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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCATGGGAGTATACTCCGATGGCTCTTACAGCGTTCCATCAGGACTTATCTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAGgtaaatatgacgcacttacaaactcaaatgctcatcaattatgaaatcctagattctgcagaccctaatgtgtattttgtttggttag

Basic information

species Arabidopsis thaliana
transcript AT1G04410.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G04410.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv07s0005g03350.t01 (Vitis vinifera), 5'ss of exon 7
TCCATGGGAGTATACTCCGATGGCTCTTACAGCGTTCCATCAGGACTTATCTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAGgtaaatatgacgcacttacaaactcaaatgctcatcaattatgaaatcct----agattctgcagaccctaatg-tgtattttgtttggttag----------
|||||||| || ||||| ||||| || ||||  |||||| |||| |||||||| |||||||||||||| ||  |   ||| || ||||  ||||| ||||||||  || | |||||   | |   |||||||  |    | || |||| |    |  |||||   ||  | ||| | | ||| |||     |           
TCCATGGGTGTGTACTCTGATGGTTCATACAATGTTCCAGCAGGGCTTATCTATTCCTTCCCTGTAACCTGCTGTGCTGGTGAATGGAAGATTGTACAAGgtaacaattatgcactatgaca---aaatgcttgtgctctttggaatcttcaccattttctgagaacatttatgctatgtttggttcccagaaattttgggga

upper sequence: AT1G04410.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv07s0005g03360.t01 (Vitis vinifera), 5'ss of exon 6
TCCATGGGAGTATACTCCGATGGCTCTTACAGCGTTCCATCAGGACTTATCTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAGgtaaatatgacgcacttacaaactcaaatgctcatcaattatgaaatc----ctagattctgcagac-cctaatgtgtattttgtttggttag----------
|||||||| |||||||| ||||| || ||||  |||||| | || |||||||| |||||||||||||||||  |   |||||| ||||  ||||| ||||||||  || | |||||   | |   ||||||||      | || ||||    ||   |||||   |    |||| | |   || |     ||           
TCCATGGGCGTATACTCTGATGGTTCATACAATGTTCCAGCGGGTCTTATCTATTCCTTCCCTGTAACTTGCTGTGCTGGAGAATGGAAGATTGTACAAGgtaacaatcatgcactatgaca---aaatgctctggctctttggaatcttcactgttttctgagaatatttaatctattcattttccttctatttaaaaaagt
















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|124803168|gb|EH891597.1|EH891597
EST:     CTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAG                         GCCTTCCGATTGATGAAGTATCAAGGAAGAAGATGGA
genomic: CTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAGgtaaatatga ... gtttggttagGCCTTCCGATTGATGAAGTATCAAGGAAGAAGATGGA
EST: gi|164066511|gb|EL995529.1|EL995529
EST:     CTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAG                         GCCTTCCGATTGA
genomic: CTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAGgtaaatatga ... gtttggttagGCCTTCCGATTGA
EST: gi|125284248|gb|EL298333.1|EL298333
EST:     CTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAG                         GCCTTCCGATTGATGAAGTATCAAGGAAGAAG
genomic: CTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAGgtaaatatga ... gtttggttagGCCTTCCGATTGATGAAGTATCAAGGAAGAAG
EST: gi|124743031|gb|EH834193.1|EH834193
EST:     CTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAG                         GCCTTCCGATTGATGAAGTATCAAGGAAG
genomic: CTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAGgtaaatatga ... gtttggttagGCCTTCCGATTGATGAAGTATCAAGGAAG
EST: gi|164192443|gb|ES030423.1|ES030423
EST:     GGAGACTGGAGTATTGTCCAAG                         GCCTTCCGATTGATGAAGTATCAAGGAAGAAGATGG
genomic: GGAGACTGGAGTATTGTCCAAGgtaaatatga ... gtttggttagGCCTTCCGATTGATGAAGTATCAAGGAAGAAGATGG
EST: gi|124881586|gb|EH960488.1|EH960488
EST:     CTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAG                         GCCTTCCGATT
genomic: CTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAGgtaaatatga ... gtttggttagGCCTTCCGATT
EST: gi|164022273|gb|ES109150.1|ES109150
EST:     GTATTGTCCAAG                         GCCTTCCGATTGATGAAGTATCAAGGAAGAAGATGGATTTGACTGCAGAGG
genomic: GTATTGTCCAAGgtaaatatga ... gtttggttagGCCTTCCGATTGATGAAGTATCAAGGAAGAAGATGGATTTGACTGCAGAGG
EST: gi|124769782|gb|EH859912.1|EH859912
EST:     TGTCGCAATGGAGACTGGAGTATTGTTCCAAG                         GCCTTCCGATTGATGAAGTATCAAGGAAGAAGATGGATTTGACTGCAGAG
genomic: TGTCGCAATGGAGACTGGAGTATTG-TCCAAGgtaaatatga ... gtttggttagGCCTTCCGATTGATGAAGTATCAAGGAAGAAGATGGATTTGACTGCAGAG
EST: gi|125208134|gb|EL223088.1|EL223088
EST:     CTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAG                         GCCTTCCGATTGATGAAG
genomic: CTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAGgtaaatatga ... gtttggttagGCCTTCCGATTGATGAAG
EST: gi|124910145|gb|EH984225.1|EH984225
EST:     AGACTGGAGTATTGTCCTAAG                         GCCTTCCGATTGATGAAGTATCAAGGAAGAAGATGGATTTGACTGCAGAA
genomic: AGACTGGAGTATTGTCC-AAGgtaaatatga ... gtttggttagGCCTTCCGATTGATGAAGTATCAAGGAAGAAGATGGATTTGACTGCAGA-
EST: gi|124919485|gb|EH993242.1|EH993242
EST:     CCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAG                         GCCTTCCGATTGATGAAGTATCAAGGAAGAAGATGGATTTGACTGCAGAGG
genomic: CCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAGgtaaatatga ... gtttggttagGCCTTCCGATTGATGAAGTATCAAGGAAGAAGATGGATTTGACTGCAGAGG
EST: gi|116378554|gb|EG421146.1|EG421146
EST:     CTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAG                         GCCTTCCGATTGATGAAGTATCAAGGAAGAAGATGGATTTGACTGCAGAGG
genomic: CTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAGgtaaatatga ... gtttggttagGCCTTCCGATTGATGAAGTATCAAGGAAGAAGATGGATTTGACTGCAGAGG
EST: gi|124892962|gb|EH971864.1|EH971864
EST:     CTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAG                         GCCTTCCGATTGATGAAGTATCAAGGAAGAAG
genomic: CTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAGgtaaatatga ... gtttggttagGCCTTCCGATTGATGAAGTATCAAGGAAGAAG
EST: gi|116378552|gb|EG421144.1|EG421144
EST:     CTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAG                         GCCTTCCGATTGATGAAGTATCAAGGAAGAAGATGGATTTGACTGCAGAGG
genomic: CTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAGgtaaatatga ... gtttggttagGCCTTCCGATTGATGAAGTATCAAGGAAGAAGATGGATTTGACTGCAGAGG
EST: gi|124789612|gb|EH879291.1|EH879291
EST:     CTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAG                         GCCTTCCGATTGATGAAGTA
genomic: CTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAGgtaaatatga ... gtttggttagGCCTTCCGATTGATGAAGTA
EST: gi|86081490|gb|DR377247.1|DR377247
EST:     CTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAG                         GCCTTCCGATTGATGAAGTATCAAGGAAGAAGATGGATTTGACTGCAGAGG
genomic: CTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAGgtaaatatga ... gtttggttagGCCTTCCGATTGATGAAGTATCAAGGAAGAAGATGGATTTGACTGCAGAGG
EST: gi|116469998|gb|EG512590.1|EG512590
EST:     CTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAG                         GCCTTCCGATTGATGAAGTATCAAGGAAGAAGATGGATTTGACTGCAGAGG
genomic: CTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAGgtaaatatga ... gtttggttagGCCTTCCGATTGATGAAGTATCAAGGAAGAAGATGGATTTGACTGCAGAGG
EST: gi|125064273|gb|EL131954.1|EL131954
EST:     CTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAG                         GCCTTCCGATTGATGAAGTATCAAGGAAGAAGATGGATTTGACTGCAGAGG
genomic: CTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAGgtaaatatga ... gtttggttagGCCTTCCGATTGATGAAGTATCAAGGAAGAAGATGGATTTGACTGCAGAGG
EST: gi|125082767|gb|EL143562.1|EL143562
EST:     CTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAG                         GCCTTCCGATTGATGAAGTATCAAGGAAGAAGATGGATTTGACTGCAG
genomic: CTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAGgtaaatatga ... gtttggttagGCCTTCCGATTGATGAAGTATCAAGGAAGAAGATGGATTTGACTGCAG
EST: gi|86080897|gb|DR376654.1|DR376654
EST:     CTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAG                         GCCTTCCGATTGATGAAGTATCAAGGAAGAAGATGGATTTGACTGCAGAGG
genomic: CTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAGgtaaatatga ... gtttggttagGCCTTCCGATTGATGAAGTATCAAGGAAGAAGATGGATTTGACTGCAGAGG
EST: gi|124705833|gb|EH797235.1|EH797235
EST:     GTCGCAATGGAGACTGGAGTATTGTCCAAG                         GCCTTCCGATTGATGAAGTATCAAGGAAGAAGATGGATTTGACTGCAGA
genomic: GTCGCAATGGAGACTGGAGTATTGTCCAAGgtaaatatga ... gtttggttagGCCTTCCGATTGATGAAGTATCAAGGAAGAAGATGGATTTGACTGCAGA
EST: gi|116376802|gb|EG419394.1|EG419394
EST:     CTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAG                         GCCTTCCGATTGATGAAGTATCAAGGAAGAAGATGGATTTGACTGCAGAGG
genomic: CTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAGgtaaatatga ... gtttggttagGCCTTCCGATTGATGAAGTATCAAGGAAGAAGATGGATTTGACTGCAGAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCATGGGAGTATACTCCGATGGCTCTTACAGCGTTCCATCAGGACTTATCTACTCCTTCCCTGTAACTTGTCGCAATGGAGACTGGAGTATTGTCCAAGgtaaatatgacgcacttacaaactcaaatgctcatcaattatgaaatcctagattctgcagaccctaatgtgtattttgtttggttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA