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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGCCCCTGTTATACATGAGTGGACATATGATGCTATGTGCCATGATTTACTGAACATGGAAGGAAACAAATATGTACATGTGgtaagttcaagtcttttccgtattagttattgtgattttgtggtggctctcttcctggatactccatgtgatgttcatttagtttttag

Basic information

species Arabidopsis thaliana
transcript AT1G12360.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G12360.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GRMZM2G012942_T01 (Zea mays), 5'ss of exon 10
ATTGCCCCTGTTATACATGAGTGGACATATGATGCTATGTGCCATGATTTACTGAACATGGAAGGAAACAAATATGTACATGTGgtaagttca------------agtctt------ttccgtattagttattgtgattttgtggtggctctcttcctgg-atactccatgtgatgttcatttagtttttag-------
||||| ||  |||| ||||||||||| ||||||||||||||||||||| || ||   ||||| || ||||| || || || | ||| ||| ||            ||||||      | ||  | |||||    | |||  ||  |  || | ||  ||    |   |   | |  || ||       | |        
ATTGCACCAATTATTCATGAGTGGACGTATGATGCTATGTGCCATGATCTATTGTGTATGGATGGCAACAAGTACGTGCAAGAGgtgagtacatcagcagcatacagtcttacactgtacctcactagtttaccttattcagttcttactatgtttttgatgcatgactcttaaaatttatgccaccctcaaacaatag

upper sequence: AT1G12360.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA17G14450.1 (Glycine max), 5'ss of exon 10
ATTGCCCCTGTTATACATGAGTGGACATATGATGCTATGTGCCATGATTTACTGAACATGGAAGGAAACAAATATGTACATGTGgtaagtt-caa----gtcttttccgtattagttattgtgattttgtggtggctctcttcctggatactcca-tgtgatgttcatttagtttttag
||||| ||||| |||||||| |||||||||||||| ||||||| ||||||  |||| ||||| ||||| |||||||| |||| ||||   | |||    || ||  || | | | || |||||| || ||| |  || ||||       || | | | |  |||    |||        
ATTGCTCCTGTGATACATGAATGGACATATGATGCCATGTGCCGTGATTTGTTGAATATGGAGGGAAATAAATATGTTCATGAGgtattctacaatattgttttccccctctaaattgttgtgactt-gtgttcactttcttgtcatgaacacaaatctactgtattcttaag------

upper sequence: AT1G12360.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA05G03970.1 (Glycine max), 5'ss of exon 11
ATTGCCCCTGTTATACATGAGTGGACATATGATGCTATGTGCCATGATTTACTGAACATGGAAGGAAACAAATATGTACATGTGgtaagttcaagtctttt-----ccgtattagttattgtgattttgtggtggctctcttcctggatactcca-tgtgatgttcatttagtttttag
||||| ||||| |||||||| |||||||||||||| ||||||| ||||||  |||| ||||| ||||| |||||||| |||| |||    |  | | | ||     || | | |  | |||||| || |||    || ||||  |  | |  | | | |  |||    |||        
ATTGCTCCTGTGATACATGAATGGACATATGATGCCATGTGCCGTGATTTGTTGAATATGGAGGGAAATAAATATGTTCATGAGgtgttctataatatctttttccccctctaaactgttgtgactt-gtgtccactttcttgttataaatacaaatatactgtattcttaag------

upper sequence: AT1G12360.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: Vv13s0019g05000.t01 (Vitis vinifera), 5'ss of exon 10
ATTGCCCCTGTTATACATGAGTGGACATATGATGCTATGTGCCATGATTTACTGAACATGGAAGGAAACAAATATGTACATGTGgtaagttcaagtcttttccgtattagttattgtgattttgtggtggctctcttcctggatactccatgtgatgttcatttagtttttag
||||| ||| | |||||||| ||||| |||||||| ||||||||||||||||| || ||||||||||| |||||||| ||||  |||||  |   ||       ||||  |  || ||  ||||   | | | |     | | |        ||| |     ||  |||||||
ATTGCACCTATCATACATGAATGGACCTATGATGCCATGTGCCATGATTTACTAAATATGGAAGGAAATAAATATGTCCATGAAgtaagc-cttttccaaattttatttatgcttttggatttgatattgtttttcctttagctgtgtgtgttgaggaattattcctttttag

upper sequence: AT1G12360.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: PP1S468_8V6.1 (Physcomitrella patens), 5'ss of exon 10
ATTGCCCCTGTTATACATGAGTGGACATATGATGCTATGTGCCATGATTTACTGAACATGGAAGGAAACAAATATGTACATGTGgtaagttcaa-gtcttttccgta-ttagttattgtgattttgtggtggctct----cttcctggatactccatgtga--tgttc---atttagtttttag
 |  | || ||||||||||||||| | |||||||| |||||||||||| |  ||||  | ||||| ||||| |||    | | |||| |   ||  | |||||   | ||| |     | ||||||    |  | |    | || | ||   |    || |  |||||   |   || |||  |
GTGACTCCGGTTATACATGAGTGGTCGTATGATGCAATGTGCCATGATCTTTTGAATTTAGAAGGCAACAAGTATTCTTACGAGgtatggaaaacatattttcttcagttaatgggcctcattttgcatagattatgcggcatcgttgactatggcagtaaattgttctggaaccaggtttagg

upper sequence: AT1G12360.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: EFJ06496 (Selaginella moellendorffii), 5'ss of exon 10
ATTGCCCCTGTTATACATGAGTGGACATATGATGCTATGTGCCATGATTTACTGAACATGGAAGGAAACAAATATGTACATGTGgtaag--ttcaagtcttttccgtattagttattgtgattttgtggtggctctcttcctggatactccatgtgatgttcatttagtttttag
 |||| ||  |||||||||||||||| ||||||||||||||||||||| | ||   ||| ||||| |||||||| ||  ||| ||| ||  ||  |||  || || | |               ||  | |  | ||||    ||                              
GTTGCGCCATTTATACATGAGTGGACGTATGATGCTATGTGCCATGATCTTCTAGGCATCGAAGGCAACAAATACGTTTATGAGgtgaggattatagttcttgccttct-----------gccctgaagcgcttttcttttctgaag----------------------------

upper sequence: AT1G12360.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: EFJ05985 (Selaginella moellendorffii), 5'ss of exon 10
ATTGCCCCTGTTATACATGAGTGGACATATGATGCTATGTGCCATGATTTACTGAACATGGAAGGAAACAAATATGTACATGTGgtaag--ttcaagtcttttccgtatt-agttattgtgattttgtggtggctctcttcctggatactccatgtgatgttcatttagtttttag
 |||| ||  |||||||||||||||| ||||||||||||||||||||| | ||   ||| ||||| |||||||| ||  ||| ||| ||  ||  |||  || |||   | |     | |  |||| ||  |                                            
GTTGCGCCATTTATACATGAGTGGACGTATGATGCTATGTGCCATGATCTTCTAGGCATCGAAGGCAACAAATACGTTTATGAGgtgaggattatagttcttgccgccctgaagcgcttttcttttctgaag--------------------------------------------

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|164018015|gb|ES008208.1|ES008208
EST:     GAACATGGAAGGAAACAAATATGTACATGTG                         ATTCCAAGCAAATCAGGCGGACAACCAGAGAAGAAAGATGTGCTCTTAGAG
genomic: GAACATGGAAGGAAACAAATATGTACATGTGgtaagttcaa ... tagtttttagATTCCAAGCAAATCAGGCGGACAACCAGAGAAGAAAGATGTGCTCTTAGAG




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGCCCCTGTTATACATGAGTGGACATATGATGCTATGTGCCATGATTTACTGAACATGGAAGGAAACAAATATGTACATGTGgtaagttcaagtcttttccgtattagttattgtgattttgtggtggctctcttcctggatactccatgtgatgttcatttagtttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA