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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGATAGAGGAGAAAATCAACAAAATCAGATGGTGTCAGCCAGCTAATGGTGCATTGTTTCTGCTTTCTACAAACGATAAAACCATCAAATATTGGAAGgtgtgacatctggatggatttttatatcacatgtctgcaaaatataggccacttatagcaattcctttctgtgtaactcggttccataatcttgtttcat...

Basic information

species Arabidopsis thaliana
transcript AT1G17720.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G17720.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA15G02640.1 (Glycine max), 5'ss of exon 4
GGAGATAGAGGAGAAAATCAACAAAATCAGATGGTGTCAGCCAGCTAATGGTGCATTGTTTCTGCTTTCTACAAACGATAAAACCATCAAATATTGGAAGgtgtgacatctggatggatttttatatcacatgtctgcaaaatataggccacttatagcaattcctttctgtgta--actcggttccataatcttgtttcat-------
|||||| || |||||||||||||||||||||||||| ||  |||||||||||||  |||| || ||||||||||| |||||||| ||||||| ||||||||| ||| ||  | |||      | ||   ||||| | ||        | || ||||  |||||| ||  |   |    | |   |    | |  ||    |        
GGAGATTGAAGAGAAAATCAACAAAATCAGATGGTGCCAAACAGCTAATGGTGCCCTGTTCCTTCTTTCTACAAATGATAAAACGATCAAATTTTGGAAGgtatgaaat--gaatgatcaccttta--gcatgttttcagtgct---gtcatttat--caattcattgataaattgtgcacaagtttgcacttctgaggaactaagttt

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA07G01440.1 (Glycine max), 5'ss of exon 4
GGAGATAGAGGAGAAAATCAACAAAATCAGATGGTGTCAGCCAGCTAATGGTGCATTGTTTCTGCTTTCTACAAACGATAAAACCATCAAATATTGGAAGgtgtgacatctggatggatttttatatcacatgtctgcaaaatataggccacttatagcaattcctttctgtgtaactcggttccataatcttgtttcat--------
||| ||||| |||||||| |||||||||| |||||| ||  ||||||||||||| ||||| || || || ||||| |||||||||||||||| ||||||||| ||| ||  | |||     || |   |      |||  |||         ||    |||||  | | ||  | || |   |   ||   || | |||         
GGAAATAGAAGAGAAAATTAACAAAATCAAATGGTGCCAAACAGCTAATGGTGCTTTGTTCCTTCTATCCACAAATGATAAAACCATCAAATTTTGGAAGgtatgaaat--gaatgctcacttgtggga------tgctgaatgctattttttttattcaatttatatatgaatgacacacatggttacatttctgtcaaaataagtt

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA13G42800.1 (Glycine max), 5'ss of exon 4
GGAGATAGAGGAGAAAATCAACAAAATCAGATGGTGTCAGCCAGCTAATGGTGCATTGTTTCTGCTTTCTACAAACGATAAAACCATCAAATATTGGAAGgtgtgacatctggatggatttttatatcacatgt------ctgcaaaatat-aggccacttatagcaattcctttctgtgtaactcggttccataatcttgtttcat
||| || || |||||||||||||||||||||||||| ||   ||||||||||||  | || || ||||||||||| |||||||| ||||||| ||||||||| ||| ||  | |||      | || ||    |      |||  |  ||| |   || | |||  ||||     |   ||  | |   |    ||    ||||   
GGAAATTGAAGAGAAAATCAACAAAATCAGATGGTGCCAAATAGCTAATGGTGCCCTCTTCCTTCTTTCTACAAATGATAAAACAATCAAATTTTGGAAGgtatgaaat--gaatgatcacctttagcatgcttttagtgctgtcatttatcaattcattgata--aattgtgcacaaggttgcacttctgaggaactaagttt---

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA08G20830.1 (Glycine max), 5'ss of exon 4
GGAGATAGAGGAGAAAATCAACAAAATCAGATGGTGTCAGCCAGCTAATGGTGCATTGTTTCTGCTTTCTACAAACGATAAAACCATCAAATATTGGAAGgtgtgacatctggatggatttttatatcacatgtctgcaaaatataggccacttatagcaattcctttctgtgtaactcggtt--ccataatcttgtttcat-------
||| ||||| |||||||| |||||||||| |||||| ||  |||| |||||||| ||||| || || || ||||| |||||||||||||||| ||||||||| |||       ||| ||| | |  |     |  |||  |||         ||||  |||||  | | ||  | || |   |    | | |  |||   |        
GGAAATAGAAGAGAAAATTAACAAAATCAAATGGTGCCAAACAGCCAATGGTGCTTTGTTCCTTCTATCCACAAATGATAAAACCATCAAATTTTGGAAGgtatga------aatgaattctcac-ttgtggga-tgctgaatgctatttttttatt-caatttatatatgaatgacacacatggttacatttctgtcgaactaagttt

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 5'ss of exon 4
GGAGATAGAGGAGAAAATCAACAAAATCAGATGGTGTCAGCCAGCTAATGGTGCATTGTTTCTGCTTTCTACAAACGATAAAACCATCAAATATTGGAAGgt-----gtgacatctgg---atggatttttatatcacatg-tctgcaaaatataggccacttatag-caattcctttctgtgtaactcggttccataatcttgtttcat------------------------------------------------------
||| ||||||||||||||||| || ||||||||||| ||| |||| ||||||||  ||||||| || ||||| || ||||||||||| || | |||||||||     | || |  ||    ||| |  |||| |   | || | |  ||  | | | |   ||||   |||   |      |  |  | |||| | | | ||  |   ||                                                      
GGAAATAGAGGAGAAAATCAATAAGATCAGATGGTGCCAGACAGCAAATGGTGCCCTGTTTCTTCTATCTACGAATGATAAAACCATTAAGTTTTGGAAGgtaggaagggaaaattgtcttatgaaactttaaacttcctgatttttaatttgttgacagattatgctcaacatcaccaactccagtttggtttctttaactactgatataatatatatcctgcacatgctgattacatagctgtcttttcgagaatgaaacag

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S100_124V6.1 (Physcomitrella patens), 5'ss of exon 4
GGAGATAGAGGAGAAAATCAACAAAATCAGATGGTGTCAGCCAGCTAATGGTGCATTGTTTCTGCTTTCTACAAACGATAAAACCATCAAATATTGGAAGgtg-tgacatctggatggatttttatatcacatgt-----ctgcaaaatat-aggccacttatagcaattcctttctgtgtaactcggttccataatcttgtttcat
||| ||||||||||| ||||||||||| |||||||| ||| |  | |||| |||   |||||| ||||||||||| || ||||| || ||||  ||||||||  |  || ||  |   || |  ||   || | |     || ||   ||| |    |   | |||| || |  ||||        |   |  |||| ||       
GGAAATAGAGGAGAAGATCAACAAAATAAGATGGTGCCAGACCACCAATGCTGCCCAGTTTCTACTTTCTACAAATGACAAAACTATTAAATCATGGAAGgtactctcagcttaagcaatgtacattgtacctattgtagcttcactttattaaattagaaaaagca-ttgcgatctgctggctctgagcctgtaattttt------

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: EFJ08844 (Selaginella moellendorffii), 5'ss of exon 4
GGAGATAGAGGAGAAAATCAACAAAATCAGATGGTGTCAGCCAGCTAATGGTGCATTGTTTCTGCTTTCTACAAACGATAAAACCATCAAATATTGGAAGgtgtgacatctggatggatttttatatcacatgt-ctgcaaaatataggccacttatagcaattcctttctgtgtaactcggttccataatcttgtttcat
|||||||||||| || |||||||||||||||||||||||  | ||||| || ||    ||| |  | || || || || || ||||||||   |||||||||  ||  |||    |||||    |  | | | |  ||||   |||   | ||    ||                                          
GGAGATAGAGGAAAAGATCAACAAAATCAGATGGTGTCACACGGCTAACGGCGCTCGTTTTGTTTTATCCACTAATGACAAGACCATCAAGCTTTGGAAGgtaggatttctattcggattaacttgacgcgtatgttgcatcctatgaacaacgagcag------------------------------------------

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: EFJ09063 (Selaginella moellendorffii), 5'ss of exon 4
GGAGATAGAGGAGAAAATCAACAAAATCAGATGGTGTCAGCCAGCTAATGGTGCATTGTTTCTGCTTTCTACAAACGATAAAACCATCAAATATTGGAAGgtgtgacatctggatggatttttatatcacatgt-ctgcaaaatataggccacttatagcaattcctttctgtgtaactcggttccataatcttgtttcat
|||||||||||| || |||||||||||||||||||||||  | ||||| || ||    ||| |  | || || || || || ||||||||   |||||||||  ||  |||    |||||    |  | | | |  || |   | |   | ||    ||                                          
GGAGATAGAGGAAAAGATCAACAAAATCAGATGGTGTCACACGGCTAACGGCGCTCGTTTTGTTTTATCCACTAATGACAAGACCATCAAGCTTTGGAAGgtaggatttctattcggattaacttgacgcgtatgttggatcctctgaacaacgagcag------------------------------------------

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|116478423|gb|EG521015.1|EG521015
EST:     GTGCATTGTTTCTGCTTTCTACAAACGATAAAACCATCAAATATTGGAAG                         GTACAAGAGAAGAAGATCAAGAAAATTAGTGAAATGAATATTGATCCGTCA
genomic: GTGCATTGTTTCTGCTTTCTACAAACGATAAAACCATCAAATATTGGAAGgtgtgacatc ... aatcaaacagGTACAAGAGAAGAAGATCAAGAAAATTAGTGAAATGAATATTGATCCGTCA
EST: gi|116411283|gb|EG453875.1|EG453875
EST:     GTGCATTGTTTCTGCTTTCTACAAACGATAAAACCATCAAATATTGGAAG                         GTACAAGAGAAGAAGATCAAGAAAATTAGTGAAATGAATATTGATCCGTCA
genomic: GTGCATTGTTTCTGCTTTCTACAAACGATAAAACCATCAAATATTGGAAGgtgtgacatc ... aatcaaacagGTACAAGAGAAGAAGATCAAGAAAATTAGTGAAATGAATATTGATCCGTCA
EST: gi|116432328|gb|EG474920.1|EG474920
EST:     GTGCGTTGTTTCTGCTTTCTACAAACGATAAAACCATCAAATATTGGAAG                         GTACAAGAGAAGAAGATCAAGAAAATTAGTGAAATGAATATTGATCCGTCA
genomic: GTGCATTGTTTCTGCTTTCTACAAACGATAAAACCATCAAATATTGGAAGgtgtgacatc ... aatcaaacagGTACAAGAGAAGAAGATCAAGAAAATTAGTGAAATGAATATTGATCCGTCA
EST: gi|164048991|gb|ES180370.1|ES180370
EST:     CAAATATTGGAAG                         GTACAAGAGAAGAAGATCAAGAAAATTAGTGAAATGAATATTGATCCGTCA
genomic: CAAATATTGGAAGgtgtgacatc ... aatcaaacagGTACAAGAGAAGAAGATCAAGAAAATTAGTGAAATGAATATTGATCCGTCA
EST: gi|116478422|gb|EG521014.1|EG521014
EST:     GTGCATTGTTTCTGCTTTCTACAAACGATAAAACCATCAAATATTGGAAG                         GTACAAGAGAAGAAGATCAAGAAAATTAGTGAAATGAATATTGATCCGTCA
genomic: GTGCATTGTTTCTGCTTTCTACAAACGATAAAACCATCAAATATTGGAAGgtgtgacatc ... aatcaaacagGTACAAGAGAAGAAGATCAAGAAAATTAGTGAAATGAATATTGATCCGTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGATAGAGGAGAAAATCAACAAAATCAGATGGTGTCAGCCAGCTAATGGTGCATTGTTTCTGCTTTCTACAAACGATAAAACCATCAAATATTGGAAGgtgtgacatctggatggatttttatatcacatgtctgcaaaatataggccacttatagcaattcctttctgtgtaactcggttccataatcttgtttcat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG