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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAATCTTTGTTGATAAGGACGGAGAGGAAATTCCTGTTAAAGTACCAATTGGAATGTCAGTGCTCGAAGCTGCTCATGAAAATGATATAGACCTTGAAGgtgcacacttctcttccattttcttctcgttttcaattgcttactctcatagctttagatgggttctattaattatattgatcctttttcgaattgaaaattcatggattgcttttacttgatctccag

Basic information

species Arabidopsis thaliana
transcript AT4G05450.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G05450.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os09g26650.1 (Oryza sativa), 5'ss of exon 4
ATAATCTTTGTTGATAAGGACGGAGAGGAAATTCCTGTTAAAGTACCAATTGGAATGTCAGTGCTCGAAGCTGCTCATGAAAATGATATAGACCTTGAAGgtgcacacttctcttccattttcttctcgttttcaattgcttactctcatagctttagatgggttctattaattatattgatcctttttcgaattgaaaattcatggattgcttttacttgatctccag
 | |  |||||||||||||| || |||||||  | |||||||||||| || ||||||||| |||| || || || ||||| ||||| ||||| |||||||||   || ||    | |    ||||          | || || |||   | | |||| ||   || |  ||| || ||| || ||| | |   ||      |||||  |||  ||      |       
GTGACTTTTGTTGATAAGGATGGCGAGGAAAAGCTTGTTAAAGTACCTATAGGAATGTCAATGCTAGAGGCAGCACATGAGAATGACATAGAACTTGAAGgt---catttgaaatgccgagtctt----------aatgtttgctcattttgatttaaatcaatttt--taagtacatttatgcttgtgcatgtt------tcatg--ttgtgttggacaaaa------

upper sequence: AT4G05450.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM5G856338_T01 (Zea mays), 5'ss of exon 1
ATAATCTTTGTTGATAAGGACGGAGAGGAAATTCCTGTTAAAGTACCAATTGGAATGTCAGTGCTCGAAGCTGCTCATGAAAATGATATAGACCTTGAAGgtgcacacttctcttccattttcttctcgttttcaattgcttactctcatagctttagatgggttctattaattatattgatcctttttcgaattgaaaattcatggattgcttttacttgatctccag
 |||  |||||| | ||||| ||    ||||   |  |    || ||| ||||||||||  || | |||||||||||||||||||| ||||| ||||||||| || |  |  |    || | |   ||  ||  | |   |   | |  |   | |     |||| | | | | |  || || |||  |   |   | |  ||||  ||                    
GTAACATTTGTTAACAAGGATGGCTCAGAAAAGACAATACGTGTTCCAGTTGGAATGTCCATGTTAGAAGCTGCTCATGAAAATGACATAGAGCTTGAAGgtacaaatattacaaagatgtgcacttctattctagtg--tgggtattgtgtttat-----ggttttgt-agtca-gttcatgcttggtgataagaatatgtcatatat--------------------

upper sequence: AT4G05450.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G013607_T02 (Zea mays), 5'ss of exon 5
ATAATCTTTGTTGATAAGGACGGAGAGGAAATTCCTGTTAAAGTACCAATTGGAATGTCAGTGCTCGAAGCTGCTCATGAAAATGATATAGACCTTGAAGgtgcacacttctcttccattttcttctcgttttcaattgcttactctcatagctttagatgggttctattaattatattgatcctttttcgaattgaaaattcatggattgcttttacttgatctccag
 |||  |||||  | ||||| ||    ||||   |  |    || ||| ||||||||||  || | ||||||||||||||||| || ||||| ||||||||| || |  |       || | |   ||  || ||    ||     |  |  |||||    |||||||| | | |    | || |  || |   | | |||  ||| |                     
GTAACATTTGTCAACAAGGATGGCTCAGAAAAGACAATATGTGTTCCAGTTGGAATGTCCATGTTAGAAGCTGCTCATGAAAACGACATAGAGCTTGAAGgtacagatattaaggaaatgtgcacttcccttcca----ctgtggtttttgcctttat---ggttctat-agtca----gttcatgcttggtgataagaatatatgcacctt-----------------

upper sequence: AT4G05450.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv11s0016g00530.t01 (Vitis vinifera), 5'ss of exon 5
ATAATCTTTGTTGATAAGGACGGAGAGGAAATTCCTGTTAAAGTACCAATTGGAATGTCAGTGCTCGAAGCTGCTCATGAAAATGATATAGACCTTGAAGgtgcacacttctcttccattttcttctcgttttcaattgcttactctcatagctttagatgggttctattaattatattgatcctttttcgaattgaaaattcatggattgcttttacttgatctccag
 |    |||||||||||||| |||||||||  ||   |||  || || |||||||||||  || | |||||||||||||||||||||||||| ||||||||||   | || |  | |||||| || |||| |    ||||  | | || | |   |   |  ||| | || || ||  | || |||      ||  | |     |                        
GTGTCATTTGTTGATAAGGATGGAGAGGAACATCACATTAGGGTCCCCATTGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGATATAGAACTTGAAGgtgtgtattt-tgatgcatttt-ttatcgtatc---ttgcacattttccttgacctcattttgttttttttataattattattcttagcatgatgcacagcattt------------------------

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|164148048|gb|ES032852.1|ES032852
EST:     TGGAATGTCAGTGCTCGAAGCTGCTCATGAAAATGATATAGACCTTGAAG                         GGGCTTGTGAGGCTTCTCTAGCGTGTTCAACGTGTC
genomic: TGGAATGTCAGTGCTCGAAGCTGCTCATGAAAATGATATAGACCTTGAAGgtgcacactt ... tgatctccagGGGCTTGTGAGGCTTCTCTAGCGTGTTCAACGTGTC
EST: gi|116443733|gb|EG486325.1|EG486325
EST:     TGGAATGTCAGTGCTCGAAGCTGCTCATGAAAATGATATAGACCTTGAAG                         GGGCTTGTGAGGCTTCTCTAGCGTGTTCAACGTGTCATGTGATTGTGATG
genomic: TGGAATGTCAGTGCTCGAAGCTGCTCATGAAAATGATATAGACCTTGAAGgtgcacactt ... tgatctccagGGGCTTGTGAGGCTTCTCTAGCGTGTTCAACGTGTCATGTGATTGTGATG
EST: gi|116443713|gb|EG486305.1|EG486305
EST:     TGGAATGTCAGTGCTCGAAGCTGCTCATGAAAATGATATAGACCTTGAAG                         GGGCTTGTGAGGCTTCTCTAGCGTGTTCAACGTGTCATGTGATTGTGATG
genomic: TGGAATGTCAGTGCTCGAAGCTGCTCATGAAAATGATATAGACCTTGAAGgtgcacactt ... tgatctccagGGGCTTGTGAGGCTTCTCTAGCGTGTTCAACGTGTCATGTGATTGTGATG
EST: gi|116443730|gb|EG486322.1|EG486322
EST:     TGGAATGTCAGTGCTCGAAGCTGCTCATGAAAATGATATAGACCTTGAAG                         GGGCTTGTGAGGCTTCTCTAGCGTGTTCAACGTGTCATGCGATTGTGATG
genomic: TGGAATGTCAGTGCTCGAAGCTGCTCATGAAAATGATATAGACCTTGAAGgtgcacactt ... tgatctccagGGGCTTGTGAGGCTTCTCTAGCGTGTTCAACGTGTCATGTGATTGTGATG
EST: gi|116443725|gb|EG486317.1|EG486317
EST:     TGGAATGTCAGTGCTCGAAGCTGCTCATGAAAATGATATAGACCTTGAAG                         GGGCTTGTGAGGCTTCTCTAGCGTGTTCAACGTGTCATGCGATTGTGATG
genomic: TGGAATGTCAGTGCTCGAAGCTGCTCATGAAAATGATATAGACCTTGAAGgtgcacactt ... tgatctccagGGGCTTGTGAGGCTTCTCTAGCGTGTTCAACGTGTCATGTGATTGTGATG
EST: gi|116443734|gb|EG486326.1|EG486326
EST:     TGGAATGTCAGTGCTCGAAGCTGCTCATGAAAATGATATAGACCTTGAAG                         GGGCTTGTGAGGCTTCTCTAGCGTGTTCAACGTGTCATGTGATTGTGATG
genomic: TGGAATGTCAGTGCTCGAAGCTGCTCATGAAAATGATATAGACCTTGAAGgtgcacactt ... tgatctccagGGGCTTGTGAGGCTTCTCTAGCGTGTTCAACGTGTCATGTGATTGTGATG
EST: gi|116443712|gb|EG486304.1|EG486304
EST:     TGGAATGTCAGTGCTCGAAGCTGCTCATGAAAATGATATAGACCTTGAAG                         GGGCTTGTGAGGCTTCTCTAGCGTGTTCAACGTGTCATGTGATTGTGATG
genomic: TGGAATGTCAGTGCTCGAAGCTGCTCATGAAAATGATATAGACCTTGAAGgtgcacactt ... tgatctccagGGGCTTGTGAGGCTTCTCTAGCGTGTTCAACGTGTCATGTGATTGTGATG
EST: gi|86076925|gb|DR372682.1|DR372682
EST:     TGGAATGTCAGTGCTCGAAGCTGCTCATGAAAATGATATAGACCTTGAAG                         GGGCTTGTGAGGCTTCTCTAGCGTGTTCAACGTGTCATGTGATTGTGATG
genomic: TGGAATGTCAGTGCTCGAAGCTGCTCATGAAAATGATATAGACCTTGAAGgtgcacactt ... tgatctccagGGGCTTGTGAGGCTTCTCTAGCGTGTTCAACGTGTCATGTGATTGTGATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAATCTTTGTTGATAAGGACGGAGAGGAAATTCCTGTTAAAGTACCAATTGGAATGTCAGTGCTCGAAGCTGCTCATGAAAATGATATAGACCTTGAAGgtgcacacttctcttccattttcttctcgttttcaattgcttactctcatagctttagatgggttctattaattatattgatcctttttcgaattgaaaattcatggattgcttttacttgatctccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG