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

gtaaatgtcttctgttgttaccaattcctgcaaaaggttaaacattatgtgtgatctttgtttacgagtgcaaaactttttcttcattgcttcctattaacaagcagtctatggagtcgtctgttttcctttctttaaataaattaaagctcttaacacttgtgctggtccagTGCAGATGGGTATTGCTTCCGTTGTTCACCTGTATGTATTCCCAGCAAAGCCTTATGGTCTAATGGGAGACCGCTTTACTGGATCCGTTTCAGTTCTTGG

Basic information

species Arabidopsis thaliana
transcript AT4G38360.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G38360.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g44910.1 (Oryza sativa), 3'ss of exon 7
gtaaatgtcttctgttgttaccaattcctgcaaaaggttaaacattatgtgtgatctttgtttacgagtgcaaaactttttcttcattgc---ttcctattaacaagcagtctatggag--tcgtctgttttcctttctttaaataaattaaagctcttaacacttgtgctggtccagTGCAGATGGGTATTGCTTCCGTTGTTCACCTGTATGTATTCCCAGCAAAGCCTTATGGTCTAATGGGAGAC---CGCTTTACTGGATCCGTTTCAGTTCTTGG--
      ||         || || | |    |        ||| | |||   | || |||  | ||   |||||     |||||  |  |    ||| |      ||     ||| ||    ||  |||    |   || | | | |  ||    |||  |     | |  |  ||||| |||||||||||||||||| ||||||||||| ||||| ||||| |||||||| |||   ||| | ||  |    || |   ||| |  | ||||||| || ||  
------gtacctcaccttt-ccgagttagacgggcttccaaagaatatcgtttatttttcataacc--tgcaagctcatttctgtaaagagagttcttgggttgaattcacctacggtatatcacctgcgggcaactcctcatacatgttttc-ctcagagtgtatttctttttccagcgcagATGGGTATTGCTTCAGTTGTTCACCTATATGTGTTCCCTGCAAAGCCCTATTCGCTATTAGGTAATCATCGTTCACCTGAAAACATTTCAGTGCTAGGGG

upper sequence: AT4G38360.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G082181_T01 (Zea mays), 3'ss of exon 7
gtaaatgtcttctgttgttaccaattcctgcaaaaggttaaacattatgtgtgatctttgtttacgagtgcaaaactttttcttcattgcttcctattaacaagcagtctatggagtcgtctgttttcctttctttaaataaattaaagctcttaaca----cttgtgctggtccagTGCAGATGGGTATTGCTTCCGTTGTTCACCTGTATGTATTCCCAGCAAAGCCTTATGGTCTAATGGGAGACCGCTTTACTGGATCCGTTTCAGTTCTTGG-----
                                                  ||  || |  ||   | |||      ||||   |  ||  |  ||||           ||    | || | |  ||    || | |   ||  |  |    | | | |    | ||   |  |||||  |||||||| |||||||| ||||||||||| ||||| |||||||| ||||| ||||  ||  |     | |  |     |||  | |||| || |||||     
--------------------------------------------------gtattcatccttccagggtgt-----ttttaactttttattctctatctttgcctttgcttaaaaatcatttcattcatgttatgtggctagttatagatacctgatagcaccatggcttcctccaggacagATGGGCATTGCTTCAGTTGTTCACCTCTATGTGTTCCCAGCCAAGCCCTATGCACTCTTAACTAATCAGTCACACGGAAACATTTCTGTACTTGGGGACT

upper sequence: AT4G38360.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G082181_T02 (Zea mays), 3'ss of exon 7
gtaaatgtcttctgttgttaccaattcctgcaaaaggttaaacattatgtgtgatctttgtttacgagtgcaaaactttttcttcattgcttcctattaacaagcagtctatggagtcgtctgttttcctttctttaaataaattaaagctcttaaca----cttgtgctggtccagTGCAGATGGGTATTGCTTCCGTTGTTCACCTGTATGTATTCCCAGCAAAGCCTTATGGTCTAATGGGAGACCGCTTTACTGGATCCGTTTCAGTTCTTGG
                                                  ||  || |  ||   | |||      ||||   |  ||  |  ||||           ||    | || | |  ||    || | |   ||  |  |    | | | |    | ||   |  |||||  |||||||| |||||||| ||||||||||| ||||| |||||||| ||||| ||||  ||  |     | |  |     |||  | |||| || |||||
--------------------------------------------------gtattcatccttccagggtgt-----ttttaactttttattctctatctttgcctttgcttaaaaatcatttcattcatgttatgtggctagttatagatacctgatagcaccatggcttcctccagGACAGATGGGCATTGCTTCAGTTGTTCACCTCTATGTGTTCCCAGCCAAGCCCTATGCACTCTTAACTAATCAGTCACACGGAAACATTTCTGTACTTGG

upper sequence: AT4G38360.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G088737_T01 (Zea mays), 3'ss of exon 7
gtaaatgtcttctgttgttaccaattcctgcaaaaggttaaacattatgtgtgatctttgtttacgagtgcaaaactttttcttcattgcttcctattaacaagcagtctatggagtcgtctgttttcctttctttaaataaattaaagctcttaacacttgtgctggtccagTGCAGATGGGTATTGCTTCCGTTGTTCACCTGTATGTATTCCCAGCAAAGCCTTATGGTCTAATGGGAGACCGCTTTACTGGATCCGTTTCAGTTCTTGG-----
             || |||| | | |  |  |     || |  ||  | |      ||||| |     ||  || ||||    | | |  ||   |  |        ||| | |     | | | | | |   |  |  | || |  |     ||||| |  |         |||||||||||| ||||| ||||||  ||||||||||| ||||| || ||||| || |  ||||| || ||  | |||  ||||   ||||||||||||||     
-------------gtggttaactactattatacgtt-ttcagtatattattcagcatttgtctgta--tgggaacctttgctgttagtagtttgaag-agggcatgttctgtaggtcaatatttatgcatgcttgcatttgaagtgta--cactaacagtcttctgtactgtgtgcagATGGGTGTTGCTGCCGTTGCCCACCTGTATGTCTTCCCTGCGAAGCCATACGAGCTAATTGGTGATTGTTTTGTTGGAGATGTTTCAGTTCTTGGAGATT

upper sequence: AT4G38360.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA04G00250.1 (Glycine max), 3'ss of exon 5
gtaaatgtcttctgttgttaccaattcctgcaaaaggttaaacattatgtgtgatctttgtttacgagtgcaaaactttttcttcattgcttcctattaacaagcagtctatggagtcgtctgttttcctttctttaaataaattaaagctcttaaca-cttgtgctggtccagTGCAGATGGGTATTGCTTCCGTTGTTCACCTGTATGTATTCCCAGCAAAGCCTTATGGTCTAATGGGAGACCGCTTTACTGGATCCGTTTCAGTTCTTGG-----
                                                                                  ||||   |||| ||||  || |   |  ||      | ||| ||    |      ||  ||| ||   |   | ||  ||||  |  || ||  |||||||| ||||||||| | |||||||||||||| || ||||||||||||||||  | |||||||||||||||| |||||  |||||||||||||||     
------------------------------------------------------------------------------cacgttcagcacttcttattttcatgttttacatttttatgactgcttcagataaggggaa-gaataaagtttaacagcaatttgtattcatcaagcacagATGGGCATTGCTTCCATAGTTCACCTGTATGTGTTTCCAGCAAAGCCTTATGAGCGAATGGGAGACCGCTTTTCTGGAAGCGTTTCAGTTCTTGGAGATT

upper sequence: AT4G38360.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA06G00300.1 (Glycine max), 3'ss of exon 5
gtaaatgtcttctgttgttaccaattcctgcaaaaggttaaacattatgtgtgatctttgtttacgagtgcaaaactttttcttcattgcttcctattaacaagcagtctatggagtcgtctgttttcctttctttaaataaattaaagctcttaaca-cttgtgctggtccagTGCAGATGGGTATTGCTTCCGTTGTTCACCTGTATGTATTCCCAGCAAAGCCTTATGGTCTAATGGGAGACCGCTTTACTGGATCCGTTTCAGTTCTTGG-----
                                                                                | ||||   |||| ||||  || |   |  ||      | ||| ||    |      ||  ||| ||   |   | ||  ||||  |  || ||  |||||||| ||||||||| | |||||||||||||| || ||||||||||||||||  | |||||||||||||||| |||||   ||||||||||| ||     
------------------------------------------------------------------------------catgttcagcacttcttattttcatgttttacatttttatgactgcttcagataaggggaa-gaataaagtttaacagcaatttgtattcatcaagcacagATGGGCATTGCTTCCATAGTTCACCTGTATGTGTTTCCAGCAAAGCCTTATGAGCGAATGGGAGACCGCTTTTCTGGAAGTGTTTCAGTTCTCGGAGATT

upper sequence: AT4G38360.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv03s0038g03670.t01 (Vitis vinifera), 3'ss of exon 7
gtaaatgtcttctgttgttaccaattcctgcaaaaggttaaacattatgtgtgatctttgtttacgagtgcaaaactttttcttcattgcttcctattaacaagcagtctatggagtcgtctgttttcctttctttaaataaattaaagctcttaacact--tgtgctggtccagTGCAGATGGGTATTGCTTCCGTTGTTCACCTGTATGTATTCCCAGCAAAGCCTTATGGTCTAATGGGAGACCGCTTTACTGGATCCGTTTCAGTTCTTGG-----
                                                                         ||||  || |    ||| |        |||  | | ||| |       |  | || | |   || | ||| ||||| |    |   |  |||  |  |||||  |||||||| || |||||  |||||||||||||||||||||| || ||||||||||  |||||||||||||| ||  |||||   ||||| ||||||||     
-----------------------------------------------------------------------tgaactccttatcttatgcctatacgctgcaa--aatttattgg------taatgtcatcttcataca-aaactaaagtttaacaggttcatgtattcatccagcacagATGGGCATCGCTTCAATTGTTCACCTGTATGTATTCCCTGCCAAGCCTTATGAGCTAATGGGAGACCGGTTATCTGGAAGTGTTTCGGTTCTTGGAGACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctgttttcctttctttaaataaattaaagctcttaacacttgtgctggtccagTGCAGATGGGTATTGCTTCCGTTGTTCACCTGTATGTATTCCCAGCAAAGCCTTATGGTCTAATGGGAGACCGCTTTACTGGATCCGTTTCAGTTCTTGG
                                tcttaac  putative branch site (score: 2)
           tttctttaaataaatt  TA-rich tract