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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacactcttgtattttctttgattaccctctcctgttcccaaacatgtctgaactcaattaacagcagtaagttatttgtattttcagATGCTGTGCCTAGCTGGGACAATATAGTTGTTGCATACGAGCCTGTATGGGCAATTGGAACTGGTAAAGTTGCATCTCCTCAGCAAGCACAAGAAGTCCA

Basic information

species Arabidopsis thaliana
transcript AT2G21170.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G002807_T01 (Zea mays), 3'ss of exon 6
-------------------gtaacactcttgtattttc-tttgattaccctctcctgttcccaaacatgtctgaactcaattaacagcagtaagttatttgtattttcagATGCTGTGCCTAGCTGGGACAATATAGTTGTTGCATACGAGCCTGTATGGGCAATTGGAACTGGTAAAGTTGCATCTCCTCAGCAAGCACAAGAAGTCCA
                      | ||| || ||||  | ||  |      | |   |      |     |||||  |       ||   | ||  | | | |   | |||||  | |  | | |||||   || | ||  |||||||||||||||| ||||| |||||||| || ||||||||  ||||| | ||||| || ||||| ||
gtgaaactttcttcatcttaagaaacttttttattggcattctagagaagtttgtaggcattgatttaatctgaggtgttgatgcatatgcaacatgtatctgcctgcagATAGTATTTCAAACTGGGCAGATGTTGTAATTGCATACGAGCCTGTTTGGGCTATTGGAACCGGAAAAGTTGCTACTCCTGAACAAGCCCAGGAAGTTCA

upper sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G20930.1 (Glycine max), 3'ss of exon 6
---gtaacactcttgtattttctttgattaccctctcctgttcccaaacatgtctgaactcaattaacagcagtaagttatttgtatt-------ttcagATGCTGTGCCTAGCTGGGACAATATAGTTGTTGCATACGAGCCTGTATGGGCAATTGGAACTGGTAAAGTTGCATCTCCTCAGCAAGCACAAGAAGTCCA
    | | |   |  | || | |||   |           |      |   |     |    |||     ||  |  |  ||| | |        | ||||||| ||||| || ||||| ||||||||| ||||||| |||||||||||||||||||||||||| ||||| ||  | ||  ||||||| || ||||||||
ttcattagaaagtcatcttctttttaggtggagaaaagaataggagcaagaggggatagcagattgtttccataacatcctttatgtccattatgtgcagATGCAGTGCCAAGTTGGGATAATATAGTTATTGCATATGAGCCTGTATGGGCAATTGGAACTGGCAAAGTGGCCACACCCGAGCAAGCCCAGGAAGTCCA

upper sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G06740.1 (Glycine max), 3'ss of exon 6
---gtaacactcttgtattttctttgattaccctctcctgttcccaaacatgtctgaactcaattaacagcagtaagttatttgtatt-------ttcagATGCTGTGCCTAGCTGGGACAATATAGTTGTTGCATACGAGCCTGTATGGGCAATTGGAACTGGTAAAGTTGCATCTCCTCAGCAAGCACAAGAAGTCCA
    |   |   |  | || | |||   |                      ||  |    | ||| |   ||  |  |  ||| | |        | ||||||  ||||| || ||||| ||||||||| ||||||| |||||||||||||||||||||||||| ||||| ||  | ||  ||||||| || ||||||||
tttatttgaaagtcattttctttttaggtggagaaaagaaaagaagggggagtgggttgccgattgattccataacatcctttatgtccattatatgcagATGTAGTGCCAAGTTGGGATAATATAGTTATTGCATATGAGCCTGTATGGGCAATTGGAACTGGCAAAGTGGCCACACCCGAGCAAGCCCAGGAAGTCCA

upper sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G36990.2 (Glycine max), 3'ss of exon 6
-----------------------gtaacactcttgtattttctttgattaccctctcctgttcccaaacatgtctgaactcaat---taacagcagtaagttatttg----tattttcagATGCTGTGCCTAGCTGGGACAATATAGTTGTTGCATACGAGCCTGTATGGGCAATTGGAACTGGTAAAGTTGCATCTCCTCAGCAAGCACAAGAAGTCCA
                        |||  |  ||  | ||  |||  ||    | |        ||||   |   | | |   |   | |  ||| ||  |  ||||    ||||| ||||||| || |||||||||||||| || ||| ||||||| || ||||||||||| |||||||| || ||||| ||  |||| |||||||| || ||||| ||
gtagtggaagttatgtttcttatataatccatttaaaattcgttttcttttgatttagaagaaacaaaaggggaaggatttggtggttgattgcattacatcgtttgccattatttacagATGCAGTTCCTAGCTGGGACAACATTGTTATTGCATATGAACCTGTATGGGCTATTGGAACGGGCAAAGTGGCCACTCCCCAGCAAGCTCAGGAAGTACA

upper sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G34300.1 (Glycine max), 3'ss of exon 6
-------------gtaacactcttgtattttctttgattaccctctcctgttcccaaacatgtctgaac--------tcaattaacagcagtaagttatttgtatttt----cagATGCTGTGCCTAGCTGGGACAATATAGTTGTTGCATACGAGCCTGTATGGGCAATTGGAACTGGTAAAGTTGCATCTCCTCAGCAAGCACAAGAAGTCCA
              ||   ||  | || |   ||| |   || | | || |    |||     ||| |            |||    |||  |  |   | || | |     |||| || ||  |||| |||||||| || ||| ||||||| || ||||||||||| |||||||| || ||||| ||  |||| || ||||| || ||||| ||
gtaggtgcaagctatatttctaatataatccatttaaagtccattttctttggaaaaaacaaactggagagggtttgctgattgcttgcataacatccatcgtgtctgtatgcagACGCAGTTGCTAGTTGGGACAACATTGTTATTGCATATGAACCTGTATGGGCCATTGGAACGGGCAAAGTGGCCACTCCCCAACAAGCTCAGGAAGTACA

upper sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv03s0038g01780.t01 (Vitis vinifera), 3'ss of exon 6
-------------------------gtaacactct-tgtattttc-tttgattaccctctcctgttccca-aacatgtctgaactcaattaacagcagtaagttatttgtattttcagATGCTGTGCCTAGCTGGGACAATATAGTTGTTGCATACGAGCCTGTATGGGCAATTGGAACTGGTAAAGTTGCATCTCCTCAGCAAGCACAAGAAGTCCA
                          |  ||     |||| | || |||  |   |||||  ||     | ||| |||     ||    ||||| |  |    |      ||   |||||||||| || || |||||  || ||||| ||||||| ||||| || ||||| ||||||||||||||||| ||  | || | ||| ||||| ||||| ||
gcaagttctcttgctgatgttctctttctcatggaatgtactgtcgttttgtggtcctcttgtgaaaagagaacttgttgactcttttgtaacatcgctcttgttcaatcatgcgcagATGCTGTACCCAGTTGGGATGATGTAGTTATTGCATATGAGCCGGTTTGGGCTATTGGAACTGGTAAAGTGGCCACACCCCTGCAGGCACAGGAAGTACA

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|164027564|gb|ES154235.1|ES154235
EST:     TTTGCTTCGCGCAACTGAAGGCGTTTGCTG                         ATGCTGTGCCTAGCTGGGACAATATAGTTGTTGCATACGAGCCTGTATGGG
genomic: TTTGCTTCGCGCAACTGAAGGCGTTTGCTGgtaacactct ... gtattttcagATGCTGTGCCTAGCTGGGACAATATAGTTGTTGCATACGAGCCTGTATGGG
EST: gi|125227822|gb|EL241907.1|EL241907
EST:     AAGACGTTTGATGTTTGCTTCGCGCAACTGAAGGCGTTTGCTG                         ATGCTGTGCCTAGCTGGGACAATATAGTTG
genomic: AAGACGTTTGATGTTTGCTTCGCGCAACTGAAGGCGTTTGCTGgtaacactct ... gtattttcagATGCTGTGCCTAGCTGGGACAATATAGTTG
EST: gi|47828644|gb|CK118328.1|CK118328
EST:     AGCAGGCAAGACGTTTGATGTTTGCTTCGCGCAACTGAAGGCGTTTGCTG                         ATGCTGTGCCTAGCTGGGACAATATAGTTGTTGCATACGAGCCTGTATGGG
genomic: AGCAGGCAAGACGTTTGATGTTTGCTTCGCGCAACTGAAGGCGTTTGCTGgtaacactct ... gtattttcagATGCTGTGCCTAGCTGGGACAATATAGTTGTTGCATACGAGCCTGTATGGG
EST: gi|47831761|gb|CK121445.1|CK121445
EST:     AGCAGGCAAGACGTTTGATGTTTGCTTCGCGCAACTGAAGGCGTTTGCTG                         ATGCTGTGCCTAGCTGGGACAATATAGTTGTTGCATACGAGCCTGTATGGG
genomic: AGCAGGCAAGACGTTTGATGTTTGCTTCGCGCAACTGAAGGCGTTTGCTGgtaacactct ... gtattttcagATGCTGTGCCTAGCTGGGACAATATAGTTGTTGCATACGAGCCTGTATGGG
EST: gi|116463095|gb|EG505687.1|EG505687
EST:     AGCAGGCAAGACGTTTGATGTTTGCTTCGCGCAACTGAAGGCGTTTGCTG                         ATGCTGTGCCTAGCTGGGACAATATAGTTGTTGCATACGAGCCTGTATGGG
genomic: AGCAGGCAAGACGTTTGATGTTTGCTTCGCGCAACTGAAGGCGTTTGCTGgtaacactct ... gtattttcagATGCTGTGCCTAGCTGGGACAATATAGTTGTTGCATACGAGCCTGTATGGG
EST: gi|164050502|gb|ES195961.1|ES195961
EST:     AGCAGGCAAGACGTTTGATGTTTGCTTCGCGCAACTGAAGGCGTTTGCTG                         ATGCTGTGCCTAGCTGGGAC
genomic: AGCAGGCAAGACGTTTGATGTTTGCTTCGCGCAACTGAAGGCGTTTGCTGgtaacactct ... gtattttcagATGCTGTGCCTAGCTGGGAC
EST: gi|116454376|gb|EG496968.1|EG496968
EST:     AGCAGGCAAGACGTTTGATGTTTGCTTCGCGCAACTGAAGGCGTTTGCTG                         ATGCTGTGCCTAGCTGGGACAATATAGTTGTTGCATACGAGCCTGTATGGG
genomic: AGCAGGCAAGACGTTTGATGTTTGCTTCGCGCAACTGAAGGCGTTTGCTGgtaacactct ... gtattttcagATGCTGTGCCTAGCTGGGACAATATAGTTGTTGCATACGAGCCTGTATGGG
EST: gi|124874394|gb|EH956039.1|EH956039
EST:     ATGTTTGCTTCGCGCAACTGAAGGCGTTTGCTG                         ATGCTGTGCCTAGCTGGGACAATATAGTTGTTACATACGAGCCTGTATGGG
genomic: ATGTTTGCTTCGCGCAACTGAAGGCGTTTGCTGgtaacactct ... gtattttcagATGCTGTGCCTAGCTGGGACAATATAGTTGTTGCATACGAGCCTGTATGGG
EST: gi|164153728|gb|EL971140.1|EL971140
EST:     GGCGTTTGCTG                         ATGCTGTGCCTAGCTGGGACAATATAGTTGTTGCATACGAGCCTGTATGGG
genomic: GGCGTTTGCTGgtaacactct ... gtattttcagATGCTGTGCCTAGCTGGGACAATATAGTTGTTGCATACGAGCCTGTATGGG
EST: gi|125283914|gb|EL297999.1|EL297999
EST:     AGCAGGCAAGACGTTTGATGTTTGCTTCGCGCAACTGAAGGCGTTTGCTG                         ATGCTGTGCCTAGCTGGGACAATATAATTGTTGCAT
genomic: AGCAGGCAAGACGTTTGATGTTTGCTTCGCGCAACTGAAGGCGTTTGCTGgtaacactct ... gtattttcagATGCTGTGCCTAGCTGGGACAATATAGTTGTTGCAT
EST: gi|124847541|gb|EH931978.1|EH931978
EST:     CTTCGCGCAACTGAAGGCGTTCGCTG                         ATGCTGTGCCTAGCTGGGACAATATAGTTGTTGCATACGAGCCTGTATGGG
genomic: CTTCGCGCAACTGAAGGCGTTTGCTGgtaacactct ... gtattttcagATGCTGTGCCTAGCTGGGACAATATAGTTGTTGCATACGAGCCTGTATGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttcccaaacatgtctgaactcaattaacagcagtaagttatttgtattttcagATGCTGTGCCTAGCTGGGACAATATAGTTGTTGCATACGAGCCTGTATGGGCAATTGGAACTGGTAAAGTTGCATCTCCTCAGCAAGCACAAGAAGTCCA
                       aattaac  putative branch site (score: 2)
                                              tattttc  putative PPT
                                   taagttatttgtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacactcttgtattttctttgattaccctctcctgttcccaaacatgtctgaactcaattaacagcagtaagttatttgtattttcagATGCTGTGCCTAGCTGGGACAATATAGTTGTTGCATACGAGCCTGTATGGGCAATTGGAACTGGTAAAGTTGCATCTCCTCAGCAAGCACAAGAAGTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT