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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTAgtaagttcttacacatttttatttttggattaatgttttaagagttaattgcaaattttcatattttgatctacaacttatattctgtggtcctaatttt...

Basic information

species Arabidopsis thaliana
transcript AT5G46110.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G46110.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os01g13770.3 (Oryza sativa), 5'ss of exon 2
GTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTAgtaagt-tcttac-acatttttatttttggattaatgttttaag----agttaattgcaaattttcatattttgatctacaactta--tattctgtggtcctaatttt-----------------
|||||||||||| || || ||||||||||| || |||||||| || || |||||||| ||||| |||||||| | |||      ||      |||  ||       | ||    ||  |  |||    | |   |||    | |  | ||    ||     | ||   ||   |                 
GTACTTCTTGAACGTTATATTCAACATCCTCAATAAGAAGATATACAACTACTTCCCCTATCCATAgtaagtgtattattgttcttccccccttgctttgcaacagtgagcatcagcaagctgcgtgatcttgcattccattttgtagctgggttacgacatagtatgaacaatcgtactgcttgctgcag

upper sequence: AT5G46110.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os05g15160.1 (Oryza sativa), 5'ss of exon 3
GTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTAgtaagttc-ttacacatttttatttttggattaatgttttaagagttaattgcaaattttcatattt-tgatctacaacttatattctgtggtcctaatttt
||| ||  |||| ||||| || ||||||||||||||||||||||   | |||||||| ||||| ||||| |||   |  | || | |   |      |  | ||||     | |  ||  ||  | ||| ||  ||||||| ||| | | |  |||     ||     
GTATTTTCTGAACGTGATATTTAACATCCTTAACAAGAAGATCTTCGACTACTTCCCCTATCCATAgtacgtttgctttatatgtgtgcctcc----ttttctttttcctttcatgtgacaacatgcatcttcatgatctaaaacctctttcttgttaatatag----

upper sequence: AT5G46110.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G070605_T01 (Zea mays), 5'ss of exon 3
GTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTAgtaagttcttacacatttttatttttggattaatgttttaagagttaattgcaaattttcatattttgatc--tacaacttatattctgtggtcctaatttt
||||||| | || || || ||||||||||| |||||||||||||| || |||||||| ||||| ||||||||    | ||  |   |   |||  | | || || |  | |  ||    |      | |||||| ||  | ||                         
GTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATAgtaagtaggcaaac-ctggcaggcttgattaattgattcataaatagatgaggaccaacaacattttgctcgttgcag------------------------

upper sequence: AT5G46110.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv10s0003g00300.t01 (Vitis vinifera), 5'ss of exon 3
GTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTAgtaagttcttacacatttttatttttggattaatgttttaagagttaattgcaaattttcatattttgatctacaacttatatt---ctgtggtcctaatttt-
||| ||| | || || || ||||||||||| |||||||||||||| || |||||||| ||||| ||||||||      | | || |   | |  || |   | | | |    |  ||      |  |  |  |||     |  ||||  |   ||||||      |    
GTATTTCCTCAACGTTATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCATATCCTTAgtaagtatggctaaaattcttggtatatatgagcttctgacggtccatctgggggcatggaattgatgaaagttagtttatggtggtctgtggggtgtgtgcag

upper sequence: AT5G46110.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S450_17V6.1 (Physcomitrella patens), 5'ss of exon 3
GTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTAgtaagttcttacacatttttatttttggattaatgttttaagagttaattgcaaattttcatattttgatctacaacttatattctgtggtcctaatttt----
||||||| ||||||| || ||||||||| | |||||||||||||| || ||||| || || || |||||||| || |      |||||    | || ||  | ||      | |        | | || |||     | || | | |   |   | |  ||  |||    
GTACTTCCTGAATGTTATCTTCAACATCATGAACAAGAAGATCTACAACTACTTTCCCTACCCTTAgtaagtcctcatgtgcgtttatg---gtatcaaaatatttgagaatgaccattggatcttatctttgctgttgcagcat-tggacgaagtttttaggtttgact

upper sequence: AT5G46110.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S450_22V6.1 (Physcomitrella patens), 5'ss of exon 3
GTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTAgtaagttcttacacatttttatttttggattaatgttttaagagttaattgcaaattttcatattttgatctacaacttatat-tctgtggtcctaatttt-------------------------------------------------------------------------------
|||||||||||| || || ||||||||| | |||||||||||||| || || || || || |||||||||||  | |     | |   |||    | | |  ||  ||  ||    | |   |    |  |||||||  |  | | ||| ||| |       | |                                                                                 
GTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTAgtaagtcttcagtacctctgcatttcatctcagtagttgcagcattgcgcgaagtatggattggtttgatcgtcttcgtgtatatctctaacaggcagtagagcggtgatctgtgagctggctcttgagcggatgcctttgcacttaggctgatacagtactggtcgcggttgcgtgcag

upper sequence: AT5G46110.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: EFJ15759 (Selaginella moellendorffii), 5'ss of exon 3
GTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTAgtaagttcttacacatttttatttttggattaatgttt--taagagttaattgcaaattttcatattttgatctacaacttatattctgtggtcctaatttt
||| ||  | |||||||| |||||||||||||||||||||||||| ||||| || |||||||| ||||||| |    ||  |    |  |||  || |     |   | ||  |  ||   |                                              
GTATTTTCTCAATGTGATCTTCAACATCCTTAACAAGAAGATCTACAATTATTTTCCTTATCCATAgtaagctacctcagctgacaaggtttttatcatctcctgacatgaactcgttcttag---------------------------------------------

upper sequence: AT5G46110.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: EFJ38162 (Selaginella moellendorffii), 5'ss of exon 2
GTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTAgtaagttcttacacatttttatttttggattaatgttttaagagttaattgcaaattttcatattttgatctacaacttatattctgtggtcctaatttt
||| ||  | |||||||| |||||||||||||||||||||||||| ||||| || |||||||| ||||||| |    ||  |    |  |||  || | | |  | | |   ||| |    || | |                                       
GTATTTTCTCAATGTGATCTTCAACATCCTTAACAAGAAGATCTACAATTATTTTCCTTATCCATAgtaagctacctcagctgacaaggtttttatca-tctcctgacatggaatcg----ttcttag--------------------------------------

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|124952343|gb|EL027622.1|EL027622
EST:     ATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTA                         TTTTGTATCGGTGATACACTTGTTCGTGGGAG
genomic: ATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTAgtaagttctt ... tttgtttcagTTTTGTATCGGTGATACACTTGTTCGTGGGAG
EST: gi|116415580|gb|EG458172.1|EG458172
EST:     ATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTA                         TTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTTTACTGCTTGATCAG
genomic: ATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTAgtaagttctt ... tttgtttcagTTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTTTACTGCTTGATCAG
EST: gi|125016402|gb|EL088671.1|EL088671
EST:     TTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTA                         TTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTTTACTGCTTGATCAG
genomic: TTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTAgtaagttctt ... tttgtttcagTTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTTTACTGCTTGATCAG
EST: gi|116474259|gb|EG516851.1|EG516851
EST:     ATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTA                         TTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTTTACTGCTTGATCAG
genomic: ATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTAgtaagttctt ... tttgtttcagTTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTTTACTGCTTGATCAG
EST: gi|124841511|gb|EH925948.1|EH925948
EST:     TTCCCTTTATCCCTA                         TTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTTTACTGCTTGATCA
genomic: TTCCC-TTATCCCTAgtaagttctt ... tttgtttcagTTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTTTACTGCTTGATCA
EST: gi|164227733|gb|ES196304.1|ES196304
EST:     AACATCCTTAACAAGAAGATCTATAATTACTTCCCTTTATCCCTA                         TTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTTTACTGCTTGATCA
genomic: AACATCCTTAACAAGAAGATCTATAATTACTTCCC-TTATCCCTAgtaagttctt ... tttgtttcagTTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTTTACTGCTTGATCA
EST: gi|116474248|gb|EG516840.1|EG516840
EST:     ATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTA                         TTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTTTACTGCTTGATCAG
genomic: ATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTAgtaagttctt ... tttgtttcagTTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTTTACTGCTTGATCAG
EST: gi|125122678|gb|EL169155.1|EL169155
EST:     ATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTA                         TTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTTTA
genomic: ATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTAgtaagttctt ... tttgtttcagTTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTTTA
EST: gi|125200360|gb|EL215314.1|EL215314
EST:     TACTTCCCTTATCCCTA                         TTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTTTACTGCTTGATCAG
genomic: TACTTCCCTTATCCCTAgtaagttctt ... tttgtttcagTTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTTTACTGCTTGATCAG
EST: gi|116431239|gb|EG473831.1|EG473831
EST:     ATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTA                         TTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTTTACTGCTTGATCAG
genomic: ATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTAgtaagttctt ... tttgtttcagTTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTTTACTGCTTGATCAG
EST: gi|164062801|gb|ES213614.1|ES213614
EST:     A-TTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTA                         TTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTT
genomic: ATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTAgtaagttctt ... tttgtttcagTTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTT
EST: gi|125306329|gb|EL320414.1|EL320414
EST:     TTTTCAACATCCTTAACAAAGAAGATCTATAATTACTTCCCTTATCCCTA                         TTTTGTATCGGTGATACACTTGTTCGTGGG
genomic: TTTTCAACATCCTTAAC-AAGAAGATCTATAATTACTTCCCTTATCCCTAgtaagttctt ... tttgtttcagTTTTGTATCGGTGATACACTTGTTCGTGGG
EST: gi|116420927|gb|EG463519.1|EG463519
EST:     ATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTA                         TTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTTTACTGCTTGATCAG
genomic: ATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTAgtaagttctt ... tttgtttcagTTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTTTACTGCTTGATCAG
EST: gi|164149578|gb|ES197706.1|ES197706
EST:     CAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTA                         TTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTTTACTGCTTGATCAG
genomic: CAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTAgtaagttctt ... tttgtttcagTTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTTTACTGCTTGATCAG
EST: gi|116431241|gb|EG473833.1|EG473833
EST:     ATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTA                         TTTTGTATCGGTGATAC
genomic: ATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTAgtaagttctt ... tttgtttcagTTTTGTATCGGTGATAC
EST: gi|164012073|gb|ES176750.1|ES176750
EST:     ATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTA                         TTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTTTACTGCTTGATCAG
genomic: ATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTAgtaagttctt ... tttgtttcagTTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTTTACTGCTTGATCAG
EST: gi|125033646|gb|EL105915.1|EL105915
EST:     ATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTA                         TTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTT
genomic: ATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTAgtaagttctt ... tttgtttcagTTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTT
EST: gi|125071184|gb|EL136325.1|EL136325
EST:     ATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTA                         TTTTGTATCGGTGATACACTTGTTCGTGGGAGTTG
genomic: ATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTAgtaagttctt ... tttgtttcagTTTTGTATCGGTGATACACTTGTTCGTGGGAGTTG
EST: gi|125200275|gb|EL215229.1|EL215229
EST:     ATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTA                         TTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTTTACTGCTTG
genomic: ATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTAgtaagttctt ... tttgtttcagTTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTTTACTGCTTG
EST: gi|164009532|gb|ES199110.1|ES199110
EST:     TAATTACTTCCCTTATCCCTA                         TTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTTTACTGCTTGATCAG
genomic: TAATTACTTCCCTTATCCCTAgtaagttctt ... tttgtttcagTTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTTTACTGCTTGATCAG
EST: gi|124851183|gb|EH935620.1|EH935620
EST:     TACTTCCCTTATCCCTA                         TTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTTTACTGCTTGATCAG
genomic: TACTTCCCTTATCCCTAgtaagttctt ... tttgtttcagTTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTTTACTGCTTGATCAG
EST: gi|116474253|gb|EG516845.1|EG516845
EST:     ATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTA                         TTTTGTATCTGTGATACACTTGTTCGTGGGAGTTGTTTACTGCTTGATCAG
genomic: ATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTAgtaagttctt ... tttgtttcagTTTTGTATCGGTGATACACTTGTTCGTGGGAGTTGTTTACTGCTTGATCAG
EST: gi|125089345|gb|EL147748.1|EL147748
EST:     ATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTA                         TTTTGTATCGGTGATACACTTAGTTCGTGGGAGTTGTTTACTGCTTGATCA
genomic: ATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTAgtaagttctt ... tttgtttcagTTTTGTATCGGTGATACACTT-GTTCGTGGGAGTTGTTTACTGCTTGATCA
EST: gi|125320377|gb|EL334462.1|EL334462
EST:     ATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTA                         TTTTGTAATCGGTGATACACTTGTTCGTGGGAGTTGT
genomic: ATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTAgtaagttctt ... tttgtttcagTTTTGTA-TCGGTGATACACTTGTTCGTGGGAGTTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTAgtaagttcttacacatttttatttttggattaatgttttaagagttaattgcaaattttcatattttgatctacaacttatattctgtggtcctaatttt

- - - - - - - - - - - - - - - - - AAGAAG