Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCGGATCTTTCTACTCAATTGAAAGAATTGAAGGCAGAGCTTGCTTCCCTACGTGTCGCTAAGGTCACTGGTGGTGCTCCTAACAAGCTCTCTAAGATgtaattgttctctactctcagccttattatacaaatgttggaatattttgagctgcttgatattggaatcactagcctctttctgagtatgatctaaagc...

Basic information

species Arabidopsis thaliana
transcript AT3G55170.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G55170.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA10G43770.1 (Glycine max), 5'ss of exon 2
AATCGGATCTTTCTACTCAATTGAAAGAATTGAAGGCAGAGCTTGCTTCCCTACGTGTCGCTAAGGTCACTGGTGGTGCTCCTAACAAGCTCTCTAAGATgtaattgttctctactctcagccttattatacaaatgttggaatattttgagctgcttgatattggaatcactagcctctttctgagtatgatctaaagc
|  | ||||| |  | |||  |||| ||  | ||||| |||||||| |  || ||||| ||||||||||| || ||||| |||||||||||||||||||||||||        | ||| |  || || || |      | |  | | ||  ||   |     |||   | |   |    |||   | |  | | |  || 
AGGCTGATCTGTTGAATCAGCTGAAGGACCTCAAGGCCGAGCTTGCCTTGCTTCGTGTTGCTAAGGTCACCGGCGGTGCACCTAACAAGCTCTCTAAGATgtaat--------aatcttaatctaataattc-----ctcgtttctcttttgcctttgaggtttgtgtttatgtgttattttgaaattgaggtttgcag-

upper sequence: AT3G55170.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA20G38480.1 (Glycine max), 5'ss of exon 2
AATCGGATCTTTCTACTCAATTGAAAGAATTGAAGGCAGAGCTTGCTTCCCTACGTGTCGCTAAGGTCACTGGTGGTGCTCCTAACAAGCTCTCTAAGATgtaattgttctctactctcagccttattatacaaatgttggaatattttgagctgcttgatattggaatcactagcctctttctgagt-atgatctaaagc
|  | |||||    | |||| |||| ||  ||||||| |||||||| |  || ||||| ||||||||||| |||||||| ||||||||||| || ||||||||||      ||| ||| |          | |||| || |  | |||||  ||    | | || |  | | |  | | |||   | |   | | |  || 
AGGCTGATCTGCTGAATCAACTGAAGGACCTGAAGGCGGAGCTTGCCTTGCTTCGTGTTGCTAAGGTCACCGGTGGTGCCCCTAACAAGCTTTCCAAGATgtaataac---ctaatctaa----------ataaatttttgtttgttttgc-ctatgaggtgtttgtgttaattacttattttgaaattggggtttgcag-

upper sequence: AT3G55170.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv06s0004g04020.t01 (Vitis vinifera), 5'ss of exon 3
AATCGGATCTTTCTACTCAATTGAAAGAATTGAAGGCAGAGCTTGCTTCCCTACGTGTCGCTAAGGTCACTGGTGGTGCTCCTAACAAGCTCTCTAAGATgtaat-tgttctctactctcagccttattatacaaatgttggaatattttgagctgcttgat-attggaatcactagcctctttctgagtatgatctaaagc
|  | ||||| |   | |||||||| ||  |||| |||||||| |||   || || ||||| |||||||||||||||||||| |||||||| ||||||||||| |   ||||||    |     ||  |||     | |   |||    | | ||| ||| |   ||  |  |   |             ||     |  | 
AGGCCGATCTGTTGGCCCAATTGAAGGAGCTGAAAGCAGAGCTCGCTCTTCTCCGAGTCGCCAAGGTCACTGGTGGTGCTCCCAACAAGCTTTCTAAGATgtactactttctctctgttttatatttatatgtgtttatca-aattgactaaactgtttggttgctgagagaatctggaaaggaaaagaaattggtaagtg-

upper sequence: AT3G55170.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv00s0317g00130.t01 (Vitis vinifera), 5'ss of exon 2
AATCGGATCTTTCTACTCAATTGAAAGAATTGAAGGCAGAGCTTGCTTCCCTACGTGTCGCTAAGGTCACTGGTGGTGCTCCTAACAAGCTCTCTAAGATgtaattgttctctactctcagccttattatacaaatgt-tggaatattttgagctgcttgatattggaatcactagcctctttctgagtatgatctaaagc
|  ||||  | |     || ||||| || |||||||| || ||||||   || || || || |||||||| |||||||| || ||||||||||| |||||||| |   | |      ||    |   |||| | || | ||  |||| |  |  |      | |||  |  | |      | | |  |     | | | | 
AGGCGGACTTGTTGGTGCAGTTGAAGGAGTTGAAGGCCGAACTTGCTCTTCTCCGAGTTGCCAAGGTCACCGGTGGTGCACCAAACAAGCTCTCCAAGATgtactctcttttcctcttccatttatgtatatatatctgtgttatatgtgtatttttcaagttttgttaagatttattggtgtttatgcggtttgttagg-

upper sequence: AT3G55170.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S6_426V6.1 (Physcomitrella patens), 5'ss of exon 3
AATCGGATCTTTCTACTCAATTGAAAGAATTGAAGGCAGAGCTTGCTTCCCTACGTGTCGCTAAGGTCACTGGTGGTGCTCCTAACAAGCTCTCTAAGATgta-attgttctc-tactctca-gccttattatacaaatgttggaatattttgagctgcttgatat-tggaatcactagcctctttctgagtatgatctaaagc
                     | || ||  | || || ||||||||| | ||  | ||||| ||||||||||| || |||||||||||||| |||||||||||   |  |||| | ||| |  |  | ||| ||    ||| | |||||| |     ||  | | | |  | |     | ||  |||| ||  |||   |||  
--------------------CTCAAGGAGCTAAAAGCTGAGCTTGCTGCTCTGAGAGTCGCAAAGGTCACTGGAGGCGCTCCTAACAAGCTGTCTAAGATgtacgcttctctcgtcctcccttggttgattgtattgctgt-gaaatattcttcatggccggttgtgttaacttgagcgtctaattctcagcctga---aaaat

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|86081163|gb|DR376920.1|DR376920
EST:     CTACGTGTCGCTAAGGTCACTGGTGGTGCTCCTAACAAGCTCTCTAAGAT                         CAAAGTGGTGAGGAAGTCGATTGCGCAAGTGTTGACTGTGAGCTCACAGAA
genomic: CTACGTGTCGCTAAGGTCACTGGTGGTGCTCCTAACAAGCTCTCTAAGATgtaattgttc ... gttgttgcagCAAAGTGGTGAGGAAGTCGATTGCGCAAGTGTTGACTGTGAGCTCACAGAA
EST: gi|116477581|gb|EG520173.1|EG520173
EST:     CTACGTGTCGCTAAGGTCACTGGTGGTGCTCCTAACAAGCTCTCTAAGAT                         CAAAGTGGTGAGGAAGTCGATTGCGCAAGTGTTGACTGTGAGCTCACAGAA
genomic: CTACGTGTCGCTAAGGTCACTGGTGGTGCTCCTAACAAGCTCTCTAAGATgtaattgttc ... gttgttgcagCAAAGTGGTGAGGAAGTCGATTGCGCAAGTGTTGACTGTGAGCTCACAGAA
EST: gi|19874839|gb|AU235670.1|AU235670
EST:     CTACGTGTCGCTAAGGTCACTGGTGGTGCTCCTAACAAGCTCTCTAAGAT                         CAAAGTGGTGAGGAAGTCGATTGCGCAAGTGTTGACTGTGAGCTCACAG
genomic: CTACGTGTCGCTAAGGTCACTGGTGGTGCTCCTAACAAGCTCTCTAAGATgtaattgttc ... gttgttgcagCAAAGTGGTGAGGAAGTCGATTGCGCAAGTGTTGACTGTGAGCTCACAG
EST: gi|124935209|gb|EL012213.1|EL012213
EST:     TGGTGCTCCTAACAAGCTCTCTAAGAT                         CAAAGTGGTGAGGAAGTCGATTGCGCAAGTGTTGACTGTGAGCTCACAGAA
genomic: TGGTGCTCCTAACAAGCTCTCTAAGATgtaattgttc ... gttgttgcagCAAAGTGGTGAGGAAGTCGATTGCGCAAGTGTTGACTGTGAGCTCACAGAA
EST: gi|222358188|gb|GH717948.1|GH717948
EST:     CTACGTGTCGCTAAGGTCACTGGTGGTGCTCCTAACAAGCTCTCTAAGAT                         CAAAGTGGTGAGGAAGTCGATTGCGCAAGTGTTGACTGTGAGCTCACAGAA
genomic: CTACGTGTCGCTAAGGTCACTGGTGGTGCTCCTAACAAGCTCTCTAAGATgtaattgttc ... gttgttgcagCAAAGTGGTGAGGAAGTCGATTGCGCAAGTGTTGACTGTGAGCTCACAGAA
EST: gi|19741057|gb|AU226410.1|AU226410
EST:     CTACGTGTCGCTAAGGTCACTGGTGGTGCTCCTAACAAGCTCTCTAAGAT                         CAAAGTGGTGA-GAAGTCGATTGCGCAAGTGTTGACTGTGAGCTCACAGAA
genomic: CTACGTGTCGCTAAGGTCACTGGTGGTGCTCCTAACAAGCTCTCTAAGATgtaattgttc ... gttgttgcagCAAAGTGGTGAGGAAGTCGATTGCGCAAGTGTTGACTGTGAGCTCACAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATCGGATCTTTCTACTCAATTGAAAGAATTGAAGGCAGAGCTTGCTTCCCTACGTGTCGCTAAGGTCACTGGTGGTGCTCCTAACAAGCTCTCTAAGATgtaattgttctctactctcagccttattatacaaatgttggaatattttgagctgcttgatattggaatcactagcctctttctgagtatgatctaaagc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT