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'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   		30  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgtgaatccaatcctccggctctcattatgtcttgcagggccgtaatcccttataatggtacgttctgatttcgtgcaatgacgtagtaatttcttcaacatttttcacatttccagGTCTGTGGGTTTGATCTTCTACGATCTGAGGGCTGTTCATATGTTTGTGATGTCAATGGATGGAGTTTTGTGAAGAACTCATACAA

Basic information

species Arabidopsis thaliana
transcript AT3G01310.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os03g48300.3 (Oryza sativa), 3'ss of exon 10
gtatgttgtgaatccaatcctccggctctcattatgtcttgcagggccgtaatcccttataatggtacgttctgatttcgtgcaatgacgtagtaatttcttcaacatttttcacatttccagGTCTGTGGGTTTGATCTTCTACGATCTGAGGGCTGTTCATATGTTTGTGATGTCAATGGATGGAGTTTTGTGAAGAACTCATACAA
|| || | ||  ||  ||| ||    | |||| ||  |       ||| |   |  |||| || |||  | || || |  | | || | ||  | || |     || | |||| |||    |||| ||||| ||||||||  || | | ||| ||  | |||||||||||||| || ||||||||||| |||||||||||||| |||||
gtttgct-tgcttctcatcttct---tttcatgataacc------gccttg--cgtttatcatagtatttcctaatat--tcctattatgttctgatat----gacttgtttc-cat----agGTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAA

upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 8
gtatgttgtgaatccaatcctccggctctcattatgtcttgcag-ggccgtaatccct-tataatggtacgttctgatttcgtgcaatga-cgtagtaatttcttcaacatttttcacatttccagGTCTGTGGGTTTGATCTTCTACGATCTGAGGGCTGTTCATATGTTTGTGATGTCAATGGATGGAGTTTTGTGAAGAACTCATACAA
                          |||| |||     || |      | ||||  | | | |    | |     | || ||   ||   | |  |    |  |  | |||| |     || ||||| ||||||||||||||  |  ||  | ||||  | ||||||||||||||||| ||||||||||| ||||| || || ||||||||
--------------------------tctctttagaatatggattaaatgaaatctttctgtgactaaaagaaaataatttgtctgatcctcttcatgtgatactataaatttgtgttgcttgcagGTTTGTGGGTTTGATCTATTGAGAAGTCAGGGACGCTCATATGTTTGTGATGTGAATGGATGGAGCTTTGTTAAAAATTCATACAA

upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 11
gtatgttgtgaatccaatcctccggctctcattatgtcttgcag-ggccgtaatccct-tataatggtacgttctgatttcgtgcaatga-cgtagtaatttcttcaacatttttcacatttccagGTCTGTGGGTTTGATCTTCTACGATCTGAGGGCTGTTCATATGTTTGTGATGTCAATGGATGGAGTTTTGTGAAGAACTCATACAA
                          |||| |||     || |      | ||||  | | | |    | |     | || || | ||   | |  |    |  |  | |||| |     || ||||| ||||||||||||||  |  ||  | ||||  | ||||||||||||||||| ||||||||||| ||||| || || ||||||||
--------------------------tctctttagaatatggattaaatgaaatctttctgtgactaaaagaaaataatttgtccgatcctcttcatgtgatactataaatttgtgttgcttgcagGTTTGTGGGTTTGATCTATTGAGAAGTCAGGGACGCTCATATGTTTGTGATGTGAATGGATGGAGCTTTGTTAAAAATTCATACAA

upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 10
gtatgttgtgaatccaatcctccggctctcattatgtcttgcagggccgtaatcccttataatggtacgttctgatttcgtgcaatgacgtagtaatttcttcaacatttttcacatttccagGTCTGTGGGTTTGATCTTCTACGATCTGAGGGCTGTTCATATGTTTGTGATGTCAATGGATGGAGTTTTGTGAAGAACTCATACAA
                      |  |  |   ||| | ||| |    |    | | ||||   | |  ||| |  ||   ||  ||| | | ||  | | |  |   |   |     || ||||| ||||||||||||||  | || | ||||||  | |||||||| |||||||| ||||||||||||||||||||||||||  ||||
-------------------acgcaaccatacatatat-ttgtaaattct---ttctttattgagatgagttgttgttaaatgttatgtctttgttctatttatattttccatattgcttgcagGTTTGTGGGTTTGATCTCTTGCGTTGTGAGGGACGCTCATATGTCTGTGATGTGAATGGATGGAGTTTTGTGAAGAACTCTCACAA

upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S112_67V6.1 (Physcomitrella patens), 3'ss of exon 10
gtatgttgtgaatccaatcctccggctctcattatgtcttgcagggccgtaatcccttataat--ggtacgttctgatttcgtgca-atgacgtagtaatttcttcaacatttttcac---atttccagGTCTGTGGGTTTGATCTTCTACGATCTGAGGGCTGTTCATATGTTTGTGATGTCAATGGATGGAGTTTTGTGAAGAACTCATACAA
                             ||  |||  ||| | |    |  ||  |  ||    ||||  |  || | |   |   ||||  |  |   || |  |||| ||   |    || | ||||| || ||||||||| | || |||||  | ||| | ||||||||||||||||| ||||| |||||||| || |||||||| |||||
-----------------------------caacatgctttgtaagctgctcttcaatgttagccaggtatctagtgttgttaggtgcatgatattctcggttatctaacagttcataattaatctgcagGTGTGCGGGTTTGATTTACTCCGATCACAAGGCCGGTCATATGTTTGTGATGTTAATGGGTGGAGTTTCGTTAAGAACTCTTACAA

upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S70_284V6.1 (Physcomitrella patens), 3'ss of exon 10
-----------------------------------------------------gtatgttgtgaatccaatcctccggctctcattatgt-cttgcagggccgtaatcccttata-atggtacgtt--ctgatttcgtgcaatga--cgtagtaatttcttcaacatttttcac--atttccagGTCTGTGGGTTTGATCTTCTACGATCTGAGGGCTGTTCATATGTTTGTGATGTCAATGGATGGAGTTTTGTGAAGAACTCATACAA
                                                     | |      |||   ||    |     ||||     | | || | |  |||||  | |   | ||  || | |  || |  |  | |  |    || | |  ||    ||| |    | |      | ||||| ||||| |||||| | || |||||  | ||| | |||||||| ||||| || ||||| ||||||||||| |||||||| |||||
gtgagcactattttttaacagacccttttagtatttaaaaagaaagagaaaaagaagagaaagaagttaaattccaaaacctcaaggcttacatgaacgtgcgtaagacttctgacatactaggattacttacctgctccggtacttcgaaatgcttctgacaaaagggataattggcctgcagGTTTGTGGATTTGATTTGCTTCGATCGCAAGGCCGGTCATATGTGTGTGACGTTAATGGGTGGAGTTTTGTTAAGAACTCTTACAA

upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: EFJ07403 (Selaginella moellendorffii), 3'ss of exon 10
gtatgttgtgaatccaatcctccggctctcattatgtcttgcagggccgtaatcccttataatggtacgttctgatttcgtgcaa-tgacgtagtaatttcttcaacatttttcacatttccagGTCTGTGGGTTTGATCTTCTACGATCTGAGGGCTGTTCATATGTTTGTGATGTCAATGGATGGAGTTTTGTGAAGAACTCATACAA
                                                           |||  |||| || || |  | | ||| ||    |||  |   || |||  ||||  ||      ||| ||||| ||||| ||  | |||||| | ||  | || |||||||| ||||||||||||||||||||||| || ||||| |||||
----------------------------------------------------------gtaa--gtacatt-tggtaacttccaagtggaagagttctcattttaacggttttggca------gGTGTGTGGTTTTGACCTCTTGCGATCTCAAGGGAGGTCTTATGTTTGCGATGTCAATGGATGGAGTTTTGTAAAAAACTCGTACAA

upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: EFJ19878 (Selaginella moellendorffii), 3'ss of exon 10
gtatgttgtgaatccaatcctccggctctcattatgtcttgcagggccgtaatcccttataatggtacgttctgatttcgtgcaa-tgacgtagtaatttcttcaacatttttcacatttccagGTCTGTGGGTTTGATCTTCTACGATCTGAGGGCTGTTCATATGTTTGTGATGTCAATGGATGGAGTTTTGTGAAGAACTCATACAA
                                                           |||  |||| || || |  | | ||| ||    |||  |   || ||| |||       |  ||||| ||||| ||||| ||  | |||||| | ||  | || |||||||| ||||||||||||||||||||||| || ||||| |||||
----------------------------------------------------------gtaa--gtacatt-tggtaacttccaagtggaagagttctcattttaacgttt-------tggcagGTGTGTGGTTTTGACCTCTTGCGATCTCAAGGGAGGTCTTATGTTTGCGATGTCAATGGATGGAGTTTTGTAAAAAACTCGTACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttctgatttcgtgcaatgacgtagtaatttcttcaacatttttcacatttccagGTCTGTGGGTTTGATCTTCTACGATCTGAGGGCTGTTCATATGTTTGTGATGTCAATGGATGGAGTTTTGTGAAGAACTCATACAA
 ttctgat  putative branch site (score: 3)
                                       tttttcacatttcc  putative PPT
                      tagtaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttgtgaatccaatcctccggctctcattatgtcttgcagggccgtaatcccttataatggtacgttctgatttcgtgcaatgacgtagtaatttcttcaacatttttcacatttccagGTCTGTGGGTTTGATCTTCTACGATCTGAGGGCTGTTCATATGTTTGTGATGTCAATGGATGGAGTTTTGTGAAGAACTCATACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC