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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGCTTGGATTAGAGTATGGGTAAAGAAGGGAGGTATGATAGTCTTACCTGCTGGAATATATCATCGCTTCACCGTAGACTCAGACAACTATATCAAGgtgcaatgttagcttcttcagagtggttaattcatcatatatatatttggttgattagaaaattgaaatatcttgttgagcag

Basic information

species Arabidopsis thaliana
transcript AT4G14710.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G14710.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA10G38940.3 (Glycine max), 5'ss of exon 5
TGAAGCTTGGATTAGAGTATGGGTAAAGAAGGGAGGTATGATAGTCTTACCTGCTGGAATATATCATCGCTTCACCGTAGACTCAGACAACTATATCAAGgtgcaatgttagcttcttcagagtggttaattcatcatatatatatttggttgattagaaaattgaaatatcttgttgagcag------------------
||| ||||||||| |||| ||||| ||||| ||||| |||||  |||||||||||||||| ||||||||||| ||  ||||      |||||| || |||||     |||   |  ||   ||| ||   | ||       | |  |  |||| | | | ||    | ||| |  |||  |                    
TGATGCTTGGATTCGAGTGTGGGTCAAGAAAGGAGGAATGATCATCTTACCTGCTGGAATTTATCATCGCTTTACACTAGATGAGAGCAACTACATTAAGgtattg-gttgcatatttacaagtagtacctgcactgctacttttgtctgttgctaatagaaaaacattatatccttgtacttctattcctctggcccatt

upper sequence: AT4G14710.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA20G28860.1 (Glycine max), 5'ss of exon 5
TGAAGCTTGGATTAGAGTATGGGTAAAGAAGGGAGGTATGATAGTCTTACCTGCTGGAATATATCATCGCTTCACCGTAGACTCAGACAACTATATCAAGgtgcaatgttagcttcttcagagtggttaatt-catcatatatatatttggttgat--tagaaaattgaaatatcttgttgagcag----------------
||||||||||||| | || ||||| ||||| ||||| |||||  |||||||||| ||||| ||||||||||| ||  ||||      |||||| || |||||    || | || | || | |    |||  | |        | | ||  |||| |  |||||||     ||||| |  |    |                 
TGAAGCTTGGATTCGTGTGTGGGTCAAGAAAGGAGGAATGATCATCTTACCTGCCGGAATTTATCATCGCTTTACGCTAGATGAGAGCAACTACATTAAGgtat--tgattgcatatttacaagtattacctgcgctgctacttttttctgttgctaatagaaaaacattatatccttgtacttatattcctctgtcccatt
















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|86080820|gb|DR376577.1|DR376577
EST:     CTGCTGGAATATATCATCGCTTCACCGTAGACTCAGACAACTATATCAAG                         GCAATGCGGCTTTTCGTGGGTGAACCGGTCTGGACACCATACAATCGCCCA
genomic: CTGCTGGAATATATCATCGCTTCACCGTAGACTCAGACAACTATATCAAGgtgcaatgtt ... tgttgagcagGCAATGCGGCTTTTCGTGGGTGAACCGGTCTGGACACCATACAATCGCCCA
EST: gi|124720239|gb|EH811641.1|EH811641
EST:     TGCTGGAATATATCATCGCTTCACCGTAGACTCAGACAACTATATCAAG                         GCAATGCGGCTTTTCGTGGGTGAACCGGTCTGGA
genomic: TGCTGGAATATATCATCGCTTCACCGTAGACTCAGACAACTATATCAAGgtgcaatgtt ... tgttgagcagGCAATGCGGCTTTTCGTGGGTGAACCGGTCTGGA
EST: gi|86074670|gb|DR370427.1|DR370427
EST:     CTGCTGGAATATATCATCGCTTCACCGTAGACTCAGACAACTATATCAAG                         GCAATGCGGCTTTTCGTGGGTGAACCGGTCTGGACACCATACAATCGCCCA
genomic: CTGCTGGAATATATCATCGCTTCACCGTAGACTCAGACAACTATATCAAGgtgcaatgtt ... tgttgagcagGCAATGCGGCTTTTCGTGGGTGAACCGGTCTGGACACCATACAATCGCCCA
EST: gi|86082287|gb|DR378046.1|DR378046
EST:     CTGCTGGAATATATCATCGCTTCACCGTAGACTCAGACAACTATATCAAG                         GCAATGCGGCTTTTCGTGGGTGAACCGGTCTGGACACCATACAATCGCCCA
genomic: CTGCTGGAATATATCATCGCTTCACCGTAGACTCAGACAACTATATCAAGgtgcaatgtt ... tgttgagcagGCAATGCGGCTTTTCGTGGGTGAACCGGTCTGGACACCATACAATCGCCCA
EST: gi|124889874|gb|EH968776.1|EH968776
EST:     CTGCTGGAATATATCATCGCTTCACCGTAGACTCAGACAACTATATCAAG                         GCAATGCGGCTTT-CGTGGGTGAAC
genomic: CTGCTGGAATATATCATCGCTTCACCGTAGACTCAGACAACTATATCAAGgtgcaatgtt ... tgttgagcagGCAATGCGGCTTTTCGTGGGTGAAC
EST: gi|164105215|gb|ES067936.1|ES067936
EST:     TAGACTCAGACAACTATATCAAG                         GCAATGCGGCTTTTCGTGGGTGAACCGGTCTGGACACCATACAATCGCCCA
genomic: TAGACTCAGACAACTATATCAAGgtgcaatgtt ... tgttgagcagGCAATGCGGCTTTTCGTGGGTGAACCGGTCTGGACACCATACAATCGCCCA
EST: gi|124727145|gb|EH818547.1|EH818547
EST:     CTGCTGGAATATATCATCGCTTCACCGTAGACTCAGACAACTATATCAAG                         GCAATGCGGCTTTTCGTGGGTGAACCGGTCTGGACACCATACAATCG
genomic: CTGCTGGAATATATCATCGCTTCACCGTAGACTCAGACAACTATATCAAGgtgcaatgtt ... tgttgagcagGCAATGCGGCTTTTCGTGGGTGAACCGGTCTGGACACCATACAATCG
EST: gi|125258671|gb|EL272756.1|EL272756
EST:     CGCTTCACCGTAGACTCAGACAACTATATCAAG                         GCAATGCGGCTTTTCGTGGGTGAACCGGTCTGGACACCATACAATCGCCCA
genomic: CGCTTCACCGTAGACTCAGACAACTATATCAAGgtgcaatgtt ... tgttgagcagGCAATGCGGCTTTTCGTGGGTGAACCGGTCTGGACACCATACAATCGCCCA
EST: gi|125294180|gb|EL308265.1|EL308265
EST:     TCAGACAACTATATCAAG                         GCAATGCGGCTTTTCGTGGGTGAACCGGTCTGGACACCATACAATCGCCCA
genomic: TCAGACAACTATATCAAGgtgcaatgtt ... tgttgagcagGCAATGCGGCTTTTCGTGGGTGAACCGGTCTGGACACCATACAATCGCCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAGCTTGGATTAGAGTATGGGTAAAGAAGGGAGGTATGATAGTCTTACCTGCTGGAATATATCATCGCTTCACCGTAGACTCAGACAACTATATCAAGgtgcaatgttagcttcttcagagtggttaattcatcatatatatatttggttgattagaaaattgaaatatcttgttgagcag

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