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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGTTTGAGAGGAGCTTTATGATCAAGTTTCCTTCCTGCACTATTTCTGCAAAGAGGCATATTGATTCAAGTACAACTATTCTTGATGTTCAAGGAGTGgtaagtattttctacagttcatgatattagttgtgaaatgagtttttttctcatgtgtttatataacttcatattcag

Basic information

species Arabidopsis thaliana
transcript AT2G21520.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G21520.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os02g04020.1 (Oryza sativa), 5'ss of exon 5
GGAGTTTGAGAGGAGCTTTATGATCAAGTTTCCTTCCTGCACTATTTCTGCAAAGAGGCATATTGATTCAAGTACAACTATTCTTGATGTTCAAGGAGTGgtaagtattt-----tctacagttcatgatattagttgtgaaatgagtttttttct-------catgtgtttatata--acttcatattcag
||| |||||  |||||||  |||||||||| ||  | ||| || || ||||||| ||||| |||||||| || ||||| |||||||||||||| || |||||| |    |     | ||   | ||   |  |  || |    |   ||| |||         |||||| | ||  |  || |  | |||||
GGAATTTGAACGGAGCTTCTTGATCAAGTTCCCAGCATGCTCTCTTGCTGCAAAAAGGCACATTGATTCGAGCACAACAATTCTTGATGTTCAGGGTGTGgtatgctgctgaagctttaatctccagactgattattctttcttttttttcttttcactcaggcatgtgctaattgagcacattcttttcag

upper sequence: AT2G21520.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G171354_T03 (Zea mays), 5'ss of exon 5
GGAGTTTGAGAGGAGCTTTATGATCAAGTTTCCTTCCTGCACTATTTCTGCAAAGAGGCATATTGATTCAAGTACAACTATTCTTGATGTTCAAGGAGTGgtaagt-att-----ttctacagttcatgatattagttgtgaaatgagtttttttctcatgtgtttatataacttcatattcag---------
||||||||||||||||||  |||| || |||||  | ||| || || ||||||| ||||| |||||||| || ||||| ||||| ||||| || || |||||| || | |     ||  |   ||||||||  |  |  |      | ||      | ||| ||     ||  ||||||   |          
GGAGTTTGAGAGGAGCTTCTTGATTAAATTTCCAGCTTGCTCTGTTGCTGCAAAAAGGCACATTGATTCCAGCACAACAATTCTGGATGTCCAGGGCGTGgtatgttactgaggatttaatctttcatgatgcttttctttgtgcaacttgacagttgatgagtgc---tactttcatacctatgtttcatag

upper sequence: AT2G21520.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G073571_T03 (Zea mays), 5'ss of exon 4
GGAGTTTGAGAGGAGCTTTATGATCAAGTTTCCTTCCTGCACTATTTCTGCAAAGAGGCATATTGATTCAAGTACAACTATTCTTGATGTTCAAGGAGTGgtaagt------attttctacagttcatgatattagttgtgaaatgagtttttttctcatgtgtttatataacttc-atattcag---
||||||||||||||||||  |||| || |||||  | ||| || || ||||||| ||||| |||||||| || || || ||||| ||||| || ||||||||| ||      |  ||      ||||||||  |  |  | |    | ||      |  || | | ||   |   | ||  |      
GGAGTTTGAGAGGAGCTTCTTGATTAAATTTCCAGCTTGCTCTCTTGCTGCAAAAAGGCACATTGATTCCAGCACGACAATTCTGGATGTCCACGGAGTGgtatgtcactgaagatttagtctttcatgatgcttctcttcatgcaacttcacaattggtgagctaattagatacctatgctttatag

upper sequence: AT2G21520.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA06G01260.1 (Glycine max), 5'ss of exon 4
GGAGTTTGAGAGGAGCTTTATGATCAAGTTTCCTTCCTGCACTATTTCTGCAAAGAGGCATATTGATTCAAGTACAACTATTCTTGATGTTCAAGGAGTGgtaa-gtattttctacagttcatg-atattagt---------tgtgaaatgagtttttttctcatgtgtttatataacttcatattcag---------
|||||||||||     |||   |||||||||||| | ||| ||||| |||| |||||||| |||||||| || || || ||  | |||||||| |||||||||   | ||  ||  | ||  |  || || |          ||| |  | |  || | |  |||       | |   |  ||  |            
GGAGTTTGAGAAAGCTTTTGCAATCAAGTTTCCTGCTTGCTCTATTGCTGCCAAGAGGCACATTGATTCCAGCACCACAATCTTAGATGTTCACGGAGTGgtattatgttacctctaatttttttatcttcgcatttactactgtaatctaaagttctataacatacaagacttttgttgtatgattgacattatcag

upper sequence: AT2G21520.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA04G01220.1 (Glycine max), 5'ss of exon 4
GGAGTTTGAGAGGAGCTTTATGATCAAGTTTCCTTCCTGCACTATTTCTGCAAAGAGGCATATTGATTCAAGTACAACTATTCTTGATGTTCAAGGAGTGgtaa-gtattttctacagttcatgatattagt---------tgtgaaatgagtttttttctcatgtgttta----tataacttcatattcag---------
|||||||||||     |||   |||||||||||| | ||| ||||| |||| |||||||| |||||||| || || || ||  | |||||||| |||||||||   | ||  ||  | ||  | || || |          ||| || | |  || | |  |||     ||    | |   |  ||| |            
GGAGTTTGAGAAAGCTTTTGCAATCAAGTTTCCTGCTTGCTCTATTGCTGCCAAGAGGCACATTGATTCCAGCACCACAATCTTAGATGTTCACGGAGTGgtattatgttacctctaatttttcatctttgcgttgactactgtaaactaaagttatataacatacaagtaacatttttgttgtataattgacatcatcag

upper sequence: AT2G21520.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv03s0038g04470.t01 (Vitis vinifera), 5'ss of exon 5
GGAGTTTGAGAGGAGCTTTATGATCAAGTTTCCTTCCTGCACTATTTCTGCAAAGAGGCATATTGATTCAAGTACAACTATTCTTGATGTTCAAGGAGTGgtaagtattttcta--cagttcatgatattagttgtgaaatgagtttttttctcatgtgtttatataacttcatattcag------------------------
|||||| ||||  ||||||    | ||||||||  |||| |||||| ||||||||||||| || ||||| || ||||||||| | ||||||||||| |||||| |  || | ||     ||| || |     |||  ||||   ||||   |  ||     | | |||  | || ||                           
GGAGTTCGAGAAAAGCTTTGCCCTAAAGTTTCCAGCCTGTACTATTGCTGCAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTGgtatgctttctgtaattttttcttggtcaccattgcaaaatatattttggcccaatcaaaatgtttaaacttatcttttctatttctgatcatcaattttccag

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|125101074|gb|EL156304.1|EL156304
EST:     CAAAGAGGCATATTGATTCAAGTACAACTATTCTTGATGTTCAAGGAGTG                         GGATTGAAAAACTTTAACAAGTCTGCTCGAGATCTTATCACACGATTACAA
genomic: CAAAGAGGCATATTGATTCAAGTACAACTATTCTTGATGTTCAAGGAGTGgtaagtattt ... tcatattcagGGATTGAAAAACTTTAACAAGTCTGCTCGAGATCTTATCACACGATTACAA
EST: gi|164165462|gb|EL987672.1|EL987672
EST:     TACAACTATTCTTGATGTTCAAGGAGTG                         GGATTGAAAAACTTTAACAAGTCTGCTCGAGATCTTATCACACGATTACAA
genomic: TACAACTATTCTTGATGTTCAAGGAGTGgtaagtattt ... tcatattcagGGATTGAAAAACTTTAACAAGTCTGCTCGAGATCTTATCACACGATTACAA
EST: gi|163994294|gb|ES119042.1|ES119042
EST:     CAAAGAGGCATATTGATTCAAGTACAACTATTCTTGATGTTCAAGGAGTG                         GGATTGAAAAACTTTAACAAGTCTGCTCGAGATC
genomic: CAAAGAGGCATATTGATTCAAGTACAACTATTCTTGATGTTCAAGGAGTGgtaagtattt ... tcatattcagGGATTGAAAAACTTTAACAAGTCTGCTCGAGATC
EST: gi|125246398|gb|EL260483.1|EL260483
EST:     TTCAAGTACAACTATTCTTGATGTTCAAGGAGTG                         GGATTGAAAAACTTTAACAAGTCTGCTCGAGATCTTATCACACGATTACAA
genomic: TTCAAGTACAACTATTCTTGATGTTCAAGGAGTGgtaagtattt ... tcatattcagGGATTGAAAAACTTTAACAAGTCTGCTCGAGATCTTATCACACGATTACAA
EST: gi|164149687|gb|ES110021.1|ES110021
EST:     CAAAGAGGCATATTGATTCAAGTACAACTATTCTTGATGTTCAAGGAGTG                         GGAT-GAAAAACTTTAACAAGTCTGCTCGAGATC
genomic: CAAAGAGGCATATTGATTCAAGTACAACTATTCTTGATGTTCAAGGAGTGgtaagtattt ... tcatattcagGGATTGAAAAACTTTAACAAGTCTGCTCGAGATC
EST: gi|164098627|gb|ES030720.1|ES030720
EST:     CAAAGAGGCATATTGATTCAAGTACAACTATTCTTGATGTTCAAGGAGTG                         GGATTGAAAAACTTTAACAAGTCTGCTCGAGATCTTATCACACGATTACAA
genomic: CAAAGAGGCATATTGATTCAAGTACAACTATTCTTGATGTTCAAGGAGTGgtaagtattt ... tcatattcagGGATTGAAAAACTTTAACAAGTCTGCTCGAGATCTTATCACACGATTACAA
EST: gi|164189845|gb|ES133704.1|ES133704
EST:     CAAAGAGGCATATTGATTCAAGTACAACTATTCTTGATGTTCAAGGAGTG                         GGATTGAAAA-CTTTAACAAGTCTGCTCGAGATCTTATCACACG
genomic: CAAAGAGGCATATTGATTCAAGTACAACTATTCTTGATGTTCAAGGAGTGgtaagtattt ... tcatattcagGGATTGAAAAACTTTAACAAGTCTGCTCGAGATCTTATCACACG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGTTTGAGAGGAGCTTTATGATCAAGTTTCCTTCCTGCACTATTTCTGCAAAGAGGCATATTGATTCAAGTACAACTATTCTTGATGTTCAAGGAGTGgtaagtattttctacagttcatgatattagttgtgaaatgagtttttttctcatgtgtttatataacttcatattcag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG