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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATCCTCTAAGTGTTTCGGTTGCAATTCTCCATCAGTTTAATATCTTGCCAGAGATGTACCAAGTTGGCTACACAAAATTGTTTTTCAGAACTGGCCAGgtactataactagtcgtctgatgtcttgactttaggggccacaaattagacattcttactgcagtatacttgcttcaccattgcag

Basic information

species Arabidopsis thaliana
transcript AT1G50360.1
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G50360.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: LOC_Os10g34710.1 (Oryza sativa), 5'ss of exon 19
AGATCCTCTAAGTGTTTCGGTTGCAATTCTCCATCAGTTTAATATCTTGCCAGAGATGTACCAAGTTGGCTACACAAAATTGTTTTTCAGAACTGGCCAGgtactataactagtc---gtctgatgtcttgactt-----taggggccacaa-attagacattcttactgcagtatacttgcttcaccattgcag-----
||| || || |||||||||||||||||||| || |||||||| || ||||| |||||||| |||||||| |||||||||||||| ||  |||||||||||||    |||  || |   || | || | || ||||     ||  |     |     |   | | ||      || |   ||  | | | ||  |      
AGACCCACTTAGTGTTTCGGTTGCAATTCTTCACCAGTTTAACATTTTGCCTGAGATGTATCAAGTTGGGTACACAAAATTGTTCTTTCGAACTGGCCAGgtgagctaagcagcctttgttttatttattcacttcctggtaatgagtgtattgccaataactgttggccttgtttttctgaatgagcgttaaatgtttg

upper sequence: AT1G50360.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: GRMZM2G113202_T01 (Zea mays), 5'ss of exon 19
AGATCCTCTAAGTGTTTCGGTTGCAATTCTCCATCAGTTTAATATCTTGCCAGAGATGTACCAAGTTGGCTACACAAAATTGTTTTTCAGAACTGGCCAGgtactataactagtcgtctgatgtcttgactttag--gggccacaaattagacattcttactgcagtatac-ttgcttcaccatt-gcag-------------------------------------------------------------------------------------------------------
|||||| || |||||||| ||||||||||| |||||||| || || || || |||||||| ||||||||||||||||| ||||| ||| ||||||| |||||  ||   ||  |  |    | || || |  | |       | ||| |  |  |  ||  | || || |  ||  |  ||||||    |                                                                                                       
AGATCCACTCAGTGTTTCAGTTGCAATTCTTCATCAGTTCAACATTTTACCTGAGATGTATCAAGTTGGCTACACAAAGTTGTTCTTCCGAACTGGTCAGgt--tagttctgtttattcagtttcctggcaatggtcacattagaaactgaagctatttgtttcattacatgtttatagaccattcattgttctggattttttaccattatatgtatgcacgaccttttttatttgttaagcatttggtgaaagtgatcttgtgttactgtgtcctttgatattgggctgaag

upper sequence: AT1G50360.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: GRMZM2G139583_T02 (Zea mays), 5'ss of exon 19
AGATCCTCTAAGTGTTTCGGTTGCAATTCTCCATCAGTTTAATATCTTGCCAGAGATGTACCAAGTTGGCTACACAAAATTGTTTTTCAGAACTGGCCAGgtactataactagtcgtctgatgtcttgactttag--gggccacaaattagacattcttactgcagtatac-ttgcttcaccatt-gcag------------------------------------------------------------------------------------------------------
|||||| || |||||||| ||||||||||| |||||||| || || || || |||||||| ||||||||||||||||| ||||| ||| ||||||| |||||  ||   ||| |  |   || |  || |  | |       | ||| || |  |  |   | || || |  ||  |  ||||||    |                                                                                                      
AGATCCACTCAGTGTTTCAGTTGCAATTCTTCATCAGTTCAACATTTTACCTGAGATGTATCAAGTTGGCTACACAAAGTTGTTCTTCCGAACTGGACAGgt--tagttctatttattcaattttctgccaatggccacattagaaactaaatctattgctttcattacatgtttatagaccattcattgtcttggatttttatctatatatgtatgtactattttatttttgttttaagcatttggtgaaactaatcttgtgttactttgtccttcgatattgggctgaag

upper sequence: AT1G50360.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: GLYMA09G42180.1 (Glycine max), 5'ss of exon 18
AGATCCTCTAAGTGTTTCGGTTGCAATTCTCCATCAGTTTAATATCTTGCCAGAGATGTACCAAGTTGGCTACACAAAATTGTTTTTCAGAACTGGCCAGgtact--ataactagtcgtctgatgtcttga----------ctttaggggccacaaattaga-cattc--ttactgcagtatacttgcttcaccattgcag
 ||||| || |||||||| ||||||||||| |||||||||||||| ||||| |||||||| |||||||||||||||||||| |||||| |||| || |||||| |  ||    | |  | ||| || ||              |||    ||   ||| |||  |||   ||| | |  | |||||  |  || |    | 
GGATCCGCTTAGTGTTTCAGTTGCAATTCTTCATCAGTTTAATATTTTGCCTGAGATGTATCAAGTTGGCTACACAAAATTATTTTTCCGAACAGGGCAGgtaatgaatgtgaatttttttgaagttttatacaatttttttcttatatccccagaatcagaatatttgattatttccatgtactttttaaactaagaaa-

upper sequence: AT1G50360.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: GLYMA20G00320.1 (Glycine max), 5'ss of exon 20
AGATCCTCTAAGTGTTTCGGTTGCAATTCTCCATCAGTTTAATATCTTGCCAGAGATGTACCAAGTTGGCTACACAAAATTGTTTTTCAGAACTGGCCAGgtactata-actagtcgtctgatgtcttgac------tttaggggccacaaattagacattcttactgca---gtatacttgcttcaccattgcag----
 ||||| || |||||||||||||||||||| |||||||||||||| ||| | |||||||| |||||||||||||||||||| |||||| | || || |||||| || |   || |  | | |    || |       |||       |      |||   | | | |      || |||||  |  || |    |     
GGATCCACTTAGTGTTTCGGTTGCAATTCTTCATCAGTTTAATATTTTGTCGGAGATGTATCAAGTTGGCTACACAAAATTATTTTTCCGGACAGGGCAGgtaataaatgttaattttttaaaagttttatacaatttttttcttatatcccccagaatctttgattatctacgtgtactttttaaactaagaaactttg

upper sequence: AT1G50360.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: GLYMA10G43230.1 (Glycine max), 5'ss of exon 18
AGATCCTCTAAGTGTTTCGGTTGCAATTCTCCATCAGTTTAATATCTTGCCAGAGATGTACCAAGTTGGCTACACAAAATTGTTTTTCAGAACTGGCCAGgtactataactagtcgtctgatgtcttgactttaggggccacaaattagacattcttactgcagtatacttgcttcaccattgcag----------------
 ||||| || |||||||| ||||| ||||| |||||||| || || ||||| |||||||| |||||||||||||||||| | || ||| |||| || |||||| ||||  |     |   || | ||      |     | ||  | | | |   ||  ||  | | |      | ||  |                     
GGATCCACTTAGTGTTTCAGTTGCTATTCTTCATCAGTTCAACATTTTGCCTGAGATGTATCAAGTTGGCTACACAAAACTATTCTTCCGAACAGGGCAGgta-tatagatgtctataaaattttttacacgaattattctcatttcatataaa-ttgttgtggcaaatgaatgtaactgtaatgattttatagaatcagca

upper sequence: AT1G50360.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: GLYMA20G23660.1 (Glycine max), 5'ss of exon 20
AGATCCTCTAAGTGTTTCGGTTGCAATTCTCCATCAGTTTAATATCTTGCCAGAGATGTACCAAGTTGGCTACACAAAATTGTTTTTCAGAACTGGCCAGgtactataactagtcgtctgatgtcttgac--tttaggggccacaaattagacattcttactgc--agtatacttgcttcaccattgcag-----------
 ||||| || |||||||| ||||| ||||| ||||| || || || ||||| |||||||| |||||||||||||| ||| | || ||  |||| || ||||||  |||  |     |  | | | |  ||  |||        || ||||    || |  |     | | || ||||       ||  ||           
GGATCCACTTAGTGTTTCAGTTGCTATTCTTCATCAATTCAACATTTTGCCTGAGATGTATCAAGTTGGCTACACGAAACTATTCTTTCGAACAGGGCAGgtaa-atagatgtctataagttttttacacatttttctcatttcatattaattgttgtggcaaacgaatgtaattgcaatgattttatagaatcagaaatt

upper sequence: AT1G50360.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: Vv10s0071g00210.t01 (Vitis vinifera), 5'ss of exon 19
AGATCCTCTAAGTGTTTCGGTTGCAATTCTCCATCAGTTTAATATCTTGCCAGAGATGTACCAAGTTGGCTACACAAAATTGTTTTTCAGAACTGGCCAGgtactataac----tagtcgtctgatgtcttgactttaggggccacaaatt---agacattcttactgcagtatact--tgcttcaccattgcag-----
|||||| || |||||||| |||||||| || |||||||| |||||  |||| |||||||| ||||||||||||||||||||||||||| |||| || |||||   || |     |  || |||||  ||          |||  |   |     |    || |  ||| |  | | |    |||    | |  |      
AGATCCACTTAGTGTTTCAGTTGCAATCCTTCATCAGTTCAATATTCTGCCTGAGATGTATCAAGTTGGCTACACAAAATTGTTTTTCCGAACGGGACAGgtgagatgaagtgattatcatctgaactcgcattcagtagggtgattgaccctaatgagttgtggctggaaaacaatgtcactttgttaataaatgctct

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|164184471|gb|ES053754.1|ES053754
EST:     TTTCAGAACTGGCCAG                         ATTGGGGTTCTTGAAGATACAAGGAATCGCACTCTGCATGGCATTTTACGT
genomic: TTTCAGAACTGGCCAGgtactataac ... accattgcagATTGGGGTTCTTGAAGATACAAGGAATCGCACTCTGCATGGCATTTTACGT




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATCCTCTAAGTGTTTCGGTTGCAATTCTCCATCAGTTTAATATCTTGCCAGAGATGTACCAAGTTGGCTACACAAAATTGTTTTTCAGAACTGGCCAGgtactataactagtcgtctgatgtcttgactttaggggccacaaattagacattcttactgcagtatacttgcttcaccattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG