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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTGTAGAGACGGATGGTAAAGGTTATGATCGGGTGAGGCGGACAGAGATTGGGAAGAAGCATTTTAAGCTTACACATTTCGAAGAGgtgagatttaaattatttactacaaaccagggtgcattgattccactaggattctggtaaatgtaactggttttgtcatcag

Basic information

species Arabidopsis thaliana
transcript AT5G19690.1
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G19690.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GLYMA16G08410.1 (Glycine max), 5'ss of exon 21
GTTTGTAGAGACGGATGGTAAAGGTTATGATCGGGTGAGGCGGACAGAGATTGGGAAGAAGCATTTTAAGCTTACACATTTCGAAGAGgtgagatt-------taaattatttacta--caaaccagggtgcattgattccactaggattctggtaaatgtaactggttttgtcatcag----------
 ||||| ||||| |||||||| | || |||  | ||||||| |||||| ||||||||||| ||||| || ||||| ||||| |||||||| |||||       |   | || || ||   ||  | |   | |    |    ||  |  ||   ||  | |   |  |||| | || |           
ATTTGTGGAGACAGATGGTAAGGCTTTTGACAGAGTGAGGCAGACAGAAATTGGGAAGAAACATTTCAAACTTACGCATTTTGAAGAGgtcagattatttaactgggtcatgtattaaataattctgtcaggaactgtcttgctgtgtatcaaatattttttttttatttt-ttattatatttagaatg

upper sequence: AT5G19690.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GLYMA01G01270.1 (Glycine max), 5'ss of exon 21
GTTTGTAGAGACGGATGGTAAAGGTTATGATCGGGTGAGGCGGACAGAGATTGGGAAGAAGCATTTTAAGCTTACACATTTCGAAGAGgtgagatt---taaattatttac-tac-aaaccagggtgcattgattccactaggattctggtaaatgtaac-tggttttgtcatcag------------
 ||||| ||||| |||||||||| ||  ||| | ||||||||||| || |||||||||||  |||| || ||||| ||||| || ||||| |||||   ||| ||  | |  ||  |||  |   |     ||     || | | | | ||   | |    || |  ||  || |             
ATTTGTGGAGACTGATGGTAAAGCTTTCGATAGAGTGAGGCGGACTGAAATTGGGAAGAAATATTTCAAACTTACGCATTTTGAGGAGgtcagattgtttaacttggtcatgtattaaataattctattaggaactgtcttgcagtgtagtttctctgttatgatcctgaaattaattttggtggatg

upper sequence: AT5G19690.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: Vv11s0016g03320.t01 (Vitis vinifera), 5'ss of exon 21
GTTTGTAGAGACGGATGGTAAAGGTTATGATCGGGTGAGGCGGACAGAGATTGGGAAGAAGCATTTTAAGCTTACACATTTCGAAGAGgtgaga---tttaaattatttactacaaaccagggtgcattgattccactaggatt--ctggtaaatgtaactggttttgtcatcag---------------
 ||||| ||||| ||||||||||| | |||||| || |||||||| || |||||||||||  |||| || || || ||||| || ||||| |||   | |||||     | |     |    ||||||  | |  | || |||    || |     |  | || | |  || |                 
ATTTGTGGAGACAGATGGTAAAGGCTTTGATCGAGTAAGGCGGACTGAAATTGGGAAGAAATATTTCAAACTCACCCATTTTGAGGAGgttagacaatctaaatccccaatt--tggcagtagtgcataaaatggagtatgatcagttgttgtgcctgtcaggctgtcacaacttatttgagagttaaaa

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|125267589|gb|EL281674.1|EL281674
EST:     GGCGGACAGAGATTGGGAAGAAGCATTTTAAGCTTACACATTTCGAAGAG                         GTTTTCACGAGT
genomic: GGCGGACAGAGATTGGGAAGAAGCATTTTAAGCTTACACATTTCGAAGAGgtgagattta ... ttgtcatcagGTTTTCACGAGT
EST: gi|164165011|gb|ES025990.1|ES025990
EST:     GCGGACAGAGATTGGGAAGAAGCATTTTAAGCTTACACATTTCGAAGAG                         GTTTTCACGAGTCACCATTGGATGGTTCGGCTATACAAGCTGAAACCTCCC
genomic: GCGGACAGAGATTGGGAAGAAGCATTTTAAGCTTACACATTTCGAAGAGgtgagattta ... ttgtcatcagGTTTTCACGAGTCACCATTGGATGGTTCGGCTATACAAGCTGAAACCTCCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTGTAGAGACGGATGGTAAAGGTTATGATCGGGTGAGGCGGACAGAGATTGGGAAGAAGCATTTTAAGCTTACACATTTCGAAGAGgtgagatttaaattatttactacaaaccagggtgcattgattccactaggattctggtaaatgtaactggttttgtcatcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA