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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgataataatttaccatttgtggtgatgagtttatgatcttggaagcatgtcatttcatcttagtctttgatcagGTACACAGAAGATATGGAACTTGATGATGCCATTCACACGGCAATATTGACATTGAAGGAAGG

Basic information

species Arabidopsis thaliana
transcript AT1G79210.3
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G79210.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os03g26970.1 (Oryza sativa), 3'ss of exon 8
------------------------gtgataataatttaccatttgtggtgatgagtttatgatcttggaagcatgtcatttcatcttagtctttgat--cagGTACACAGAAGATATGGAACTTGATGATGCCATTCACACGGCAATATTGACATTGAAGGAAGG
                         | ||         ||          | ||    ||||   || |   || |||| |    ||| | ||| ||  ||| ||||||||||||||||| ||||| ||||||||||| || || || || ||  |||| |||||
atttaagtgtcaagtttatacaggctcatgcccccccccccccaaaaaaaaagaaggcatgaa--tgcattaatttcatattcatttattgtttcattgcagATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAACTCTGAAAGAAGG

upper sequence: AT1G79210.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 7
----------------------------------------------------------------------------gtgataataatttaccatttgtggtgatgagtttatgatcttggaagcatgtc--atttcatcttagtctttgatcagGTACACAGAAGATATGGAACTTGATGATGCCATTCACACGGCAATATTGACATTGAAGGAAGG
                                                                             | |  |  || |    |||     | ||  |   ||  |||| |    |||   |  || |  |   ||    |||| ||||||||||| ||||| |||||||||||||| || || || || |||||  |||| |||||
gtacatagcataccactaatattgtattgtactacactctgttttcctcaatctgatcagaaataaagtggatttgtttacgaggatatcttctttccaaagttgtatgactgcacttgtactgttgttcaacctctttatgtcctcatttcagATACACAGAAGACATGGAGCTTGATGATGCCATCCATACTGCCATTTTGACTCTGAAAGAAGG

upper sequence: AT1G79210.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM5G850355_T06 (Zea mays), 3'ss of exon 2
-------------gtgataataat-ttaccatttgtggt------gatgagtttatgatcttggaagcatgtcatttcatcttagt---ctttgatc--agGTACACAGAAGATATGGAACTTGATGATGCCATTCACACGGCAATATTGACATTGAAGGAAGG
             | || | |  |   ||| | ||||        ||| | | | |  |  ||    ||  || ||  || ||| |    ||| ||   || |||||||| ||||||||||||||||||||||| ||||| ||||| ||||| ||||| |||||
ccactccttgttggagacagtcttaccaccctgtgtgccataacagatcattctttccttctgatttcacatc-ttatattttaatatgttttcattgtagATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGG

upper sequence: AT1G79210.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G115948_T01 (Zea mays), 3'ss of exon 5
---------------------gtgataataatttaccatttgtggtgatgagtttatgatcttggaa---gcatgtcatttcatcttagtctttgatcagGTACACAGAAGATATGGAACTTGATGATGCCATTCACACGGCAATATTGACATTGAAGGAAGG
                      ||  |  |   |      | |  |  |   |   |   ||  ||     ||||| || |     | || |      || ||||||||||||||||| |||||||||||||| ||||| ||||| ||||| ||||| |||||
tatctacctcatcagtgattaatgtaaggagcatgtgtgctataattgttcatcctttccctctgatttcacatgttatatttgtatggtttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGG

upper sequence: AT1G79210.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM5G824831_T03 (Zea mays), 3'ss of exon 9
---------------------gtgataataatttaccatttgtggtgatgagtttatgatcttggaa---gcatgtcatttcatcttagtctttgatcagGTACACAGAAGATATGGAACTTGATGATGCCATTCACACGGCAATATTGACATTGAAGGAAGG
                      ||  |  |   |      | |  |  |   |   |   ||  ||     ||||| || |     | || |      || ||||||||||||||||| |||||||||||||| ||||| ||||| ||||| ||||| |||||
tatctacctcatcagtgattaatgtaagcagcatgtgtgctataattgttcatcctttccctctgatttcacatgttatatttgtatggtttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGG

upper sequence: AT1G79210.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM5G850355_T08 (Zea mays), 3'ss of exon 8
-------------gtgataataatttaccatttgtggt------gatgagtttatgatcttggaagcatgtcat---ttcatcttagtctttgatc--agGTACACAGAAGATATGGAACTTGATGATGCCATTCACACGGCAATATTGACATTGAAGGAAGG
             | |   || |    || | ||||        ||| | | | |  |  ||    ||  || |   || ||  ||   ||| ||   || |||||||| |||||||| |||||||||||||| ||||| ||||| ||||| ||||| |||||
agtgtaagatttagagcccattaccacccctgtgtgccataacagatcattctttccttctgatttcacatcttatatttataatatgttttcattgtagATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGG

upper sequence: AT1G79210.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G085243_T01 (Zea mays), 3'ss of exon 9
---------------gtgataataatttaccatttgtggt----gatgagtttatgatcttggaagcatgtcat---ttcatcttagtctttgatc--agGTACACAGAAGATATGGAACTTGATGATGCCATTCACACGGCAATATTGACATTGAAGGAAGG
                  || |  |    |  | ||   |    ||| |   | |  |  ||    ||  || |   || ||  ||   ||| ||   || |||||||| |||||||| |||||||||||||| ||||| ||||| ||||| ||||| |||||
gtgtaagatttagagcccattaccaccccctgtgtgccataacagatcatcctttccttctgatttcacatcttatatttataatatgttttcattgtagATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGG

upper sequence: AT1G79210.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA01G25940.2 (Glycine max), 3'ss of exon 8
gtgataataatttaccatttgtggtgat--gagtt-tatgatcttggaagcatgtcattt-------catcttagtctttgat---------------cagGTACACAGAAGATATGGAACTTGATGATGCCATTCACACGGCAATATTGACATTGAAGGAAGG
 |||| |||   ||    ||   |||||  |||||  || |  ||     ||| ||||||       ||| |   |  ||||                |||||||||||| |||||||| |||||||||||  | |||||  |||||||||| |||||||||||
-tgattatataatatttctttgagtgatttgagttgcattagttttacttcatttcattttccctatcatttctatggttgacttgattgtccacttacagGTACACAGATGATATGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGG

upper sequence: AT1G79210.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G17810.3 (Glycine max), 3'ss of exon 9
-----------------------gtgataataatttaccatttgtggtgatgagtttatgatcttggaagcatgtcatttcatcttagtctttgat--cagGTACACAGAAGATATGGAACTTGATGATGCCATTCACACGGCAATATTGACATTGAAGGAAGG
                       ||||| ||  || |   |   | || |    |   |   |||   |         || |  | | | |    |  |||||||||||| |||||||| |||||||||||  | ||||| |||||||||||  ||||||||||
actttctttctttggagataattgtgattatg-ttgagtttcattagttacacctcattttccttatcatttctatggttgacttgattgtccacttacagGTACACAGATGATATGGAGCTTGATGATGCAGTCCACACAGCAATATTGACTCTGAAGGAAGG

upper sequence: AT1G79210.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA15G41330.1 (Glycine max), 3'ss of exon 9
---------gtgataataatttaccatttg--tggtgatgagtttatgatcttggaa---gcatgtcatttc-------atcttagtctttgat---cagGTACACAGAAGATATGGAACTTGATGATGCCATTCACACGGCAATATTGACATTGAAGGAAGG
         ||||| ||  ||  |    ||  | | |||   ||| | ||     |     |   |||||||         |||  |  |  |    |||||||||||| |||||||| |||||||||||  | ||||| ||||| |||||  ||||||||||
aagataattgtgattatgtttccctgagtgatttgagattcatttgttatacctcattttccccatcatttctatggttgacttgattgtccacttacagGTACACAGATGATATGGAGCTTGATGATGCAGTCCACACAGCAATGTTGACTCTGAAGGAAGG

upper sequence: AT1G79210.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA03G16660.2 (Glycine max), 3'ss of exon 9
gtgataataattt--accatttgtggtg-atgagtttatgatcttggaa----gcatgtcatttc-------atcttagtctttgat---cagGTACACAGAAGATATGGAACTTGATGATGCCATTCACACGGCAATATTGACATTGAAGGAAGG
 | ||| |  |||  |  ||||| | || || |||||    || |   |     | | |||||||         |||| |  |  |    |||||||||||| |||||||| ||||||||| |  | ||||| |||||||||||  ||||||||||
-ttatatttctttgaatgatttgagttgcattagttttacctcatttcattttccctatcatttctatggttgacttaattgtccacttacaggtacacagATGATATGGAGCTTGATGATTCAGTCCACACAGCAATATTGACTCTGAAGGAAGG

upper sequence: AT1G79210.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA03G16660.1 (Glycine max), 3'ss of exon 9
gtgataataatttaccatttgtggtgat--gagtt-tatgatcttggaagcatgtcattt-------catcttagtctttgat---------------cagGTACACAGAAGATATGGAACTTGATGATGCCATTCACACGGCAATATTGACATTGAAGGAAGG
 |||| ||| | ||    ||    ||||  |||||  || |  ||     ||| ||||||       ||| |   |  ||||                |||||||||||| |||||||| ||||||||| |  | ||||| |||||||||||  ||||||||||
-tgattatattatatttctttgaatgatttgagttgcattagttttacctcatttcattttccctatcatttctatggttgacttaattgtccacttacagGTACACAGATGATATGGAGCTTGATGATTCAGTCCACACAGCAATATTGACTCTGAAGGAAGG

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|86065885|gb|DR361642.1|DR361642
EST:     AAAGACGTTTCTTGAGAAGAG                         GTACACAGAAGATATGGAACTTGATGATGCCATTCACACGGCAATATTGAC
genomic: AAAGACGTTTCTTGAGAAGAGgtgataataa ... ctttgatcagGTACACAGAAGATATGGAACTTGATGATGCCATTCACACGGCAATATTGAC
EST: gi|116484723|gb|EG527315.1|EG527315
EST:     TTTGCAATGGGAAAGAATGTTTCGAATGCAAAGACGTTTCTTGAGAAGAG                         GTACACAGAAGATATGGAACTTGATGATGCCATTCACACGGCAATATTGAC
genomic: TCTGCAATGGGAAAGAATGTTTCGAATGCAAAGACGTTTCTTGAGAAGAGgtgataataa ... ctttgatcagGTACACAGAAGATATGGAACTTGATGATGCCATTCACACGGCAATATTGAC
EST: gi|116484724|gb|EG527316.1|EG527316
EST:     TCTGCAATGGGAAAGAATGTTTCGAATGCAAAGACGTTTCTTGAGAAGAG                         GTACACAGAAGATATGGAACTTGATGATGCCATTCACACGGCAATATTGAC
genomic: TCTGCAATGGGAAAGAATGTTTCGAATGCAAAGACGTTTCTTGAGAAGAGgtgataataa ... ctttgatcagGTACACAGAAGATATGGAACTTGATGATGCCATTCACACGGCAATATTGAC
EST: gi|86065886|gb|DR361643.1|DR361643
EST:     TCTGCAATGGGAAAGAATGTTTCGAATGCAAAGACGTTTCTTGAGAAGAG                         GTACACAGAAGATATGGAACTTGATGATGCCATTCACACGGCAATATTGAC
genomic: TCTGCAATGGGAAAGAATGTTTCGAATGCAAAGACGTTTCTTGAGAAGAGgtgataataa ... ctttgatcagGTACACAGAAGATATGGAACTTGATGATGCCATTCACACGGCAATATTGAC
EST: gi|47831532|gb|CK121216.1|CK121216
EST:     TCTGCAATGGGAAAGAATGTTTCGAATGCAAAGACGTTTCTTGAGAAGAG                         GTACACAGAAGATATGGAACTTGATGATGCCATTCACACGGCAATATTGAC
genomic: TCTGCAATGGGAAAGAATGTTTCGAATGCAAAGACGTTTCTTGAGAAGAGgtgataataa ... ctttgatcagGTACACAGAAGATATGGAACTTGATGATGCCATTCACACGGCAATATTGAC
EST: gi|164154533|gb|ES045674.1|ES045674
EST:     TCTGCAATGGGAAAGAATGTTTCGAATGCAAAGACGTTTCTTGAGAAGAG                         GTACACAGAAGATATGGAACT
genomic: TCTGCAATGGGAAAGAATGTTTCGAATGCAAAGACGTTTCTTGAGAAGAGgtgataataa ... ctttgatcagGTACACAGAAGATATGGAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtgatgagtttatgatcttggaagcatgtcatttcatcttagtctttgatcagGTACACAGAAGATATGGAACTTGATGATGCCATTCACACGGCAATATTGACATTGAAGGAAGG
                                            tcttt  CT-rich tract
          tttatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgataataatttaccatttgtggtgatgagtttatgatcttggaagcatgtcatttcatcttagtctttgatcagGTACACAGAAGATATGGAACTTGATGATGCCATTCACACGGCAATATTGACATTGAAGGAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA