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'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctctcttcttttcttcttaccacagtctaaatgctttccgttttattcctcttaacactttttttatctgatgcaaacagCTATATCTTGAGTTCTTGGATAAGTTCGAGAGGAAGTTTGTGGCTCAGGGAGCTTATGATACCCGAAACATCTTCCAGTCACTCGACCTGGCATGGACTC

Basic information

species Arabidopsis thaliana
transcript AT4G38510.4
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GRMZM2G094497_T02 (Zea mays), 3'ss of exon 13
gtctctcttcttttcttcttaccacagtctaaatgctttccgttttattcctcttaa---cactttttttatctgatgcaaacagCTATATCTTGAGTTCTTGGATAAGTTCGAGAGGAAGTTTGTGGCTCAGGGAGCTTATGATACCCGAAACATCTTCCAGTCACTCGACCTGGCATGGACTC
     |||  |     |   |  |     ||| |   |||  ||| |  || |  ||    | | || |  ||        |||||| ||  | |||||| | || ||||| ||||||||||||||| | || ||||| ||||| || || |||||||||||||||||||| || ||||||||  
----gtctgttgcgagtgaaataaattcgtaagttagttctttttcagacccccaaaacttaatgttctgttccttattgcacagCTTTACTTAGAGTTCCTTGACAAGTTTGAGAGGAAGTTTGTGACACAAGGAGCATATGACACACGGAACATCTTCCAGTCACTCGATCTTGCATGGACAT

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GRMZM2G181151_T04 (Zea mays), 3'ss of exon 5
----------------------------------------gtctctcttcttttcttcttaccacagtctaaatgctttccgttttattcctcttaacac-----tttttttatctgatgcaaacagCTATATCTTGAGTTCTTGGATAAGTTCGAGAGGAAGTTTGTGGCTCAGGGAGCTTATGATACCCGAAACATCTTCCAGTCACTCGACCTGGCATGGACTC
                                        ||  |            |  | ||    |||| |   |||  ||| |    ||  ||  |     || | |||  |  |||   ||||| ||  | |||||| | || ||||| ||||||||||||||| | || ||||| || || || || ||||||||||||||||| || || ||||||||  
gtctgtttcgagtgaaataaattcctaagggcttgttcgggttgcgtgcagacgtaaccgaacaagccctaagttagttctttttcagatgtccaaaacctaatgttctgttacttcttgct--cagCTTTACTTAGAGTTCCTTGACAAGTTTGAGAGGAAGTTTGTGACACAAGGAGCATACGACACACGGAACATCTTCCAGTCACTAGATCTTGCATGGACAT

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 15
----------------------gtctctcttcttttcttcttaccacagtctaaatgctttccgttttattcctcttaacactttttttatc-tgatgcaaacagCTATATCTTGAGTTCTTGGATAAGTTCGAGAGGAAGTTTGTGGCTCAGGGAGCTTATGATACCCGAAACATCTTCCAGTCACTCGACCTGGCATGGACTC
                      |          | | || || |  ||    ||||       |   |  | ||  |   |||     |  | |  |   ||||||| ||||| || || ||||| ||||| |||||||||||||| || |||||||| ||||| ||||| || || ||||||||||| || || ||||||||| 
gtctctaataactttctatcttgataagtactatattttgtttcttcaagtgaaatttcccttgaagtggtactaatggaactccccctccccttttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAGGGAGCCTATGACACCCGCAATATATTCCAGTCACTTGATCTTGCATGGACTT

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA10G42940.3 (Glycine max), 3'ss of exon 14
-----------------------gtctctcttcttttcttcttaccacagtctaaatgctttccgttttattcctctt-aacactttttttatctgatgcaaacagCTATATCTTGAGTTCTTGGATAAGTTCGAGAGGAAGTTTGTGGCTCAGGGAGCTTATGATACCCGAAACATCTTCCAGTCACTCGACCTGGCATGGACTC
                        |   |  | | || |  ||   |  ||  || |||  |     | ||     |  ||| |||||     ||  |   ||||||| ||||| || || ||||| ||||| ||||| |||||||| || |||||||||||||| ||||| || || ||||||||||| || || ||||||||| 
gtctctaataactttctatcttaataagtactatattttgtttcttaatgtgaaattgcccttgaagtgatattaatggaactcttttccccccttttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGAAAGTTTGTTGCCCAGGGAGCTTATGACACCCGCAATATATTCCAGTCACTAGATCTTGCATGGACTT

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA09G38110.1 (Glycine max), 3'ss of exon 14
-----------gtctctctt----cttttcttcttaccacagtctaaatgctttccgttttattcctcttaacactttttttatctgatgcaaacagCTATATCTTGAGTTCTTGGATAAGTTCGAGAGGAAGTTTGTGGCTCAGGGAGCTTATGATACCCGAAACATCTTCCAGTCACTCGACCTGGCATGGACTC
            | ||||||     || |  | | |  |  || |   ||   |     |  |    || |  | |||| || | |      ||||||| ||| | || || ||||| ||||| |||||||||||||| || || |||||||| ||||| || || |||||||||||||| || || ||||||||| 
gtctctactacttttctcttgggaattcttgtttgagtatggtgtgtttgtccttgaagtggtggtactaattaattttattctttttgatcaacagCTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGAGCTTACGATACACGCAATATCTTCCAGTCACTAGATCTTGCATGGACTT

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA18G48280.1 (Glycine max), 3'ss of exon 14
----------gtctctcttc----ttttcttcttaccacagtctaaatgctttccgttttattcctcttaacactttttttatctgatgcaaacagCTATATCTTGAGTTCTTGGATAAGTTCGAGAGGAAGTTTGTGGCTCAGGGAGCTTATGATACCCGAAACATCTTCCAGTCACTCGACCTGGCATGGACTC-
           | ||||||     || |  | | |    |||   | ||   |     |  |    || |  |  ||| || | |      ||||||| ||| | || || ||||| ||||| |||||||||||||| || || ||||| || ||||| || || |||||||||||||| || || |||||||||  
tctctactacttttctcttgggaattcttgtttgagtgtagtgagattgtccttgaagtggtggtactaattaagtttattctttatgatcaacagcTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGAGCATACGATACACGCAATATCTTCCAGTCACTAGATCTTGCATGGACTTT

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 14
----gtctctcttcttttc-ttcttaccacagtctaaatgctttccgtttt----attcctcttaacacttttttta----tctgatgcaaacagCTATATCTTGAGTTCTTGGATAAGTTCGAGAGGAAGTTTGTGGCTCAGGGAGCTTATGATACCCGAAACATCTTCCAGTCACTCGACCTGGCATGGACTC
     |||| ||  | |   || | |   ||    |||||  | ||  ||     |   |   |||||  || |       |    || |||||||||||||| || ||| | || || |||||||| || ||||||||||||||||| ||||| ||||| |||||||||||||| || || ||||||||||| |
gtacatctcactcttataaattatcatttcatctgaaatgaatccctattgtaagaaaacaactaacaggttgtccgacccttcactggaaacagCTATATCTGGAATTCCTAGACAAATTCGAGAGAAAATTTGTGGCTCAGGGAGCCTATGACACCCGCAACATCTTCCAGTCCCTTGATCTGGCATGGACGC

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 13
----------------------------------------------gtctctcttcttttcttcttaccacagtctaaatgctttccgttttattcctcttaacactttttttatctgatgca-aacagCTATATCTTGAGTTCTTGGATAAGTTCGAGAGGAAGTTTGTGGCTCAGGGAGCTTATGATACCCGAAACATCTTCCAGTCACTCGACCTGGCATGGACTC
                                                ||||||  | | ||    | |  ||| ||       || | | | |     | |  |    ||  |  || | |   |||| | ||||| |||||| | || ||||||||| |||||||||| || || ||  |||||||||||||  |||| ||||||||||| ||||| || ||| |  
gtacctgttgcttcatattttctgtttatgatatttcatcatttgatgctctctgttatcctgtagagcttagttta--ctgagtcagatctgtctgcgtgataatgacttcaaattgttacttgacagTTGTATCTCGAGTTCCTTGACAAGTTCGAGCGGAAGTTTGTCGCCCAAGGTCCTTATGATACCCGTGACATTTTCCAGTCACTGGACCTTGCCTGGTCAT

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|116473937|gb|EG516529.1|EG516529
EST:     CCATGAAAGCCGTGGTTGGAGAAGAAGCTCTTTCTTCCGAGGATCTG                         CTATATCTTGAGTTCTTGGATAAGTTCGAGAGGAAGTTTGTGGCTCAGGGA
genomic: CCATGAAAGCCGTGGTTGGAGAAGAAGCTCTTTCTTCCGAGGATCTGgtctctcttc ... atgcaaacagCTATATCTTGAGTTCTTGGATAAGTTCGAGAGGAAGTTTGTGGCTCAGGGA
EST: gi|125326230|gb|EL340310.1|EL340310
EST:     GGCCATGAAAGCCGTGGTTGGAGAAGAAGCTCTTTCTTCCGAGGATCTAG                         CTATATCTTGAGTTCTTGGATAAGTTC
genomic: GGCCATGAAAGCCGTGGTTGGAGAAGAAGCTCTTTCTTCCGAGGATCT-Ggtctctcttc ... atgcaaacagCTATATCTTGAGTTCTTGGATAAGTTC
EST: gi|116473935|gb|EG516527.1|EG516527
EST:     CCATGAAAGCCGTGGTTGGAGAAGAAGCTCTTTCTTCCGAGGATCTG                         CTATATCTTGAGTTCTTGGATAAGTTCGAGAGGAAGTTTGTGGCTCAGGGA
genomic: CCATGAAAGCCGTGGTTGGAGAAGAAGCTCTTTCTTCCGAGGATCTGgtctctcttc ... atgcaaacagCTATATCTTGAGTTCTTGGATAAGTTCGAGAGGAAGTTTGTGGCTCAGGGA
EST: gi|164056535|gb|ES177296.1|ES177296
EST:     GAAAGCCGTGGTTGGAGAAGAAGCTCTTTCTTCCGAGGATCTG                         CTATATCTTGAGTTCTTGGATAAGTTCGAGAGGAAGTTTGTGGCTCAGGGA
genomic: GAAAGCCGTGGTTGGAGAAGAAGCTCTTTCTTCCGAGGATCTGgtctctcttc ... atgcaaacagCTATATCTTGAGTTCTTGGATAAGTTCGAGAGGAAGTTTGTGGCTCAGGGA
EST: gi|116476764|gb|EG519356.1|EG519356
EST:     AGGCCATGAAAGCCGTGGTTGGAGAAGAAGCTCTTTCTTCCGAGGATCTG                         CTATATCTTGAGTTCTTGGATAAGTTCGAGAGGAAGTTTGTGGCTCAGGGA
genomic: AGGCCATGAAAGCCGTGGTTGGAGAAGAAGCTCTTTCTTCCGAGGATCTGgtctctcttc ... atgcaaacagCTATATCTTGAGTTCTTGGATAAGTTCGAGAGGAAGTTTGTGGCTCAGGGA
EST: gi|124749076|gb|EH839206.1|EH839206
EST:     TTGGAGAAGAAGCTCTTTCTTCCGAGGATCCG                         CTATATCTTGAGTTCTTGGATAAGTTCGAGAGGAAGTTTGTGGCTCAGGGA
genomic: TTGGAGAAGAAGCTCTTTCTTCCGAGGATCTGgtctctcttc ... atgcaaacagCTATATCTTGAGTTCTTGGATAAGTTCGAGAGGAAGTTTGTGGCTCAGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaaatgctttccgttttattcctcttaacactttttttatctgatgcaaacagCTATATCTTGAGTTCTTGGATAAGTTCGAGAGGAAGTTTGTGGCTCAGGGAGCTTATGATACCCGAAACATCTTCCAGTCACTCGACCTGGCATGGACTC
                          ttaacactttttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctctcttcttttcttcttaccacagtctaaatgctttccgttttattcctcttaacactttttttatctgatgcaaacagCTATATCTTGAGTTCTTGGATAAGTTCGAGAGGAAGTTTGTGGCTCAGGGAGCTTATGATACCCGAAACATCTTCCAGTCACTCGACCTGGCATGGACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA