATATCAGCTTCGTCAG                         GTCAACGAACTTAGACTCGTGGAGTCCTGAGCAGCTAAGAACAAT
genomic: GATTGTTCTGCTGTTCATCGAAGTCTAGGTGTTCATATCAGCTTCGTCAGgtaaaacttt ... ttttgtgcagGTCAACGAACTTAGACTCGTGGAGTCCTGAGCAGCTAAGAACAAT
EST: gi|125292793|gb|EL306878.1|EL306878
EST:     GATTGTTCTGCTGTTCATCGAAGTCTAGGTGTTCATATCAGCTTCGTCAG                         GTCAACGAACTTAGACTCGTGG
genomic: GATTGTTCTGCTGTTCATCGAAGTCTAGGTGTTCATATCAGCTTCGTCAGgtaaaacttt ... ttttgtgcagGTCAACGAACTTAGACTCGTGG
EST: gi|116474060|gb|EG516652.1|EG516652
EST:     GATTGTTCTGCTGTTCATCGAAGTCTAGGTGTTCATATCAGCTTCGTCAG                         GTCAACGAACTTAGACTCGTGGAGTCCTGAGCAGCTAAGAACAATGATGTT
genomic: GATTGTTCTGCTGTTCATCGAAGTCTAGGTGTTCATATCAGCTTCGTCAGgtaaaacttt ... ttttgtgcagGTCAACGAACTTAGACTCGTGGAGTCCTGAGCAGCTAAGAACAATGATGTT
EST: gi|124748900|gb|EH839030.1|EH839030
EST:     GTTCATCGAAGTCTAGGTGTTCATATCAGCTTCGTCTG                         GTCAACGAACTTAGACTCGTGGAGTCCTGAGCAGCTAAGAACAATGATGTT
genomic: GTTCATCGAAGTCTAGGTGTTCATATCAGCTTCGTCAGgtaaaacttt ... ttttgtgcagGTCAACGAACTTAGACTCGTGGAGTCCTGAGCAGCTAAGAACAATGATGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAAGAATCCAACATGGGCTTCTGTTCCTTATGGGATCTTCCTATGCATCGATTGTTCTGCTGTTCATCGAAGTCTAGGTGTTCATATCAGCTTCGTCAGgtaaaactttgaatcttgaggaacacaaatttgaactctttaggcttaatttttagcttcatggacttgtagcaatgtttcaccttctggctagggttta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaacacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caccttct