Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGAGAAAGCAGCTTTCGATGAGGCTGAGAAGAAGAATGAGGAAGAGgtaaatatctctcctaattatttagcttaattcatttgaatctctctaaaacaagtagtttggacttttgtggagtttctactgccaattatgtaattgttgtaaccaagttgggaatagataatctaagacggcattctcctttttctgtgttgatacag

Basic information

species Arabidopsis thaliana
transcript AT1G09210.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G09210.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GRMZM2G074687_T01 (Zea mays), 5'ss of exon 11
GCGGAGAAAGCAGCTTTCGATGAGGCTGAGAAGAAGAATGAGGAAGAGgtaaatatctctcctaattatttagcttaattcatttga-atctctctaaaacaagtagtttggacttttgtggagtttctactgccaattatgtaattgttgtaaccaagttgggaatagataatctaagacggcattctcctttttctgtgttgatacag
|| |||||  | |||||||||||||||||||| ||||| || ||||||||| || ||    | |  || |  | ||   | ||  |  || ||  || |   |  ||| |    | |  |||  |||||   |    || |||  ||||  |                                                          
GCAGAGAAGACTGCTTTCGATGAGGCTGAGAAAAAGAAGGAAGAAGAGgtatatttcaacaccatatagt--gtttttgtgatggggtatatccgtatatgcatgagtgtctggtatattggtatttct---gtatgttctgtctttgtcatg---------------------------------------------------------
















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|124974075|gb|EL047659.1|EL047659
EST:     GAATGAGGAAGAG                         GAATCCAAGGACGCACCTGCGGAATCTGAT
genomic: GAATGAGGAAGAGgtaaatatct ... gttgatacagGAATCCAAGGACGCACCTGCGGAATCTGAT
EST: gi|164004691|gb|ES155932.1|ES155932
EST:     GCGGAGAAAGCAGCTTTCGATGAGGCTGAGAAGAAGAATGAGGAAGAG                         GAATCCAAGGACGCACCTGCGGAATCTGAT
genomic: GCGGAGAAAGCAGCTTTCGATGAGGCTGAGAAGAAGAATGAGGAAGAGgtaaatatct ... gttgatacagGAATCCAAGGACGCACCTGCGGAATCTGAT
EST: gi|164080378|gb|ES075330.1|ES075330
EST:     ATGCGGAGAAAGCAGCTTTCGATGAGGCTGAGAAGAAGAATGAGGAAGAG                         GAATCCAAGGACGCACCTGCGGAATCTGATGC
genomic: ATGCGGAGAAAGCAGCTTTCGATGAGGCTGAGAAGAAGAATGAGGAAGAGgtaaatatct ... gttgatacagGAATCCAAGGACGCACCTGCGGAATCTGATGC
EST: gi|164200510|gb|ES171420.1|ES171420
EST:     AGGCTGAGAAGAAGAATGAGGAAGAG                         GAATCCAAGGACGCACCTGCGGAATCTGATGC
genomic: AGGCTGAGAAGAAGAATGAGGAAGAGgtaaatatct ... gttgatacagGAATCCAAGGACGCACCTGCGGAATCTGATGC
EST: gi|116412926|gb|EG455518.1|EG455518
EST:     GCGGAGAAAGCAGCTTTCGATGAGGCTGAGAAGAAGAATGAGGAAGAG                         GAATCCAAGGACGCACCTGCGGAATCTGAT
genomic: GCGGAGAAAGCAGCTTTCGATGAGGCTGAGAAGAAGAATGAGGAAGAGgtaaatatct ... gttgatacagGAATCCAAGGACGCACCTGCGGAATCTGAT
EST: gi|125145396|gb|EL180593.1|EL180593
EST:     ATGCGGAGAAAGCAGCTTTCGATGAGGCTGAGAAGAAGAATGAGGAAGAG                         GAATCCAAGGACGCACCTGCGGAATCTGATG
genomic: ATGCGGAGAAAGCAGCTTTCGATGAGGCTGAGAAGAAGAATGAGGAAGAGgtaaatatct ... gttgatacagGAATCCAAGGACGCACCTGCGGAATCTGATG
EST: gi|86078431|gb|DR374188.1|DR374188
EST:     GCGGAGAAAGCAGCTTTCGATGAGGCTGAGAAGAAGAATGAGGAAGAG                         GAATCCAAGGACGCAC-TGCGGAATCTGAT
genomic: GCGGAGAAAGCAGCTTTCGATGAGGCTGAGAAGAAGAATGAGGAAGAGgtaaatatct ... gttgatacagGAATCCAAGGACGCACCTGCGGAATCTGAT
EST: gi|116412928|gb|EG455520.1|EG455520
EST:     GCGGAGAAAGCAGCTTTCGATGAGGCTGAGAAGAAGAATGAGGAAGAG                         GAATCCAAGGACGCACCTGCGGAATCTGAT
genomic: GCGGAGAAAGCAGCTTTCGATGAGGCTGAGAAGAAGAATGAGGAAGAGgtaaatatct ... gttgatacagGAATCCAAGGACGCACCTGCGGAATCTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGGAGAAAGCAGCTTTCGATGAGGCTGAGAAGAAGAATGAGGAAGAGgtaaatatctctcctaattatttagcttaattcatttgaatctctctaaaacaagtagtttggacttttgtggagtttctactgccaattatgtaattgttgtaaccaagttgggaatagataatctaagacggcattctcctttttctgtgttgatacag

- GGAGAA
- - - -  GCAGCT
- - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - -  GGAAGA