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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttctatctaacttgtgtttttcttttttctttcagatttttaatcaatgggaaaattttgaactgttcttgctggtatcttgggattttctcctcagGTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTCCGTTCAGTACCCACAGAGCTGAACAAAGACCATAACCAGATTTTGGAGT

Basic information

species Arabidopsis thaliana
transcript AT4G27040.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G27040.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA18G11630.1 (Glycine max), 3'ss of exon 3
-gt-ttctatctaacttgtgtttttcttttttctttcagatttttaatcaatgggaaaattttgaactgttcttgctggtatcttgggat--tttctcctcagGTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTCCGTTCAGTACCCACAGAGCTGAACAAAGACCATAACCAGATTTTGGAGT-
 || ||  || |  ||| ||||  ||||| ||||        || |   | | |  | || |     ||||| | ||| | | |  |  |   |     ||||||  ||||||| || ||||| |||||  || |||| |||||||| ||||| |||||||| || || ||| ||||||||||||| ||  ||||| | ||   
agtattacattttccttttgttcatctttgttctcca----cttgagaaatttgttacatgtgtccttgttcatactgatgtgtaagtgtaactaaatttcaggTGCTGGGTAGTGGTTTTGAAGTTATTTCTGTTGGAAAGAAAAAACTTGTTCGTTCAGTTCCAACTGAGTTGAACAAAGACCACAATGAGATTCTAGAACT

upper sequence: AT4G27040.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv19s0090g00070.t01 (Vitis vinifera), 3'ss of exon 4
-----gtttctatctaacttgtgtttttcttttttctttcagatttttaatcaatgggaaaattttgaactgttcttgctggtatcttgggattttctcctcagGTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTCCGTTCAGTACCCACAGAGCTGAACAAAGACCATAACCAGATTTTGGAGT
       |||| |   |     ||     |   |    | ||   | |  |  ||||  |   |      | ||     | |   ||||    ||||    |||||||||||||| || |||||||| ||  || |||| |||  |||||||||  | || || || |||||| ||||||||||||||||    ||| | ||| 
agtgaacttctttaatataaaagtcaggatgcatctcctaagcagtcttcttgatggttatgatacactgtattaacattcggtgcttgaacctttc----cagGTATTGGGTAGTGGTTTTGAGGTGATATCTGTTGGAAAGCGAAAGCTTGTTAGGTCTGTCCCTACAGAGTTGAACAAAGACCATAATGCAATTCTAGAGC

upper sequence: AT4G27040.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv19s0090g00110.t01 (Vitis vinifera), 3'ss of exon 1
-----gtttctatctaacttgtgtttttcttttttctttcagatttttaatcaatgggaaaattttgaactgttcttgctggtatcttgggattttctcctcagGTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTCCGTTCAGTACCCACAGAGCTGAACAAAGACCATAACCAGATTTTGGAGT
       |||| |   |     ||     |   |    | ||   | |  |  |||   |   |      | ||     | |   || |    ||||    |||||||||||||| || |||||||| ||  || |||| |||  |||||||||  | || || || |||||| ||||||||||||||||    ||| | ||| 
agcgaacttctttaatataaacgtcaggatgcatctcctaagcagtgttcttgatgtttatgatacactgtattaacattcggtgctcgaacctttc----cagGTATTGGGTAGTGGTTTTGAGGTGATATCTGTTGGAAAGCGAAAGCTTGTTAGGTCTGTCCCTACAGAGTTGAACAAAGACCATAATTCAATTCTAGAGC

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|164175608|gb|ES059895.1|ES059895
EST:     GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAG                         GTATTGGGTAGCGGATTTGAGGTTATCACTATTGG
genomic: GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAGgtttctatct ... ttctcctcagGTATTGGGTAGCGGATTTGAGGTTATCACTATTGG
EST: gi|116404460|gb|EG447052.1|EG447052
EST:     GTGAAGCTGTGACTGAAGATGATT-TCTTCGAGCTATTAGCAAGCTAAAG                         GTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
genomic: GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAGgtttctatct ... ttctcctcagGTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
EST: gi|116404485|gb|EG447077.1|EG447077
EST:     GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAG                         GTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
genomic: GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAGgtttctatct ... ttctcctcagGTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
EST: gi|116404457|gb|EG447049.1|EG447049
EST:     GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAG                         GTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
genomic: GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAGgtttctatct ... ttctcctcagGTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
EST: gi|116404471|gb|EG447063.1|EG447063
EST:     GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAG                         GTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
genomic: GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAGgtttctatct ... ttctcctcagGTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
EST: gi|116404479|gb|EG447071.1|EG447071
EST:     ATTAGCAAGCTAAAG                         GTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
genomic: ATTAGCAAGCTAAAGgtttctatct ... ttctcctcagGTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
EST: gi|116404489|gb|EG447081.1|EG447081
EST:     GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAG                         GTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
genomic: GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAGgtttctatct ... ttctcctcagGTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
EST: gi|116404468|gb|EG447060.1|EG447060
EST:     GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAG                         GTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
genomic: GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAGgtttctatct ... ttctcctcagGTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
EST: gi|116404480|gb|EG447072.1|EG447072
EST:     GTGAAGCCGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAG                         GTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
genomic: GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAGgtttctatct ... ttctcctcagGTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
EST: gi|116404481|gb|EG447073.1|EG447073
EST:     GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAG                         GTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
genomic: GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAGgtttctatct ... ttctcctcagGTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
EST: gi|116404466|gb|EG447058.1|EG447058
EST:     GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAG                         GTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
genomic: GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAGgtttctatct ... ttctcctcagGTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
EST: gi|116404478|gb|EG447070.1|EG447070
EST:     GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAG                         GTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
genomic: GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAGgtttctatct ... ttctcctcagGTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
EST: gi|116404474|gb|EG447066.1|EG447066
EST:     GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAG                         GTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
genomic: GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAGgtttctatct ... ttctcctcagGTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
EST: gi|116404364|gb|EG446956.1|EG446956
EST:     GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCGAGCTAAAG                         GTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
genomic: GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAGgtttctatct ... ttctcctcagGTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
EST: gi|116404464|gb|EG447056.1|EG447056
EST:     GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAG                         GTATTGGGTAGCGGATTTGA
genomic: GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAGgtttctatct ... ttctcctcagGTATTGGGTAGCGGATTTGA
EST: gi|116404356|gb|EG446948.1|EG446948
EST:     GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAG                         GTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
genomic: GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAGgtttctatct ... ttctcctcagGTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
EST: gi|116404487|gb|EG447079.1|EG447079
EST:     GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAG                         GTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
genomic: GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAGgtttctatct ... ttctcctcagGTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
EST: gi|116404482|gb|EG447074.1|EG447074
EST:     GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAG                         GTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
genomic: GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAGgtttctatct ... ttctcctcagGTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
EST: gi|116404362|gb|EG446954.1|EG446954
EST:     GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAG                         GTATTGGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGT
genomic: GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAGgtttctatct ... ttctcctcagGTATTGGG-TAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGT
EST: gi|116404459|gb|EG447051.1|EG447051
EST:     GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAG                         GTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
genomic: GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAGgtttctatct ... ttctcctcagGTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
EST: gi|116404477|gb|EG447069.1|EG447069
EST:     GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAG                         GTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
genomic: GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAGgtttctatct ... ttctcctcagGTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
EST: gi|116404461|gb|EG447053.1|EG447053
EST:     GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAG                         GTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
genomic: GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAGgtttctatct ... ttctcctcagGTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
EST: gi|116404467|gb|EG447059.1|EG447059
EST:     GTGAAGCTGTGACTGAAGATGATT-TCTTCGAGCTATTAGCAAGCTAAAG                         GTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
genomic: GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAGgtttctatct ... ttctcctcagGTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
EST: gi|116404472|gb|EG447064.1|EG447064
EST:     GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAG                         GTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
genomic: GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAGgtttctatct ... ttctcctcagGTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
EST: gi|116404455|gb|EG447047.1|EG447047
EST:     GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAG                         GTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC
genomic: GTGAAGCTGTGACTGAAGATGATTGTCTTCGAGCTATTAGCAAGCTAAAGgtttctatct ... ttctcctcagGTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcaatgggaaaattttgaactgttcttgctggtatcttgggattttctcctcagGTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTCCGTTCAGTACCCACAGAGCTGAACAAAGACCATAACCAGATTTTGGAGT
 ttttaat  putative branch site (score: 3)
                                           ttttctcctc  putative PPT
         aaaattttgaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttctatctaacttgtgtttttcttttttctttcagatttttaatcaatgggaaaattttgaactgttcttgctggtatcttgggattttctcctcagGTATTGGGTAGCGGATTTGAGGTTATCACTATTGGCAAGAAAAAGCTTGTCCGTTCAGTACCCACAGAGCTGAACAAAGACCATAACCAGATTTTGGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG