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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGCCAAAAACACTGCAGCTTTGAAGTCTCAGATTGAAAAGTTACAGCAGGAGAGGGATGAATTCCAAAGGATGGTGATTGGTAACCAGgtctgattgtgtttgctcttggattaactactttatcttagaggaaattgtactgatgatggattctctgcatttcttcttttatttctgaatag

Basic information

species Arabidopsis thaliana
transcript AT5G57410.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G57410.3 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os08g14460.3 (Oryza sativa), 5'ss of exon 6
GAAGCCAAAAACACTGCAGCTTTGAAGTCTCAGATTGAAAAGTTACAGCAGGAGAGGGATGAATTCCAAAGGATGGTGATTGGTAACCAGgtctgattg------------tgtttgctcttggattaac------------------tactttatcttagaggaaattgtac-------tgatgatggattctctgcatttcttcttttatttctgaatag-
|| ||||||||||||||| |||||||| |||||||||| ||| | || |||||  | ||||| |||||||  ||||| ||||| || |||||   ||||              | |  | || ||| ||                   |||||| | || |  ||| || |         |  ||||||   |  |   || |||  |   |||||   ||  
GAGGCCAAAAACACTGCAACTTTGAAGGCTCAGATTGACAAGCTGCAACAGGAACGCGATGAGTTCCAAAAAATGGTTATTGGCAATCAGgtagaattgccatgccatagtcttatttttttagatcaatctgttcatcttgcttgcttactttgttttcggagaagttattaatgtgtatactgatgggaccaatatcttgctttctaattttctttttaag

upper sequence: AT5G57410.3 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G147500_T04 (Zea mays), 5'ss of exon 6
GAAGCCAAAAACACTGCAGCTTTGAAGTCTCAGATTGAAAAGTTACAGCAGGAGAGGGATGAATTCCAAAGGATGGTGATTGGTAACCAGgtctga-----ttgtgtttgctcttggattaactactttatcttagaggaa--attgtactgatg-atggattctctgc-atttcttcttttatttctgaatag-----------------------
|| |||||||||||||| ||| |||||||||||||||| ||| | || || ||  | |||||||| || |  ||||| || || || |||||  ||     || | ||    ||| || || |  | | | | |||       ||| |  |  || || |||  |  |  ||    | | ||    |||    |                       
GAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAAGAACGTGATGAATTTCAGAAAATGGTTATAGGAAATCAGgttagactgccttattttattccttcgagtatcatcctaaccatagcatgtttattttgttattgcattgatatttggtgatgaggtatgttgaacctgtcctgaccttctttggttcttctgcaag

upper sequence: AT5G57410.3 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA17G07040.2 (Glycine max), 5'ss of exon 6
GAAGCCAAAAACACTGCAGCTTTGAAGTCTCAGATTGAAAAGTTACAGCAGGAGAGGGATGAATTCCAAAGGATGGTGATTGGTAACCAGgtctga---ttgtgtttgctcttggattaactactttatcttagaggaaattgtactgat---gatggattctctgcatttcttc--ttttatttctgaatag--------
||||| ||||||||||||||| ||||| | || ||||| ||| | || |||||||||||||||||||| || ||||| |||||||| |||||  ||   |||   ||  |     |||      | |   || || ||   |      |    |||  |  |||||  | |  |   ||| | |  ||||| |        
GAAGCTAAAAACACTGCAGCTCTGAAGGCCCAAATTGAGAAGCTGCAACAGGAGAGGGATGAATTCCAGAGAATGGTTATTGGTAATCAGgttagaagtttgatcttctttgcttattgtggcgtcttgtttggatgaccctacttcaaaatggataaagcctctgactcttgtgaatttgactcttgaatggtgttaaag

upper sequence: AT5G57410.3 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA13G00980.1 (Glycine max), 5'ss of exon 6
GAAGCCAAAAACACTGCAGCTTTGAAGTCTCAGATTGAAAAGTTACAGCAGGAGAGGGATGAATTCCAAAGGATGGTGATTGGTAACCAGgtctgattgtgtttgctcttggatta--actactttatcttagaggaaattgtactgatgatggat---tctctgcatttctt--cttttatttctgaatag--------
|| || ||||||||||||||| ||||| |||| ||||| ||| | || ||||||||||||||||| || || ||||| |||||||| |||||  ||  || |   ||||| | |||      | |  | || |    |       | |  ||||||    |||||  | |  |   ||| | |  ||||| |        
GAGGCTAAAAACACTGCAGCTCTGAAGGCTCAAATTGAGAAGCTGCAACAGGAGAGGGATGAATTTCAGAGAATGGTTATTGGTAATCAGgttagaa-gtttgatctctttgcttattgtggcgtcttgtttggatgaccctacttcaaaatggataagcctctgactcttgtgaatttgactattgaatggtgttaaag

upper sequence: AT5G57410.3 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv11s0052g00890.t01 (Vitis vinifera), 5'ss of exon 6
GAAGCCAAAAACACTGCAGCTTTGAAGTCTCAGATTGAAAAGTTACAGCAGGAGAGGGATGAATTCCAAAGGATGGTGATTGGTAACCAGgtctgattgtgtttgctcttggattaactactttatcttagaggaaattgtactgatgatggattctctgcatttcttct-tttatttctgaatag
||||| |||   || |||||||| ||| |||| || ||||| || ||||||||| |||||||||| ||||||||||| |||||||| |||||  |      |||| |  |    ||  || |   | |||   |||| || |  |||  |  |  |  |  ||    | | |||||      | ||
GAAGCAAAAGCTACAGCAGCTTTTAAGGCTCAAATAGAAAAATTGCAGCAGGAGCGGGATGAATTTCAAAGGATGGTTATTGGTAATCAGgttaggactcttttgttaattatctagttagtgcttgttatgtgaaaatgcatagattctaaaagcattcaatcctatttgtttatggtgccaaag

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|86047423|gb|DR343178.1|DR343178
EST:     AGTTACAGCAGGAGAGGGATGAATTCCAAAGGATGGTGATTGGTAACCAG                         CAAGTGAAGGCTCAACAGATACACGAAATGAAGAAAAAGGAGAAGGATTAC
genomic: AGTTACAGCAGGAGAGGGATGAATTCCAAAGGATGGTGATTGGTAACCAGgtctgattgt ... ttctgaatagCAAGTGAAGGCTCAACAGATACACGAAATGAAGAAAAAGGAGAAGGATTAC
EST: gi|86047424|gb|DR343179.1|DR343179
EST:     AGTTACAGCAGGAGAGGGATGAATTCCAAAGGATGGTGATTGGTAACCAG                         CAAGTGAAGGCTCAACAGATACACGAAATGAAGAAAAAGGAGAAGGATTAC
genomic: AGTTACAGCAGGAGAGGGATGAATTCCAAAGGATGGTGATTGGTAACCAGgtctgattgt ... ttctgaatagCAAGTGAAGGCTCAACAGATACACGAAATGAAGAAAAAGGAGAAGGATTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGCCAAAAACACTGCAGCTTTGAAGTCTCAGATTGAAAAGTTACAGCAGGAGAGGGATGAATTCCAAAGGATGGTGATTGGTAACCAGgtctgattgtgtttgctcttggattaactactttatcttagaggaaattgtactgatgatggattctctgcatttcttcttttatttctgaatag

- - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG