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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtttttgtataaatgatatgtgaaaggggagttgcctcaaaaaccaaagcttctcatttcttttagtatagcaagtaccctaatattcctcatattttgtgctgcagGAAAGACTGTTATCACAAGTGATCATGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGA

Basic information

species Arabidopsis thaliana
transcript AT4G16155.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 4
gtatgtgtttttgtataaatgatatgtgaaaggggagttgcctcaaaaaccaaagcttctcatttcttttagtatagcaagtaccctaatattcctcatattttgtgctgcagGAAAGACTGTTATCACAAGTGATCATGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGA
      | |  | | ||| |   || |  |       ||  |   ||||     | | |  ||     ||     |  |  |     |    ||     ||  | |  |||||| || || ||  | || |||||||||||| | ||| | ||||| ||||||||||||||||| || || ||||| ||||| || || || || ||||||||
------gctcctttctaa-taccatttacatatattatt--caggaaaatatgtgttgcatatgcacatt----cactagttcttacagagctcgctgaatggttttatgcagGTAAAACCGTATTTACTAGTGATCATGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGA

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 4
gtatgtgtttttgtataaatgatatgtgaaaggggagttgcctcaaaaaccaaagcttctcatttcttttagtatagcaagtaccc-taatattcc-tcatattttgtgctgcagGAAAGACTGTTATCACAAGTGATCATGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGA
               |   ||   | |  |  | ||  ||  |   |    | |  || |   | ||||   | | | | || | |  || ||||      ||  |    |||||| || |||||  | || |||||||||||| ||||| | ||||| ||||| |||||||| || || || ||||||||||| || || ||||||||||||||
---------------tgggtgcattttttattgtgacatgtgtattagttgacattttttgtgtactttccttgttgtatgttctcacaaaattctactggatgattatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 3
gtatgtgtttttgtataaatgatatgtgaaaggggagttgcctcaaaaaccaaagcttctcatttcttttagtatagcaagtaccctaatattcctcatattttgtgctgcagGAAAGACTGTTATCACAAGTGATCATGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGA
       || |  ||||  |   ||   | ||   |  ||| |      |||    |||  ||||| ||     |||||        ||   |      ||  | |  |||||| || |||||  | || |||||||||||| | ||| | ||||| || ||||| |||||||| || || ||||||||||| || || ||||| ||||||||
-----ccttatcatatatgttgcatactacagcttaaatgcatttgttgcca----ttcctatttcattc----tagcatccctttaaaagcttgcaccatggttttatgcagGTAAAACTGTATTTACTAGTGATCATGCACTAAAACTTGAGTCAGTCCCTGAATGGATTGCTATTGTTGGAAGTGGTTACATTGGACTTGAATTCAGTGA

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 4
gtatgtgtttttgtataaatgatatgtgaaaggggagttgcctcaaaaaccaaagcttctcatttcttttagtatagcaagtaccctaatattcctcatattttgtgc-tgcagGAAAGACTGTTATCACAAGTGATCATGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGA
    |  | ||||| | | |||||  ||        |||               | |  |  ||  | || ||||    | |     ||   ||  || | |   ||| | ||||||||||||| || || ||||| |||||| | ||| ||||| | |||||||| ||||| || || ||||||||||||||||| || ||||| ||||||||
--ggggatctttgt-tcactgatac-tgtccctcttgtttttctg-----ttttgttatttcttcttcttggtatcattaatg----aaagctcacca-agtaaatgcattcagGAAAGACTGTGATTACCAGTGACCATGCACTCAAACTGGAGACTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGTTATATTGGCCTTGAATTCAGTGA

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 4
-gtatgtgtttttgtataaatgatatgtgaaaggggagttgcctcaaaa-accaaagcttctcatttcttttagtatagcaagtaccctaatattcctcatattttgtgctgcagGAAAGACTGTTATCACAAGTGATCATGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGA
      ||||| | |||   |      |    ||    |||| |||||  |     |  | | ||| |||||    |||  |       ||| ||||| | | ||    || |||| |||||||| || || ||||| || ||| | ||| ||||||| |||||||| ||||| || || ||||||||||| ||||| |||||||| ||||||||
aaaccttgtttctttatgtttttcccatctctgga---ttgcttcaaagtattgttgagtatgattactttt----tagtgaa------aattttcctaaaaattac--cttcagGGAAGACTGTGATTACCAGTGACCACGCACTCAAACTGGAGTCTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGATATATTGGTCTTGAATTCAGTGA

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G37050.2 (Glycine max), 3'ss of exon 4
gtatgtgtttttgtataaatgatatgtgaaaggggagttgcctc-aaaaaccaaagcttctcatttcttttagtatagcaagtaccctaatattcctcatattttgtgctgcagGAAAGACTGTTATCACAAGTGATCATGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGA
  |  | | | | | ||  |  | |   |        |||| || ||        |  | | ||| |||||    |   || |  ||||| | || || |           |||| |||||||| || || |||||||| ||| | ||| |||| || |||||||| ||||| || || ||||||||||| ||||| |||||||| ||||||||
--acctttgtatctttatgtttttttccatctcttgattgcttctaagttttgttgggtataattacttttta-gtgaaaactttcctaaaaatcatctt-----------cagGGAAGACTGTGATTACCAGTGATCACGCACTCAAACTGGAATCTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGATATATTGGTCTTGAATTCAGTGA

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S352_68V6.1 (Physcomitrella patens), 3'ss of exon 4
gtatgtgtttttgtataaatgatatgtgaaaggggagttgcctcaaaaaccaaagcttctcatttcttttagtatagcaagtaccctaatattcctcatattttgtgctgcagGAAAGACTGTTATCACAAGTGATCATGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGA
          | | | |||| || |  |    |    |   || ||  |   |       || |  ||||     ||  |      |  |    |  | |  | ||  |||||||||||| ||| | ||||||||||| || ||||| || ||||   |||| |||||||||||||| || || || ||||| || ||||| |||||||||||
----------taggaaaaattatgtaggtgttgcccatgttctgaacgatatagctgcagcactgtttttga---agtgaacttgatgcttactcaaaaacctggttatgcagGAAAGACCGTTTTTACAAGTGATCACGCTTTGAAGTTAGAGTGGATTCCAGACTGGATTGCGATCGTTGGCAGCGGTTACATTGGTCTAGAGTTCAGTGA

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 4
gtatgtgtttttgtataaatgatatgtgaaaggggagttgcctcaaaaaccaaagcttctcatttcttttagtatagcaagtaccctaatattcctcatattttgtgc-tgcagGAAAGACTGTTATCACAAGTGATCATGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGA
||| |   |  ||  |   || |   | |||       ||| |  |||    | |||  ||  || |      | |   | || |      ||  ||| | |  |||  | |||||||||| ||  |||| || ||||||||  ||||  ||||||   | || ||||||||||| || || ||||||||||| || |||||||||||||| ||
gtaagaagtcatg-gtcgttggtggattaaaa------tgcttttaaagtttatgctggtcgattgt-----aaaaatgattatctc----ttgatcaaactgcgtgtatccagGAAAGACGGTGTTCACCAGCGATCATGCGCTGAAGCTGGAGTGGATCCCAGACTGGATTGCCATTGTTGGAAGTGGTTACATTGGTCTTGAGTTCAGCGA

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S35_94V6.1 (Physcomitrella patens), 3'ss of exon 4
gtatgtgtttttgtataaatgatatgtgaaaggggagttgcctcaaaaaccaaagcttctcatttcttttagtatagcaagtaccctaatattc--ctcatattttg--tgctgcagGAAAGACTGTTATCACAAGTGATCATGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGA
                        |  ||||      | |  | | |    | |   | |||  |||| || |   || |  |    || ||     ||||||   |  |||| |||||||||| ||  |||| ||||| ||||| |||||  ||||||   |||| ||||||||  | || || ||||||||||| || |||||||||||||||||
-----------------------gtaagaaactatcatcgt-tgatactttagatgctttcaaatcttgtattgccgcgataagaacaaaatctgattcatatggaggatgct-cagGAAAGACGGTGTTCACGAGTGACCATGCGTTGAAGCTGGAGTGGATTCCCGACTGGATCACTATTGTCGGAAGTGGTTACATTGGTCTTGAGTTCAGTGA

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|125282729|gb|EL296814.1|EL296814
EST:     TTGAAGTTGATG                         GAAAGACTGTTATCACAAGTGATCATGCATTGAAATTGGAGTCCGTTCCTG
genomic: TTGAAGTTGATGgtatgtgttt ... tgtgctgcagGAAAGACTGTTATCACAAGTGATCATGCATTGAAATTGGAGTCCGTTCCTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcatttcttttagtatagcaagtaccctaatattcctcatattttgtgctgcagGAAAGACTGTTATCACAAGTGATCATGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGA
                         ccctaat  putative branch site (score: 3)
        ttttagtata  TA-rich tract