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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaacttcttttactggcggctttactcgtaaacttaaaatttcgatatagtagtcatgttttattttcttgggaaaaagGTTACTTTGATGTGAGAGATCGTAATGAAGCTTGGATTAGGGTATTGGTAAAGAAGGGAGGTATGATAGTCTTACCTGCTGGGATCTATCATCGCTTCAC

Basic information

species Arabidopsis thaliana
transcript AT4G14716.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G14716.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G28860.2 (Glycine max), 3'ss of exon 4
gtaagaact--tcttttact---ggcggctttactcgtaa----acttaaaatttcgatatagtagtcatgttttattttcttgggaaaaagGTTACTTTGATGTGAGAGATCGTAATGAAGCTTGGATTAGGGTATTGGTAAAGAAGGGAGGTATGATAGTCTTACCTGCTGGGATCTATCATCGCTTCAC
||| |||||  | |||| ||       | ||| || |  |     | ||  ||||  |  |  ||   || |  | |||   |       ||| || |||||||| || ||||| ||||||||||||||| | || | ||| ||||| ||||| |||||  |||||||||| || || ||||||||||| ||
gtatgaactaattttttgctttactttgattttcttgccaccttgcctaccattttaagttgctaaatatatcatgtttgtcttt-----agGCTATTTTGATGTTAGGGATCGCAATGAAGCTTGGATTCGTGTGTGGGTCAAGAAAGGAGGAATGATCATCTTACCTGCCGGAATTTATCATCGCTTTAC

upper sequence: AT4G14716.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G38940.3 (Glycine max), 3'ss of exon 4
gtaagaact--tcttttact---ggcggctttactcgtaaacttaaaatttcgatatagtagtcatgttttattttcttgggaaaaagGTTACTTTGATGTGAGAGATCGTAATGAAGCTTGGATTAGGGTATTGGTAAAGAAGGGAGGTATGATAGTCTTACCTGCTGGGATCTATCATCGCTTCAC
|||  ||||  | || | ||       | ||| || |  | |||          |  ||| |  |  | | ||  | || |     ||| || |||||||| || ||| | ||||| ||||||||| | || | ||| ||||| ||||| |||||  ||||||||||||| || ||||||||||| ||
gtacaaactaattttctgctttactttgattttcttgccaccttgcctaccatgttaagttgctaaatat-atcctgtttgtctttagGGTATTTTGATGTTAGGGATTGCAATGATGCTTGGATTCGAGTGTGGGTCAAGAAAGGAGGAATGATCATCTTACCTGCTGGAATTTATCATCGCTTTAC
















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|19878312|gb|AU239143.1|AU239143
EST:     AGAACATTTACACACTGATGAGGAGATCCGTTACTGCGTTGCAGGAACTG                         GTTACTTTGATGTGAGAGATCGTACTGAAGCTTGGATTANGGTATTGGTTA
genomic: AGAACATTTACACACTGATGAGGAGATCCGTTACTGCGTTGCAGGAACTGgtaagaactt ... tgggaaaaagGTTACTTTGATGTGAGAGATCGTAATGAAGCTTGGATTAGGGTATTGGTAA
EST: gi|116403060|gb|EG445652.1|EG445652
EST:     AGAACATTTACACACTGATGAGGAGATCCGTTACTGCGTTGCAGGAACTG                         GTTACTTTGATGTGAGAGATCGAAATGAAGCTTGGATTAGGGTATTGGTAA
genomic: AGAACATTTACACACTGATGAGGAGATCCGTTACTGCGTTGCAGGAACTGgtaagaactt ... tgggaaaaagGTTACTTTGATGTGAGAGATCGTAATGAAGCTTGGATTAGGGTATTGGTAA
EST: gi|19874934|gb|AU235765.1|AU235765
EST:     AGAACATTTACACACTGATGAGGAGATCCGTTACTGCGTTGCAGGAACTG                         GTTACTTTGATGTGAGAGATCGTAATGAAGCNTTGGATTANGGTNTTGGT
genomic: AGAACATTTACACACTGATGAGGAGATCCGTTACTGCGTTGCAGGAACTGgtaagaactt ... tgggaaaaagGTTACTTTGATGTGAGAGATCGTAATGAAGC-TTGGATTAGGGTATTGGT
EST: gi|124794677|gb|EH884356.1|EH884356
EST:     AGAACATTTACACACTGATGAGGAGATCCGTTACTGCGTTGCAGGAACTG                         GTTACTTTGAT
genomic: AGAACATTTACACACTGATGAGGAGATCCGTTACTGCGTTGCAGGAACTGgtaagaactt ... tgggaaaaagGTTACTTTGAT
EST: gi|116403021|gb|EG445613.1|EG445613
EST:     AGAACATTTACACACTGATGAGGAGATCCGTTACTGCGTTGCAGGAACTG                         GTTACTTTGATGTGAGAGATCGTAATGAAGCTTGGATTAGGGTATTGGTAA
genomic: AGAACATTTACACACTGATGAGGAGATCCGTTACTGCGTTGCAGGAACTGgtaagaactt ... tgggaaaaagGTTACTTTGATGTGAGAGATCGTAATGAAGCTTGGATTAGGGTATTGGTAA
EST: gi|125040367|gb|EL112636.1|EL112636
EST:     CTGATGAGGAGATCCGTTACTGCGTTGCAGGAACTG                         GTTACTTTGATGTGAGAGATCGTAATGAAGCTTGGATTAGGGTATTGGTAA
genomic: CTGATGAGGAGATCCGTTACTGCGTTGCAGGAACTGgtaagaactt ... tgggaaaaagGTTACTTTGATGTGAGAGATCGTAATGAAGCTTGGATTAGGGTATTGGTAA
EST: gi|124759329|gb|EH849459.1|EH849459
EST:     TACACACTGATGAGGAGATCCGTTACNGCGTTGCAGGAACTG                         GTTACTTTGATGTGAGAGATCGTAATGAAGCTTGGATTAGGGTATTGGTAA
genomic: TACACACTGATGAGGAGATCCGTTACTGCGTTGCAGGAACTGgtaagaactt ... tgggaaaaagGTTACTTTGATGTGAGAGATCGTAATGAAGCTTGGATTAGGGTATTGGTAA
EST: gi|125041711|gb|EL113980.1|EL113980
EST:     AGAACATTTACACACTGATGAGGAGATCCGTTACTGCGTTGCAGGAACTG                         GTTACTTTGATGTGAGAGATCGTAATGAAG
genomic: AGAACATTTACACACTGATGAGGAGATCCGTTACTGCGTTGCAGGAACTGgtaagaactt ... tgggaaaaagGTTACTTTGATGTGAGAGATCGTAATGAAG
EST: gi|124717617|gb|EH809019.1|EH809019
EST:     GAACATTTACACACTGATGAGGAGATCCGTTACTGCGTTGCAGGAACTG                         GTTACTTTGATGTGAGAGATCGTAATGAAGCTTGGATTAGGGTATTGGTAA
genomic: GAACATTTACACACTGATGAGGAGATCCGTTACTGCGTTGCAGGAACTGgtaagaactt ... tgggaaaaagGTTACTTTGATGTGAGAGATCGTAATGAAGCTTGGATTAGGGTATTGGTAA
EST: gi|124909352|gb|EH983432.1|EH983432
EST:     GTTACTGCGTTGCAGGAACTG                         GTTACTTTGATTTGTGAGAGATCGTAATGAAGCTTGGATTAGGGTATTGGT
genomic: GTTACTGCGTTGCAGGAACTGgtaagaactt ... tgggaaaaagGTTACTTTGA--TGTGAGAGATCGTAATGAAGCTTGGATTAGGGTATTGGT
EST: gi|124934976|gb|EL011999.1|EL011999
EST:     AACATTTACACACTGATGAGGAGATCCGTTACTGCGTTGCAGGAACTG                         GTTACTTTGATGTGAGAGATACGTAATGAAGCTTGGATTAGGGTATTGGTA
genomic: AACATTTACACACTGATGAGGAGATCCGTTACTGCGTTGCAGGAACTGgtaagaactt ... tgggaaaaagGTTACTTTGATGTGAGAGAT-CGTAATGAAGCTTGGATTAGGGTATTGGTA
EST: gi|124977878|gb|EL051152.1|EL051152
EST:     AGAACATTTACACACTGATGAGGAGATCCGTTACTGCGTTGCAGGAACTG                         GTTACTTTGATGTGAGAGATCGTAATGA
genomic: AGAACATTTACACACTGATGAGGAGATCCGTTACTGCGTTGCAGGAACTGgtaagaactt ... tgggaaaaagGTTACTTTGATGTGAGAGATCGTAATGA
EST: gi|125274269|gb|EL288354.1|EL288354
EST:     AGAACATTTACACACTGATGAGGAGATCCGTTACTGCGTTGCAGGAACTG                         GTTACTTTGATGTGAGAGA
genomic: AGAACATTTACACACTGATGAGGAGATCCGTTACTGCGTTGCAGGAACTGgtaagaactt ... tgggaaaaagGTTACTTTGATGTGAGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcgtaaacttaaaatttcgatatagtagtcatgttttattttcttgggaaaaagGTTACTTTGATGTGAGAGATCGTAATGAAGCTTGGATTAGGGTATTGGTAAAGAAGGGAGGTATGATAGTCTTACCTGCTGGGATCTATCATCGCTTCAC
                                tgttttattttctt  CT-rich tract
         ttaaaatttcgatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaacttcttttactggcggctttactcgtaaacttaaaatttcgatatagtagtcatgttttattttcttgggaaaaagGTTACTTTGATGTGAGAGATCGTAATGAAGCTTGGATTAGGGTATTGGTAAAGAAGGGAGGTATGATAGTCTTACCTGCTGGGATCTATCATCGCTTCAC

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