Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTATGTTCAGTATAATGTCTATGGCAATCTCTTCGAAGTTTCTAGAAAGTATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTGgtgagttccaaaattaatcagattgggtttttgaaacatgtaatgttcacttctggggttcttagatttgggaattagggttttggaatctgttgttattataataacttgtgttgataattgttgatcag

Basic information

species Arabidopsis thaliana
transcript AT4G01370.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G01370.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA16G03670.1 (Glycine max), 5'ss of exon 1
GCTATGTTCAGTATAATGTCTATGGCAATCTCTTCGAAGTTTCTAGAAAGTATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTGgtgagttccaaaattaatcagattgggtttttgaaacatgtaatgttcacttctggggttcttagatttgggaattagggttttggaatctgttgttattataataacttgtgttgataattgttgatcag
||||||||||||| ||| ||||||||||||||||||||||||| ||||||||||| |||||| |||| ||| |||||||||| |||||||| ||||| |||| ||  ||| || |  |    |||      ||||     ||   ||   |  ||  ||| ||   |||     || |||    ||  | |  |  | ||    | |||                      
GCTATGTTCAGTACAATATCTATGGCAATCTCTTCGAAGTTTCCAGAAAGTATGTCCCTCCTATTCGCCCTGTCGGTAGAGGTGCTTATGGTATTGTTTGgtaagc-ccagaactcttttatttg-----ctgaatttattagcatttgttgttgttgttgttgttttttt---tttgggcaaaggggtatccttgttttgagctgact----------------------

upper sequence: AT4G01370.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA07G07270.1 (Glycine max), 5'ss of exon 1
GCTATGTTCAGTATAATGTCTATGGCAATCTCTTCGAAGTTTCTAGAAAGTATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTGgtgagttccaaaattaatcagattgggttt-ttgaaacatgtaatgttcacttctggggttc-ttagatttgggaattagggttttggaatctgttgttattataataacttgtgttgataattgttgatcag
||||||||||||| ||| |||||||||||||||| |||||||| ||||||||||| |||||| |||| ||| | ||||||||||||||||| ||||| |||| |||   | | |   |     ||  ||| ||   |  |||  | ||   |||||  |||  ||  ||||    |||    ||||| ||     |||  ||                               
GCTATGTTCAGTACAATATCTATGGCAATCTCTTTGAAGTTTCCAGAAAGTATGTCCCTCCTATTCGCCCTGTGGGTAGAGGCGCTTATGGTATTGTTTGgtaagtcaaagactctttttcgctgaatttattagcatttgtttttttt-tttctgttgttggtttcatttatatattta--ttttgtaaaggagtgtccttg------------------------------

upper sequence: AT4G01370.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA09G39190.1 (Glycine max), 5'ss of exon 1
GCTATGTTCAGTATAATGTCTATGGCAATCTCTTCGAAGTTTCTAGAAAGTATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTGgtgagttccaaaattaatca---gattgggtttttgaaacatgtaatgttcacttctggggttcttagatttgggaattagggttttggaatctgttgttattataataacttgtgttgataattgttgatcag
||||||||||||||||| ||||||| || ||||| || || ||||| |||||||| |||||| |||| ||| | || ||||| || ||||||||||| |||| ||    ||| ||  ||    | ||  ||||||       |     |||| ||     ||| |  |  |||    ||    |||  ||   |||| |    ||                             
GCTATGTTCAGTATAATATCTATGGAAACCTCTTTGAGGTCTCTAGGAAGTATGTCCCTCCTATTCGCCCTGTGGGAAGAGGAGCATATGGAATTGTTTGgtaaggaagaaattttttcgtggggttcagttttttgttttggctgaattcattt-----gttttatgtgttgctttttgttatttgtgagggtgttttggggat-----------------------------

upper sequence: AT4G01370.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA18G47140.1 (Glycine max), 5'ss of exon 1
GCTATGTTCAGTATAATGTCTATGGCAATCTCTTCGAAGTTTCTAGAAAGTATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTGgtgagttccaaaattaatc---agattgggtttttgaaacatgtaatgttcacttctggggttcttagatttgggaattagggttttggaatctgttgttattataataacttgtgttgataattgttgatcag
 |||||||||||| ||| ||||||| || ||||| || || ||||| ||||||||||||||| |||| ||| | || ||||| || ||||| ||||| |||| ||    ||| ||  |     | ||| | |||||       | |  |||| || |    ||  |   ||  |   ||   ||||  ||   |||| | |  ||||                           
-CTATGTTCAGTACAATATCTATGGAAACCTCTTTGAGGTCTCTAGGAAGTATGTTCCTCCTATTCGCCCTGTGGGAAGAGGAGCATATGGTATTGTTTGGtaaggaagaaacttttttgtggggttgagcttttgttttggctga-attcatttgt----tttctgtgtt--gtttttgttgtttgtgagggtgttttgaggataaa--------------------------

upper sequence: AT4G01370.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv15s0046g02010.t01 (Vitis vinifera), 5'ss of exon 1
GCTATGTTCAGTATAATGTCTATGGCAATCTCTTCGAAGTTTCTAGAAAGTATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTGgtgagttccaaaattaatcagattgggtttttgaaacatgtaa-tgttcacttctggggttcttagatttgggaattagggttttggaatctgttgttattataataacttgtgttgataattgttgatcag
| ||||||||||| ||||| ||||| || ||||||||||||||||| ||||| || || ||  |||| ||| | ||| | || |||||||| || || |||| ||  |    ||   |   |     |||||    | |  || | || | | || || || | |   ||  || |     ||| |  || |||| |  ||    |                          
GGTATGTTCAGTACAATGTGTATGGGAACCTCTTCGAAGTTTCTAGGAAGTACGTGCCGCCAATTCGGCCTGTGGGTCGTGGTGCTTATGGTATCGTGTGgtaagaactgttatgggtttaagcttttttttctttctttcaaatatttattgcttggattttcatggttttgatt-----tttggagatttgtt-tctttgagct--------------------------

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|86026209|gb|DR321962.1|DR321962
EST:     TATGWTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTG                         TGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
genomic: TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTGgtgagttcca ... tgttgatcagTGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
EST: gi|86026213|gb|DR321966.1|DR321966
EST:     TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTG                         TGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
genomic: TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTGgtgagttcca ... tgttgatcagTGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
EST: gi|86026222|gb|DR321975.1|DR321975
EST:     TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTG                         TGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
genomic: TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTGgtgagttcca ... tgttgatcagTGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
EST: gi|86026210|gb|DR321963.1|DR321963
EST:     TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTG                         TGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
genomic: TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTGgtgagttcca ... tgttgatcagTGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
EST: gi|86026217|gb|DR321970.1|DR321970
EST:     TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTG                         TGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
genomic: TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTGgtgagttcca ... tgttgatcagTGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
EST: gi|86026226|gb|DR321979.1|DR321979
EST:     TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTG                         TGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
genomic: TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTGgtgagttcca ... tgttgatcagTGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
EST: gi|116416232|gb|EG458824.1|EG458824
EST:     TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTG                         TGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
genomic: TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTGgtgagttcca ... tgttgatcagTGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
EST: gi|86026211|gb|DR321964.1|DR321964
EST:     TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTG                         TGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
genomic: TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTGgtgagttcca ... tgttgatcagTGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
EST: gi|86026223|gb|DR321976.1|DR321976
EST:     ATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCGTTATGGAATTGTCTG                         TGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
genomic: ATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGC-TTATGGAATTGTCTGgtgagttcca ... tgttgatcagTGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
EST: gi|86026216|gb|DR321969.1|DR321969
EST:     TATGTACCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTG                         TGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
genomic: TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTGgtgagttcca ... tgttgatcagTGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
EST: gi|86026224|gb|DR321977.1|DR321977
EST:     TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTG                         TGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
genomic: TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTGgtgagttcca ... tgttgatcagTGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
EST: gi|86026229|gb|DR321982.1|DR321982
EST:     TATTTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTG                         TGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
genomic: TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTGgtgagttcca ... tgttgatcagTGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
EST: gi|86026214|gb|DR321967.1|DR321967
EST:     TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTG                         TGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
genomic: TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTGgtgagttcca ... tgttgatcagTGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
EST: gi|86026208|gb|DR321961.1|DR321961
EST:     TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTG                         TGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
genomic: TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTGgtgagttcca ... tgttgatcagTGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
EST: gi|124908636|gb|EH982716.1|EH982716
EST:     TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTG                         TGCTGCTACAAACTCAGAGACTGGAGAGGAGGT
genomic: TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTGgtgagttcca ... tgttgatcagTGCTGCTACAAACTCAGAGACTGGAGAGGAGGT
EST: gi|86026227|gb|DR321980.1|DR321980
EST:     TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTG                         TGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
genomic: TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTGgtgagttcca ... tgttgatcagTGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
EST: gi|86026207|gb|DR321960.1|DR321960
EST:     TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTG                         TGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
genomic: TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTGgtgagttcca ... tgttgatcagTGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
EST: gi|86026228|gb|DR321981.1|DR321981
EST:     TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTG                         TGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
genomic: TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTGgtgagttcca ... tgttgatcagTGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
EST: gi|86026215|gb|DR321968.1|DR321968
EST:     TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTG                         TGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
genomic: TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTGgtgagttcca ... tgttgatcagTGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
EST: gi|86026230|gb|DR321983.1|DR321983
EST:     TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTG                         TGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
genomic: TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTGgtgagttcca ... tgttgatcagTGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
EST: gi|86026212|gb|DR321965.1|DR321965
EST:     TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTG                         TGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
genomic: TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTGgtgagttcca ... tgttgatcagTGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
EST: gi|86026218|gb|DR321971.1|DR321971
EST:     TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTG                         TGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
genomic: TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTGgtgagttcca ... tgttgatcagTGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
EST: gi|86026206|gb|DR321959.1|DR321959
EST:     TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTG                         TGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
genomic: TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTGgtgagttcca ... tgttgatcagTGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
EST: gi|116451512|gb|EG494104.1|EG494104
EST:     TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTG                         TGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG
genomic: TATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTGgtgagttcca ... tgttgatcagTGCTGCTACAAACTCAGAGACTGGAGAGGAGGTAGCTATCAAGAAGATTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTATGTTCAGTATAATGTCTATGGCAATCTCTTCGAAGTTTCTAGAAAGTATGTTCCTCCTCTTCGTCCTATCGGTAGAGGCGCTTATGGAATTGTCTGgtgagttccaaaattaatcagattgggtttttgaaacatgtaatgttcacttctggggttcttagatttgggaattagggttttggaatctgttgttattataataacttgtgttgataattgttgatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC