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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTCTTGCTGATCTTCAAGGTGATGAGGATAACGCTTACAGGAAGATCCGTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatagtttgttgtaaacattgatttacatcagtaattctggtcattggttaaaaaacccagattatggttgtggagcttgactgttttttttaatcatctttag

Basic information

species Arabidopsis thaliana
transcript AT3G04840.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G04840.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G030915_T02 (Zea mays), 5'ss of exon 3
TTCTCTTGCTGATCTTCAAGGTGATGAGGATAACGCTTACAGGAAGATCCGTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggat----agtttgttgtaaacattgatttacatcagtaattctggtcattggttaaaaaacccagattatggttgtggagcttgactgttttttttaatcatctttag
||  || ||||||||||| || || |||||| | ||||||||||| ||| | ||| | ||||||||||| ||||||||||| || ||     | || ||||||| |||    | | | |||  | ||    ||  | |  ||  |  || | ||   |     ||      || |  |  | | |  ||| | ||     | ||         
TTGCCTAGCTGATCTTCAGGGCGACGAGGATCAAGCTTACAGGAAAATCAGGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGGgtaatgatcggcattcttttgctagcagctgttgccctttgttgtgttgtttatcact-----aatttgttttctattactagggtatgaattttaccactgata--------

upper sequence: AT3G04840.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G145258_T01 (Zea mays), 5'ss of exon 3
TTCTCTTGCTGATCTTCAAGGTGATGAGGATAACGCTTACAGGAAGATCCGTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatag----tttgttgtaaacattgatttacatcagtaattctggtcattggttaaaaaacccagattatggttgtggagcttgactgttttttttaatcatctttag
||  || ||||||||||| || || |||||| | ||||||||||| ||| | ||| | ||||||||||| ||||||||||| || ||     | || ||||||| ||| |    | |||||   |||    ||  | |  ||  || || | ||   |     |||     || |  |  | |                              
TTGCCTAGCTGATCTTCAGGGCGACGAGGATCAAGCTTACAGGAAAATCAGGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGGgtaatgatcggcattatgttgctcacagctgttgccctttgttgttttgtttatcact-----aacttgttttctattactag------------------------------

upper sequence: AT3G04840.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G030915_T08 (Zea mays), 5'ss of exon 3
TTCTCTTGCTGATCTTCAAGGTGATGAGGATAACGCTTACAGGAAGATCCGTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatag----tttgttgtaaacattgatttacatcagtaattctggtcattggttaaaaaacccagattatggttgtggagcttgactgttttttttaatcatctttag
||  || ||||||||||| || || |||||| | ||||||||||| ||| | ||| | ||||||||||| ||||||||||| || ||     | || |||||||  || |    | | |||  ||||    ||  | |  ||  |  || | ||   |     |||     || |  || | |                              
TTGCCTAGCTGATCTTCAGGGCGACGAGGATCAAGCTTACAGGAAAATCAGGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGGgtaataatcggcattcttttgctaacagctgttgccctttgttgtggtgtttatcact-----aacttgttttctatttctag------------------------------

upper sequence: AT3G04840.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G013457_T01 (Zea mays), 5'ss of exon 3
TTCTCTTGCTGATCTTCAAGGTGATGAGGATAACGCTTACAGGAAGATCCGTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggat-agtttgttgtaaacattgatttacatcagtaattctggtcattggttaaaaaacccagattatggttgtggagcttgactgttttttttaatcatctttag
|| ||| ||||||||||| ||||| |||||| | ||||||||||| ||| | ||| | ||||||||||| || |||||||| || ||     | |||||||||| ||| ||  |  ||| |        |     |  |||||||| ||  |      | |||     || |  ||                                  
TTGTCTAGCTGATCTTCAGGGTGACGAGGATCAGGCTTACAGGAAAATCAGGCTCCGTGCTGAAGATGTGCAAGGCAGGAATGTGCTCACAAACTTCTGGgtaatgatcagcattctgttactcactgctgttgcccttaattctgttctctatc---ataacttgtttttttattactag-----------------------------

upper sequence: AT3G04840.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G030915_T03 (Zea mays), 5'ss of exon 3
TTCTCTTGCTGATCTTCAAGGTGATGAGGATAACGCTTACAGGAAGATCCGTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatag----tttgttgtaaacattgatttacatcagtaattctggtcattggttaaaaaacccagattatggttgtggagcttgactgttttttttaatcatctttag
||  || ||||||||||| || || |||||| | ||||||||||| ||| | ||| | ||||||||||| ||||||||||| || ||     | || ||||||| ||| |    | | |||  | ||    ||  | |  ||  |  || | ||   | |          ||||                                       
TTGCCTAGCTGATCTTCAGGGCGACGAGGATCAAGCTTACAGGAAAATCAGGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGGgtaatgatcggcattcttttgctagcagctgttgccctttgttgtgttgtttatcactaatttgttttctattactag-----------------------------------

upper sequence: AT3G04840.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv05s0020g03900.t01 (Vitis vinifera), 5'ss of exon 4
TTCTCTTGCTGATCTTCAAGGTGATGAGGATAACGCTTACAGGAAGATCCGTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatagtttgttgtaaac--attgatttacatc--agtaattctggtcattggttaaaaaacccagattatggttgtggagctt------gactgttttttttaatcatctttag-------
 || |||||||| ||||| | |||||||||| | ||||| || ||||| || || |||||||||||||| || || ||||| ||||||    | || |||||| |       |  ||    |  ||  |||| |||   |   | |||  | |||  ||  |          | |  || |  |  ||       | ||||||| ||   | | |  |        
ATCACTTGCTGACCTTCAGGCTGATGAGGATCAGGCTTATAGAAAGATTCGACTGAGAGCTGAAGATGTTCAAGGGAGGAATGTTCTGACAAACTTTTGGgtatgacagagatcctgaggtcctataaattttcattctatgtaatcttatgattatttttatttttatttatgtatttatttattttttaacaaaatgtttttcttttccttttggaaaatacag

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|116436618|gb|EG479210.1|EG479210
EST:     CTGTGCCAATTCTGG                         GGCATGGACTTC-CCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
genomic: CTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
EST: gi|125006514|gb|EL078783.1|EL078783
EST:     GCCAATTCTGG                         GGCATGGACTTCACCACCGTATAAACTTAGGTCATTGGTTAAGAAGTGGCA
genomic: GCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCG-ATAAACTTAGGTCATTGGTTAAGAAGTGGCA
EST: gi|124903164|gb|EH977244.1|EH977244
EST:     ATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGG                         GGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
genomic: ATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
EST: gi|125198295|gb|EL213249.1|EL213249
EST:     GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGG                         GGCATGGACTTCACCACCGATAAACTTAGGTCATTGG
genomic: GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATTGG
EST: gi|125094796|gb|EL152170.1|EL152170
EST:     TCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTCGTGCCAATTCTGG                         GGCATGGACTTCA
genomic: TCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCT-GTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCA
EST: gi|164178285|gb|EL971970.1|EL971970
EST:     GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGG                         GGCATGGACTTC
genomic: GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTC
EST: gi|124738495|gb|EH829775.1|EH829775
EST:     AGGAACGTTCTGTGCCAATTCTGG                         GGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
genomic: AGGAACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
EST: gi|164037895|gb|ES154790.1|ES154790
EST:     GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGG                         GGCGATGGACTTCACCACCGATAAACTTAGGTCATTG
genomic: GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGC-ATGGACTTCACCACCGATAAACTTAGGTCATTG
EST: gi|124912755|gb|EH986745.1|EH986745
EST:     ATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGG                         GGCATGGACTTCACCACCGATAAACTTAGGTCATTAGGTTAAGAAGTGGCA
genomic: ATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATT-GGTTAAGAAGTGGCA
EST: gi|116425121|gb|EG467713.1|EG467713
EST:     GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGG                         GGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
genomic: GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
EST: gi|124865708|gb|EH950145.1|EH950145
EST:     TGTGCCAATTCTGG                         GGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCGG
genomic: TGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
EST: gi|116436720|gb|EG479312.1|EG479312
EST:     CTGTGCCAATTCTGG                         GGCATGGACTTC-CCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
genomic: CTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
EST: gi|125258688|gb|EL272773.1|EL272773
EST:     CGTTCTGTGCCAATTCTGG                         GGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
genomic: CGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
EST: gi|125044772|gb|EL117041.1|EL117041
EST:     GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGG                         GGCATGGACTTCACCACCGA
genomic: GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGA
EST: gi|125306848|gb|EL320933.1|EL320933
EST:     GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGG                         GGCATGGACTTCACCACCGATAAACTTAGGTCATTGGT
genomic: GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATTGGT
EST: gi|124887667|gb|EH966569.1|EH966569
EST:     AACGTTCTGTGCCAATTCTGG                         GGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
genomic: AACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
EST: gi|125319767|gb|EL333852.1|EL333852
EST:     AACGCTCTGTGCCAATTCTGG                         GGCNTGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
genomic: AACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
EST: gi|125170110|gb|EL193765.1|EL193765
EST:     GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGG                         GGCATGGACTTCACCAC
genomic: GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCAC
EST: gi|124732806|gb|EH824208.1|EH824208
EST:     AGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGG                         GGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGT
genomic: AGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGT
EST: gi|124724280|gb|EH815682.1|EH815682
EST:     GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGG                         GGCATGGACTTCACCACCG
genomic: GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCG
EST: gi|124966709|gb|EL040795.1|EL040795
EST:     GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGG                         GGCATGGACTTCACCACCGATAAACTTAGGT
genomic: GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGATAAACTTAGGT
EST: gi|124734648|gb|EH826050.1|EH826050
EST:     GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGG                         GGCATGGACTTCACCACCGATAAACTTA
genomic: GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGATAAACTTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCTCTTGCTGATCTTCAAGGTGATGAGGATAACGCTTACAGGAAGATCCGTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatagtttgttgtaaacattgatttacatcagtaattctggtcattggttaaaaaacccagattatggttgtggagcttgactgttttttttaatcatctttag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG