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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtttggctacctacgatttcggcttcttcttgtcattttaatatatggaatgctaaacatcggcctcggacttacaccattttatttgtgttttgcagCAATACCCATTTGACATACCAACTGAAGCTTTTTCATTTGAGATTTTCAAACAGGCATTTGTTGCCATTCAGTCATGTGTGGTGCATTTACAA

Basic information

species Arabidopsis thaliana
transcript AT5G14260.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G14260.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os12g13460.1 (Oryza sativa), 3'ss of exon 4
gtgtttggctacctacgatttcggcttcttcttgtcattttaatatatggaatgctaa-acatcggcctcggacttacaccattttatttgtgttttgcagCAATACCCATTTGACATACCAACTGAAGCTTTTTCATTTGAGATTTTCAAACAGGCATTTGTTGCCATTCAGTCATGTGTGGTGCATTTACAA
         | | | |  ||| | | | | |      ||    | | ||| || ||    ||   ||  |    |     ||| | |  |||  | |||||||||| || ||||||||||| || || |||||| |||||||||| ||||| || || ||||| ||  | ||||| || ||||| ||||| || 
--------gtgctttc--ttttgacct-tccaaaatgttcctgtctctgggattctgttgcactagctgcttgttgttctcatgtcaactgt--tatgcagCAATATCCTTTTGACATACCTACCGAGGCTTTTCCATTTGAGATCTTCAAGCAAGCTTTTGTCGCAGTACAGTCTTGCGTGGTCCATTTGCAG

upper sequence: AT5G14260.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: AC198982.3_FGT006 (Zea mays), 3'ss of exon 2
gtgtttggctacctacgatttcggcttcttcttgtcattttaatatatggaatgctaaacatcggcctcggacttacaccattttatttgtgttttgcagCAATACCCATTTGACATACCAACTGAAGCTTTTTCATTTGAGATTTTCAAACAGGCATTTGTTGCCATTCAGTCATGTGTGGTGCATTTACAA
       |    |   ||| |      | | ||  |  || ||    |||     |    | |    ||    |  |||  ||  |||  ||||||||||||||| || ||||||||||| ||||| |||||| | ||||| || ||||| ||||| ||||||||  | ||||| ||||| || ||||| || 
-------gtattccttgatcttccaagcatatttcc--ttcaaggattggctatttcgttaacttattctatttctcacagtt--attattgttttgcagCAATATCCTTTTGACATACCTACTGAGGCTTTTCCGTTTGAAATATTCAAGCAGGCTTTTGTTGCAGTACAGTCTTGTGTTGTTCATTTGCAG

upper sequence: AT5G14260.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G047695_T01 (Zea mays), 3'ss of exon 4
gtgtttggctacctacgatttcggcttcttcttgtcattttaatatatggaatgctaaacatcgg-cctcggacttacaccattttatttgtgttttgcagCAATACCCATTTGACATACCAACTGAAGCTTTTTCATTTGAGATTTTCAAACAGGCATTTGTTGCCATTCAGTCATGTGTGGTGCATTTACAA
       |    |   ||| |      | | || || || ||  ||  |  ||   |   |  |  ||||   || ||| |     |||| |||||| |||||||| || ||||||||||| ||||| |||||| | ||||| || ||||| ||||| ||||||||  | ||||| |||||||| ||||| || 
-------gtattccttgatctttcaagcatattttctttctaggattggctatatcatcaactgatcctctttctcacagcg----atttttgtttt-cagCAATATCCTTTTGACATACCTACTGAGGCTTTTCCGTTTGAAATATTCAAGCAGGCTTTTGTTGCAGTACAGTCTTGTGTGGTTCATTTGCAG

upper sequence: AT5G14260.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G07100.1 (Glycine max), 3'ss of exon 4
gtgtttggctacctacgatttcggcttcttcttgtcattttaatatatggaatgctaaacatcggcctc--ggacttacaccat-tttatttgtgttttgcagCAATACCCATTTGACATACCAACTGAAGCTTTTTCATTTGAGATTTTCAAACAGGCATTTGTTGCCATTCAGTCATGTGTGGTGCATTTACAA
                 ||      | |    |  ||  || |    | |     || |  | | | |   |  ||||||  || |  ||   | |  |||||||||| |||| |||||| || |||||||| ||||||||||||||||||||||| || |||| ||| |||||||| ||||||||||||||||| 
--------------gtaataaaaaataccctataacaagttca---gtagttatttacattttgacatttagtgcttacattatatgcataaatataatgcagCAATATCCATATGACATTCCTACTGAAGCCTTTTCATTTGAGATTTTCAAACAAGCCTTTGCTGCTATTCAGTCTTGTGTGGTGCATTTACAG

upper sequence: AT5G14260.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G22520.2 (Glycine max), 3'ss of exon 4
gtgtttggctacctacgatttcggcttcttcttgtcattttaatatatggaatgctaaacatcggcctcgg-acttacaccattt-tatttgtgttttgcagCAATACCCATTTGACATACCAACTGAAGCTTTTTCATTTGAGATTTTCAAACAGGCATTTGTTGCCATTCAGTCATGTGTGGTGCATTTACAA
                 | |     |||  |     | || | ||  |   |||   |   |  |  |  |  ||||||  ||||  ||   | |  |||||||||| |||| |||||| || ||||| || ||||||||||||||||||||||| || |||| ||| |||||||| ||||||||||||||||| 
---------------gtaataaaatttccccgaacaagttcagtagtt---atgtacattttgagatttagtgcttacattatttgcataaatataatgcagCAATATCCATATGACATTCCTACTGAGGCCTTTTCATTTGAGATTTTCAAACAAGCCTTTGCTGCTATTCAGTCTTGTGTGGTGCATTTACAG

upper sequence: AT5G14260.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv14s0171g00310.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------------------------------------------gtgtttggctacctacgatttcggcttcttcttgtca-----ttttaatatatggaatgctaaacatcggcc--tcggacttacaccattttatttgtgttttgcagCAATACCCATTTGACATACCAACTGAAGCTTTTTCATTTGAGATTTTCAAACAGGCATTTGTTGCCATTCAGTCATGTGTGGTGCATTTACAA
                                                                  | | | |||   | | |||  |   |  | |  | |     || |  ||  ||   || ||||  | |     |  ||||   |   | ||| ||   |||||||||||||||||| ||| || || ||||| || ||| ||||||||||||||||||| || |||||||| |||||||| ||||||||||||||||| 
gtcattctcttacacatctgttgttgaaactagataatatatgccttccccttttgttaatttaaatatattgctgtttcctattgggagattctttgattacattgttcttttaggtgatttgttaaatgtagatgaatgtgactatgattttcttaatttctttttgcagCAATACCCATATGATATTCCTACTGAGGCCTTTCCATTTGAGATTTTCAAACAAGCTTTTGTTGCAATTCAGTCTTGTGTGGTGCATTTACAG

upper sequence: AT5G14260.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S181_117V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------gtgtttggctacctacgatttcggcttcttcttgtcattttaatatatggaat----gctaaacatcggcctcggactt-----acaccattttatttgtgttttg--cagCAATACCCATTTGACATACCAACTGAAGCTTTTTCATTTGAGATTTTCAAACAGGCATTTGTTGCCATTCAGTCATGTGTGGTGCATTTACAA
                          ||    |   |  | || |  |     |  | || |  |   |  |  | ||    |  | |  |  ||    || |      |||    ||   | ||  |||   |||||||| || || ||| |||| || |||||||| ||||||||||| ||||| ||||| ||||| ||  | ||||| || || || ||  | || 
gtaattccactgccgactttacattatgagatgaagctgaagagtatgttccatcttggtgagatatttgcagaggattacggggagaagtttgctgatgattcttcaaacattggttgcctggttatttaaacagCAATATCCCTTCGACCTACCTACGGAAGCTTTCTCATTTGAGATATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAG

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|116473444|gb|EG516036.1|EG516036
EST:     AATACAATGAGCTTGACACTGTCTGGTTCATGGCTGGATCTTTGTTTCAG                         CAATACCCATTTGACATACCAACTGAAGCTTTTTCATTTGAGATTTTCAAA
genomic: AATACAATGAGCTTGACACTGTCTGGTTCATGGCTGGATCTTTGTTTCAGgtgtttggct ... tgttttgcagCAATACCCATTTGACATACCAACTGAAGCTTTTTCATTTGAGATTTTCAAA
EST: gi|125073574|gb|EL137855.1|EL137855
EST:     CTGGTTCATGGCTGGATCTTTGTTTCAG                         CAATACCCATTTGACATACCAACTGAAGCTTTTTCATTTGAGATTTTCAAA
genomic: CTGGTTCATGGCTGGATCTTTGTTTCAGgtgtttggct ... tgttttgcagCAATACCCATTTGACATACCAACTGAAGCTTTTTCATTTGAGATTTTCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatggaatgctaaacatcggcctcggacttacaccattttatttgtgttttgcagCAATACCCATTTGACATACCAACTGAAGCTTTTTCATTTGAGATTTTCAAACAGGCATTTGTTGCCATTCAGTCATGTGTGGTGCATTTACAA
                         gacttac  putative branch site (score: 2)
                                   attttatttgtgtttt  TA-rich tract