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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATGGCGATTGATTGTTTCTTTGCGGTGTGGTTTGTTGTGGGGAATGTATGGATATTTGGAGGTCACTCATCTCCTTCTGATTCTCCTAAACTGTACAGgtacacgccttcgacttcatccgctattatgtcccaatgaggaactgaaattctaacactcatgtttttcttgcag

Basic information

species Arabidopsis thaliana
transcript AT1G80400.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G80400.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os01g08340.1 (Oryza sativa), 5'ss of exon 4
AGATGGCGATTGATTGTTTCTTTGCGGTGTGGTTTGTTGTGGGGAATGTATGGATATTTGGAGGTCACTCATCTCCTTCTGATTCTCCTAAACTGTACAGgtacacgccttcgact--tcatccgctat-tatgtcccaatgaggaactgaaattctaacac------tcatgtttttcttgcag
|  ||||  | |||||||||||||| |||||||||||||| |||||||| |||||||| || || |   | ||||    |||  |||||||  |||||||||    |      |     |||   | || | |  |    |    |||| | ||  | || |      |  || |  | || |||
AATTGGCTCTGGATTGTTTCTTTGCTGTGTGGTTTGTTGTTGGGAATGTGTGGATATTCGGGGGCCGTACTTCTCTCCATGACGCTCCTAACTTGTACAGgtctgtgatgctaagcagccatagacaatgtgttccttgcttctcaacttagatgtttactcatttgttagtgatcatttttcag

upper sequence: AT1G80400.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os05g08610.4 (Oryza sativa), 5'ss of exon 4
AGATGGCGATTGATTGTTTCTTTGCGGTGTGGTTTGTTGTGGGGAATGTATGGATATTTGGAGGTCACTCATCTCCTTCTGATTCTCCTAAACTGTACAGgtac-acgcct-tcgacttcatccgcta---ttatgtcccaatgaggaact------gaaattctaacactca-tgtttttcttgcag
| |||||  | || ||||||||||| |||||||| |||||||| ||||||||| ||||||| || || || ||| ||   ||  | || ||  ||||||||||  | || |  | || |  |    ||    | || |  ||  |  || |      ||  ||  | ||  || | ||| |    |||
AAATGGCTCTGGACTGTTTCTTTGCTGTGTGGTTCGTTGTGGGAAATGTATGGGTATTTGGTGGACATTCTTCTGCTCACGACGCGCCCAACTTGTACAGgtatgatgcttgcctacattgtgttgtagatctgtgacttaaccaaaaatttatttggatgtttcatcatgcaatatttcttccccag

upper sequence: AT1G80400.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os02g54624.1 (Oryza sativa), 5'ss of exon 3
AGATGGCGATTGATTGTTTCTTTGCGGTGTGGTTTGTTGTGGGGAATGTATGGATATTTGGAGGTCACTCATCTCCTTCTGATTCTCCTAAACTGTACAGgtacacgccttcgacttcatccgctattatgtcccaatgaggaactgaaattctaacactcatgtttttcttgcag
|||||||  | |||||||||||||| ||||||||||| || || ||||| ||||||||||| || |  || ||| || | ||| |||| ||  |||||||||| |  |     | ||  |  |    || |     |||      |||  || |  |   | | |||  ||  |||
AGATGGCCTTGGATTGTTTCTTTGCTGTGTGGTTTGTCGTAGGAAATGTGTGGATATTTGGCGGGCGTTCTTCTGCTGCCGATGCTCCAAACTTGTACAGgtaaatacaaat-attttttgtgtggataag-----atgctcccttgatcttgttgctgacttttttccctgccag

upper sequence: AT1G80400.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G004799_T01 (Zea mays), 5'ss of exon 3
AGATGGCGATTGATTGTTTCTTTGCGGTGTGGTTTGTTGTGGGGAATGTATGGATATTTGGAGGTCACTCATCTCCTTCTGATTCTCCTAAACTGTACAGgtacacgccttcgacttcatccgctattatgtcccaatgaggaact-gaaattctaacactcatgtttttc---ttgcag
|  ||| | | |||||||||||||| || |||||||||||||| ||||| ||||| |||||  | |  || ||| |   |||  ||||||| || ||||||||   |        || ||  | |   ||   | |   |  |  | ||  || || | ||  | | |  |   || |||
AATTGGTGTTGGATTGTTTCTTTGCCGTCTGGTTTGTTGTGGGAAATGTGTGGATGTTTGGTAGCCGTTCTTCTGCCCATGACGCTCCTAACCTATACAGgtatgtg--------ttgattggttgcaatcctctagccacaacttagatgttttatctcttgtttgtaaccatttccag

upper sequence: AT1G80400.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G089466_T01 (Zea mays), 5'ss of exon 3
AGATGGCGATTGATTGTTTCTTTGCGGTGTGGTTTGTTGTGGGGAATGTATGGATATTTGGAGGTCACTCATCTCCTTCTGATTCTCCTAAACTGTACAGgtacacgccttcgact--tcatccgctattatgtcccaatgaggaactgaa-attctaacactcatgtttttcttgcag----
|||||||  | |||||||||||||| || ||||||||||| || || || ||||||||||| || |  || ||| || ||||| | || ||  |||||||||| | |    |  ||  |||   | |   ||||| | |||      |    || ||    || |  || | ||| |      
AGATGGCCCTGGATTGTTTCTTTGCCGTCTGGTTTGTTGTTGGAAACGTGTGGATATTTGGTGGCCGTTCTTCTGCTGCTGATGCACCGAACTTGTACAGgtaaatgtgaactgctcttcaattgatgagatgtcactatgtcagcttctttatcctgcagctgactttctacttcccaccag

upper sequence: AT1G80400.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA13G43770.1 (Glycine max), 5'ss of exon 3
AGATGGCGATTGATTGTTTCTTTGCGGTGTGGTTTGTTGTGGGGAATGTATGGATATTTGGAGGTCACTCATCTCCTTCTGATTCTCCTAAACTGTACAGgtacacg--ccttcgact----tcatccgctattatgtcccaatgaggaactgaa-attctaacactcatgtttttcttgcag
|||||||  | ||||| |||||||| || |||||||| || || ||||| ||||| |||||||||||| | |||||||||||| ||||  || |||||||||||  |  ||   |  |    ||| ||  |||| |        |||     ||  | |||     ||||||    | |||||
AGATGGCCTTGGATTGCTTCTTTGCAGTTTGGTTTGTAGTAGGAAATGTTTGGATCTTTGGAGGTCACACTTCTCCTTCTGATGCTCCACAATTGTACAGgtacctgtaccactgtttttgctcaaccagtattttactttctcgagtcttcgagtaatctgggcttcatgt----catgcag

upper sequence: AT1G80400.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA15G01570.1 (Glycine max), 5'ss of exon 3
AGATGGCGATTGATTGTTTCTTTGCGGTGTGGTTTGTTGTGGGGAATGTATGGATATTTGGAGGTCACTCATCTCCTTCTGATTCTCCTAAACTGTACAGgtacacgccttcgact--------tcatccgctattatgtcccaatgaggaactgaa-attctaacactcatgtttttcttgcag
|||||||  | ||||| |||||||| || |||||||| || || ||||| ||||| |||||||||||| | |||||||||||| ||||  || |||| ||||||  |  |   | |        ||| ||  |||| |        |||      || | |||     ||||    ||| |||||
AGATGGCCCTGGATTGCTTCTTTGCAGTTTGGTTTGTAGTAGGAAATGTTTGGATCTTTGGAGGTCACACTTCTCCTTCTGATGCTCCACAATTGTATAGgtacttgtatctcattgtttttgctcaacctgtattttactttctcgagtcttcaaataatctgggcttcat----ttcatgcag

upper sequence: AT1G80400.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv09s0002g05120.t01 (Vitis vinifera), 5'ss of exon 3
AGATGGCGATTGATTGTTTCTTTGCGGTGTGGTTTGTTGTGGGGAATGTATGGATATTTGGAGGTCACTCATCTCCTTCTGATTCTCCTAAACTGTACAGgtacacgccttcgacttcatccgctattatgtcccaatgaggaactgaaa--ttctaa--cactcatgtttttcttgcag---------
|||||||  | || || |||||||| ||||||||||||||||| ||||| |||||||||||||||||||| ||||| |||||| |||| ||| |||||||||| |    |     |   |    || |   |  | || || |    |    || | |  |||||| || | ||||||           
AGATGGCCTTGGACTGCTTCTTTGCAGTGTGGTTTGTTGTGGGCAATGTGTGGATATTTGGAGGTCACTCTTCTCCCTCTGATGCTCCCAAATTGTACAGgta-atagttgtagttatgtata-tagtccatttctattagaattccaccccttttgagccactcaagtgtctcttgcccttcctgcag

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|124798742|gb|EH888421.1|EH888421
EST:     TTTGGAGGTCACTCATCTCCTTCTGATTTCTCCTAAACTGTACAG                         GTTATGCATAGCGTTCCTTACTTTCAGTTGCATTGGATATGCAATGCCATT
genomic: TTTGGAGGTCACTCATCTCCTTCTGA-TTCTCCTAAACTGTACAGgtacacgcct ... tttcttgcagGTTATGCATAGCGTTCCTTACTTTCAGTTGCATTGGATATGCAATGCCATT
EST: gi|125204488|gb|EL219442.1|EL219442
EST:     TTTGGAGGTCACTCATCTCCTTCTGATTCTCCTAAACTGTACAG                         GTTATGCATAGCGTTCCTTACTTTCAGTTGCATTGGATATGCAATGCCATT
genomic: TTTGGAGGTCACTCATCTCCTTCTGATTCTCCTAAACTGTACAGgtacacgcct ... tttcttgcagGTTATGCATAGCGTTCCTTACTTTCAGTTGCATTGGATATGCAATGCCATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATGGCGATTGATTGTTTCTTTGCGGTGTGGTTTGTTGTGGGGAATGTATGGATATTTGGAGGTCACTCATCTCCTTCTGATTCTCCTAAACTGTACAGgtacacgccttcgacttcatccgctattatgtcccaatgaggaactgaaattctaacactcatgtttttcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG