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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAATGGAAGGCTGAACAAGTGTGGAGTTATCAGTCCTCGTTTCGATGTCGGTGTTAAGGAGATTGAAGGATGGACTGCTCGTCTACTTCCTTCCAGACAGgttagtctagagactatatagtagtggtaccaatcaatgttttagctattgatctgctgccttactttgctgttcctattatggtttaattggatgtttagtgtcattactttgccttactttatctttcaatgttacaacttcattgaacacttctctatgtgcag

Basic information

species Arabidopsis thaliana
transcript AT3G46040.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G46040.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G018228_T02 (Zea mays), 5'ss of exon 2
TAATGGAAGGCTGAACAAGTGTGGAGTTATCAGTCCTCGTTTCGATGTCGGTGTTAAGGAGATTGAAGGATGGACTGCTCGTCTACTTCCTTCCAGACAGgttagtctagag-actatatagtagtggtaccaatcaatgttttagctattgatctgctgccttactttgctgttcctattatggtttaattggatgtttagtgtcattactttgccttactttatctttcaatgttacaacttcattgaacacttctctatgtgcag
 |||||||| ||||| || ||||| ||||| || || ||||| ||||| |||||||||||||| || |||||||| ||  | || ||||| ||  | |||||||||| ||    || | |  ||      |  || |  ||||          | ||   ||     |  |||| ||| || ||  |    | |                                                                          
GAATGGAAGACTGAATAAATGTGGTGTTATTAGCCCACGTTTTGATGTAGGTGTTAAGGAGATCGAGGGATGGACGGCGAGGCTTCTTCCATCTCGCCAGgttagtccaggctgctgtctc-tacaaaatctgattagagtttgtctgtacactttgaccccagtgctaactgtgcctctt-tgactggtgtag--------------------------------------------------------------------------

upper sequence: AT3G46040.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G059624_T01 (Zea mays), 5'ss of exon 2
TAATGGAAGGCTGAACAAGTGTGGAGTTATCAGTCCTCGTTTCGATGTCGGTGTTAAGGAGATTGAAGG-------ATGGACTGCTCGTCTACTTCCTTCCAGACAGgttagtctagagactatatagtagtggtaccaatcaatgttttagctattgatctgctgc-cttactttgctgttcc-tattatggtttaattggatgtttagtgtcattactttgccttactttatctttcaatgttacaacttcattgaacacttctctatgtgcag
    || |||||||||||||||||| | |||||||||||||| ||| | ||||  ||||| ||||||||        | ||| ||| | || ||||| ||  |  | ||  ||       ||| | | |  || | | ||  |  | | |||| |||||     ||  | | |  |    |||  ||||||  ||||| | | | |       ||||                                                           
---CGGCAGGCTGAACAAGTGTGGACTGATCAGTCCTCGTTTTGATATTGGTGGGAAGGAAATTGAAGGCGGACGACTAGACGGCTAGGCTCCTTCCCTCTCGgtacgtccgttccttcgctacacattcttgtttctaactatagatctagc-attgagtatttgtacatgcagtttgattctatattataatttaactagctttccctgtccattgt---------------------------------------------------------

upper sequence: AT3G46040.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G012117_T01 (Zea mays), 5'ss of exon 2
TAATGGAAGGCTGAACAAGTGTGGAGTTATCAGTCCTCGTTTCGATGTCGGTGTTAAGGAGATTGAAGGATGGACTGCTCGTCTACTTCCTTCCAGACAGgttagtctagag-actatatagtagtggtaccaatcaatgttttagctattgatctgctgccttactttgctgttcctattatggtttaattggatgtttagtgtcattactttgccttactttatctttcaatgttacaacttcattgaacacttctctatgtgcag
 ||||| |||||||| || ||||| ||||| || || || || ||||| |||||||||||||| || ||||||||  |  | || ||||| ||  | |||||||||| ||    || | |  ||      |  || |  ||| |   ||   |||||   ||         ||| ||| ||      | | | | ||| |||                                                                  
GAATGGCAGGCTGAATAAATGTGGTGTTATTAGCCCACGATTTGATGTAGGTGTTAAGGAGATCGAGGGATGGACGACGAGGCTTCTTCCATCTCGCCAGgttagtccagtccgctgtctc-tacaaaagctgattagagttgtctgtac-aatctgaaaccaatgcaaaatgtgcctctt------tgactag-tgtgtag------------------------------------------------------------------

upper sequence: AT3G46040.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S41_94V6.2 (Physcomitrella patens), 5'ss of exon 3
TAATGGAAGGCTGAACAAGTGTGGAGTTATCAGTCCTCGTTTCGATGTCGGTGTTAAGGAGATTGAAGGATGGACTGCTCGTCTACTTCCTTCCAGACAGgttagtctagagactatatagtagtggtaccaatcaatgtttt----agctattgatctgctgccttactttgctgttcctattatggtttaattggatgtttagtgtcattactttgccttactttatctttcaatgttacaacttcattgaacacttctctatgtgcag---------------
 || ||||| || |||||||| ||||||||||||||||||| | | || || |||   ||| |||| | ||||||||| ||||| || |||||  ||||||||| | |  |     | |  | ||||| | | ||||| || |    |     || |    ||   | || ||  | |    | | |  |     || ||  |  |   | |||||  | ||  ||  || || |  ||          || |   ||| | | | |                   
AAACGGAAGACTTAACAAGTGCGGAGTTATCAGTCCTCGTTACAACGTTGGAGTTGGCGAGCTTGAGGCATGGACTGCCCGTCTGCTCCCTTCTCGACAGgttattatttaccacctgtcatcgtggt-ctactcaatattattcaaaatcggtggtacaatgtggtgctgtggagatagcttaacgcatgtgacggttgcgtcatcctagtacttctctttttttcttcgtttagagtcggtggaatcttcattccttatatgtattttatttttgcctgtgcag

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|164037706|gb|ES145991.1|ES145991
EST:     TGTTAAGGAAGATTGAAGGATGGACTGCTCGTCTACTTCCTTCCAGACAG                         TTTGGTTTCATTGTTCTGACGACCTCAGCGGGAAT
genomic: TGTTAAGG-AGATTGAAGGATGGACTGCTCGTCTACTTCCTTCCAGACAGgttagtctag ... ctatgtgcagTTTGGTTTCATTGTTCTGACGACCTCAGCGGGAAT
EST: gi|116412289|gb|EG454881.1|EG454881
EST:     GTGTTAAGGAGATTGAAGGATGGACTGCTCGTCTACTTCCTTCCAGACAG                         TTTGGTTTCATTGTTCTGACGACCTCAGCGGGAATCATGGATCATGAAGAA
genomic: GTGTTAAGGAGATTGAAGGATGGACTGCTCGTCTACTTCCTTCCAGACAGgttagtctag ... ctatgtgcagTTTGGTTTCATTGTTCTGACGACCTCAGCGGGAATCATGGATCATGAAGAA
EST: gi|124854595|gb|EH939032.1|EH939032
EST:     GTGTTAAGGAGATTGAAGGATGGACTGCTCGTCTACTTCCTTCCAGACAG                         TTTGGTTTCATTGTTCTGACGA
genomic: GTGTTAAGGAGATTGAAGGATGGACTGCTCGTCTACTTCCTTCCAGACAGgttagtctag ... ctatgtgcagTTTGGTTTCATTGTTCTGACGA
EST: gi|116402443|gb|EG445035.1|EG445035
EST:     GTGTTAAGGAGATTGAAGGATGGACTGCTCGTCTACTTCCTTCCAGACAG                         TTTGGTTTCATTGTTCTGACGACCTCAGCGGGAATCATGGATCATGAAGAA
genomic: GTGTTAAGGAGATTGAAGGATGGACTGCTCGTCTACTTCCTTCCAGACAGgttagtctag ... ctatgtgcagTTTGGTTTCATTGTTCTGACGACCTCAGCGGGAATCATGGATCATGAAGAA
EST: gi|116401733|gb|EG444325.1|EG444325
EST:     GTGTTAAGGAGATTGAAGGATGGACTGCTCGTCTACTTCCTTCCAGACAG                         TTTGGTTTCATTGTTCTGACGCCCTCAGCGGGAATCATGGATCATGAAGAA
genomic: GTGTTAAGGAGATTGAAGGATGGACTGCTCGTCTACTTCCTTCCAGACAGgttagtctag ... ctatgtgcagTTTGGTTTCATTGTTCTGACGACCTCAGCGGGAATCATGGATCATGAAGAA
EST: gi|164000533|gb|ES050690.1|ES050690
EST:     GTGTTAAGGAGATTGAAGGATGGACTGCTCGTCTACTTCCTTCCAGACAG                         TTTGGTTTCATT
genomic: GTGTTAAGGAGATTGAAGGATGGACTGCTCGTCTACTTCCTTCCAGACAGgttagtctag ... ctatgtgcagTTTGGTTTCATT
EST: gi|116401724|gb|EG444316.1|EG444316
EST:     GTGTTAAGGAGATTGAAGGATGGACTGCTCGTCTACTTCCTTCCAGACAG                         TTTGGTTTCATTGTTCTGACGACCTCAGCGGGAATCATGGATCATGAAGAA
genomic: GTGTTAAGGAGATTGAAGGATGGACTGCTCGTCTACTTCCTTCCAGACAGgttagtctag ... ctatgtgcagTTTGGTTTCATTGTTCTGACGACCTCAGCGGGAATCATGGATCATGAAGAA
EST: gi|163980598|gb|EL987800.1|EL987800
EST:     GTGTTAAGGAGATTGAAGGATGGACTGCTCGTCTACTTCCTTCCAGACAG                         TTTGGTTTCATTGTTCTGACGACCTCAGCGGGAATCAT
genomic: GTGTTAAGGAGATTGAAGGATGGACTGCTCGTCTACTTCCTTCCAGACAGgttagtctag ... ctatgtgcagTTTGGTTTCATTGTTCTGACGACCTCAGCGGGAATCAT
EST: gi|116412290|gb|EG454882.1|EG454882
EST:     GTGTTAAGGAGATTGAAGGATGGACTGCTCGTCTACTTCCTTCCAGACAG                         TTTGGTTTCATTGTTCTGACGACCTCAGCGGGAATCATGGATCATGAAGAA
genomic: GTGTTAAGGAGATTGAAGGATGGACTGCTCGTCTACTTCCTTCCAGACAGgttagtctag ... ctatgtgcagTTTGGTTTCATTGTTCTGACGACCTCAGCGGGAATCATGGATCATGAAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAATGGAAGGCTGAACAAGTGTGGAGTTATCAGTCCTCGTTTCGATGTCGGTGTTAAGGAGATTGAAGGATGGACTGCTCGTCTACTTCCTTCCAGACAGgttagtctagagactatatagtagtggtaccaatcaatgttttagctattgatctgctgccttactttgctgttcctattatggtttaattggatgtttagtgtcattactttgccttactttatctttcaatgttacaacttcattgaacacttctctatgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA