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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTATGTGACAATGTACCTCAATGACTGCCAAAGAACTAATTTCTACGAGGGTATCGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAGgtaaaggaacttgaaacaagaagattaatattaacctgtgttatgttcctttttctgaaaatgttgagatttgtttcag

Basic information

species Arabidopsis thaliana
transcript AT3G56940.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G56940.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA03G27380.1 (Glycine max), 5'ss of exon 4
GTTTATGTGACAATGTACCTCAATGACTGCCAAAGAACTAATTTCTACGAGGGTATCGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAGgtaaag--gaacttgaaacaa--gaagattaatattaacctgt-gttatgttcctttttctgaaaatgttgagatttgtt-tcag---------------
|||||||| |||||||| |||||||| |||||| | ||   ||||||||| || || ||  | |||||||| || || || ||||||||||| |||||||| |    |   ||| |       |  || |  |||   |  | ||||| ||   |  ||   |  ||||   ||   || |||                
GTTTATGTCACAATGTATCTCAATGATTGCCAACGTACAGCTTTCTACGAAGGCATTGGACTTAACACAAAAGAATTTGACATGCATGTCATTATCGAGgttagtttgtgtttgcatttttctataatcaccattcctccattgttattttgtataatcaatatttgtttttatccattctcaattacataatcaattt

upper sequence: AT3G56940.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv08s0040g00390.t01 (Vitis vinifera), 5'ss of exon 4
GTTTATGTGACAATGTACCTCAATGACTGCCAAAGAACTAATTTCTACGAGGGTATCGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAGgtaaaggaacttgaaacaagaagattaatattaacctgtgttatgttcctttttctgaaa-atgtt---gagatttgtttcag---
|||||||| ||||||||||||||||| |||||  | ||  ||||||| || || || ||| | |||||||| || || || |||||||| ||||| ||||| |     | |  |   |     |  |  ||   |  ||||||      |  || ||   ||| |   || ||||  ||  |   
GTTTATGTAACAATGTACCTCAATGATTGCCAGCGTACGGATTTCTATGAAGGAATTGGGCTCAACACAAAAGAATTTGACATGCATGTGATCATAGAGgtgagcctgcat--attcatgccctccagctttttccatgttataagtaatgatccgagtcatgcttatgaaattttgttttgcag

upper sequence: AT3G56940.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: EFJ28505 (Selaginella moellendorffii), 5'ss of exon 4
GTTTATGTGACAATGTACCTCAATGACTGCCAAAGAACTAATTTCTACGAGGGTATCGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAGgtaaaggaacttgaaacaagaagattaatattaacctgtgttatgttcctttttctgaaaatgttgagatttgtttcag
|| || |||||||||||||| ||||||||||||||||||   || ||||| || || ||  |  |||| || || ||||| |||||||||||||||||||||       || ||   ||| ||  ||||  |||    | |   ||  ||| ||||| |                   
GTGTACGTGACAATGTACCTAAATGACTGCCAAAGAACTGCCTTTTACGAAGGAATAGGCCTCGACACTAAAGATTTCGACATGCATGTCATCATCGAGgtat-----tttaaagtgagatgag-aataggaactcacgatcgtttgttttctctgacag------------------

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|125165211|gb|EL191594.1|EL191594
EST:     AGGAGTTCGATATGCATGTCATCATCGAG                         ACAAACCGAACCACGGCAAGAATATTCCCTGCGGTGCTGGATGTTGAGAAC
genomic: AGGAGTTCGATATGCATGTCATCATCGAGgtaaaggaac ... tttgtttcagACAAACCGAACCACGGCAAGAATATTCCCTGCGGTGCTGGATGTTGAGAAC
EST: gi|124848942|gb|EH933379.1|EH933379
EST:     GGGTATCGGGTTAAACACAAAGGTAGTTCGATATGCATGTCATCATCGAG                         ACAAACCGAACCACGGCAAGAATATTCCCTGCGGTG
genomic: GGGTATCGGGTTAAACACAAAGG-AGTTCGATATGCATGTCATCATCGAGgtaaaggaac ... tttgtttcagACAAACCGAACCACGGCAAGAATATTCCCTGCGGTG
EST: gi|124928188|gb|EL005852.1|EL005852
EST:     TGCATGTCATCATCGAG                         ACAAACCGAACCACGGCAAGAATATTCCCTGCGGTGCTGGATGTTGAGAAC
genomic: TGCATGTCATCATCGAGgtaaaggaac ... tttgtttcagACAAACCGAACCACGGCAAGAATATTCCCTGCGGTGCTGGATGTTGAGAAC
EST: gi|124741302|gb|EH832464.1|EH832464
EST:     CACAAAGGAGTTCGATATGCATGTCATCATCGAG                         ACAAACCGAACCACGGCAAGAATATT
genomic: CACAAAGGAGTTCGATATGCATGTCATCATCGAGgtaaaggaac ... tttgtttcagACAAACCGAACCACGGCAAGAATATT
EST: gi|125087986|gb|EL146918.1|EL146918
EST:     AGGGTATCGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAG                         ACAAACCGAACCACGGCAAGAATATTCCCT
genomic: AGGGTATCGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAGgtaaaggaac ... tttgtttcagACAAACCGAACCACGGCAAGAATATTCCCT
EST: gi|125176994|gb|EL196295.1|EL196295
EST:     CAAAGGAGTTCGATATGCATGTCATCATCGAG                         ACAAACCGAACCACGGCAAGAATATTCCCTGCGGTGCTGGATGTTGAGAAC
genomic: CAAAGGAGTTCGATATGCATGTCATCATCGAGgtaaaggaac ... tttgtttcagACAAACCGAACCACGGCAAGAATATTCCCTGCGGTGCTGGATGTTGAGAAC
EST: gi|124891208|gb|EH970110.1|EH970110
EST:     AACACAAAGGAGTTCGATATGCATGTCATCATCGAG                         ACAAACCGAACCACGGCAAGAATATTCCCTGCGG
genomic: AACACAAAGGAGTTCGATATGCATGTCATCATCGAGgtaaaggaac ... tttgtttcagACAAACCGAACCACGGCAAGAATATTCCCTGCGG
EST: gi|125104797|gb|EL158764.1|EL158764
EST:     AGGGTATCGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAG                         ACAAACCGAACCACGGCAAGAATATTCCCT
genomic: AGGGTATCGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAGgtaaaggaac ... tttgtttcagACAAACCGAACCACGGCAAGAATATTCCCT
EST: gi|164067966|gb|ES038823.1|ES038823
EST:     CGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAG                         ACAAACCGAACCACGGCAAGAATATTCCC
genomic: CGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAGgtaaaggaac ... tttgtttcagACAAACCGAACCACGGCAAGAATATTCCC
EST: gi|125169926|gb|EL193677.1|EL193677
EST:     AGGGTATCGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAG                         ACAAACCGAACCACGGCAAGAATATTCCCTGCGGTGCTGGATGTTGAGAA
genomic: AGGGTATCGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAGgtaaaggaac ... tttgtttcagACAAACCGAACCACGGCAAGAATATTCCCTGCGGTGCTGGATGTTGAGAA
EST: gi|164031195|gb|ES080340.1|ES080340
EST:     AGGGTATCGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAG                         ACAAACCGAACCACGGCAAGAATATTCCCTGCGGTGTTGGATGTTGAGAA
genomic: AGGGTATCGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAGgtaaaggaac ... tttgtttcagACAAACCGAACCACGGCAAGAATATTCCCTGCGGTGCTGGATGTTGAGAA
EST: gi|124869978|gb|EH954415.1|EH954415
EST:     CATGTCATCATCGAG                         ACAAACCGAACCACGGCAAGAATATTCCCTGCGGTGCTGGATGTTGAGAAC
genomic: CATGTCATCATCGAGgtaaaggaac ... tttgtttcagACAAACCGAACCACGGCAAGAATATTCCCTGCGGTGCTGGATGTTGAGAAC
EST: gi|124705925|gb|EH797327.1|EH797327
EST:     AGGGTATCGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAG                         ACAAACCGAACCA
genomic: AGGGTATCGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAGgtaaaggaac ... tttgtttcagACAAACCGAACCA
EST: gi|125034742|gb|EL107011.1|EL107011
EST:     AGGGTATCGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAG                         ACAAACCGAACCAC
genomic: AGGGTATCGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAGgtaaaggaac ... tttgtttcagACAAACCGAACCAC
EST: gi|125222778|gb|EL236863.1|EL236863
EST:     AGGGTATCGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAG                         ACAAACCGAACCACGGCAAGAATATTCCCTGCGGTGCTGGATGTT
genomic: AGGGTATCGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAGgtaaaggaac ... tttgtttcagACAAACCGAACCACGGCAAGAATATTCCCTGCGGTGCTGGATGTT
EST: gi|124855376|gb|EH939813.1|EH939813
EST:     AGGGTATCGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAG                         ACAAACCGAACCACGGCAAGAATATTCCCTGCGGTGCTGGATGTTGAG
genomic: AGGGTATCGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAGgtaaaggaac ... tttgtttcagACAAACCGAACCACGGCAAGAATATTCCCTGCGGTGCTGGATGTTGAG
EST: gi|124742345|gb|EH833507.1|EH833507
EST:     AGGGTATCGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAG                         ACAAACCGAACCACGGCAAGAA
genomic: AGGGTATCGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAGgtaaaggaac ... tttgtttcagACAAACCGAACCACGGCAAGAA

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTATGTGACAATGTACCTCAATGACTGCCAAAGAACTAATTTCTACGAGGGTATCGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAGgtaaaggaacttgaaacaagaagattaatattaacctgtgttatgttcctttttctgaaaatgttgagatttgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG