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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcgtttcttttccgttttacatttttactggcctttgctagggttctgtgtgattatactttgcaaccttgggttattgttgaccaacattgtttgactttttagcggttgcttatgcttgtcgttggtttttcttgttttcttcagGTGTGGCATTTGGCTGATGTCCCCAAAAACGACAACTTTCAGTACACTCACTTTGCTCACAAGATAAACAGCTTCGACACAGCGCCTGCTAAGCTCTTGG

Basic information

species Arabidopsis thaliana
transcript AT5G59420.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 8
gtatgtcgtttcttttccgttttacatt--tttactggcctttgcta-gggttctgtgtgattatactttgcaaccttgggttattgttgaccaacattgtttgactttttagcggttgcttatgcttgtcgttggtttttcttgtttt-cttcagGTGTGGCATTTGGCTGATGTCCCCAAAAACGACAACTTTCAGTACACTCACTTTGCTCACAAGATAAACAGCTTCGACACAGCGCCTGCTAAGCTCTTGG
                  ||  ||| ||  || |||  |   | ||| || |   ||||| ||||| | |  | || |  | |         |||   || |    | |||   | |  || ||||       ||||  | |||| ||  || ||| | |||    | |||  || |||  |   |||||| | ||||||||| ||||| || ||||| ||||||||||||||||| || |||   ||||| ||||
------------------gtcgtactttctttcactttctgctactatggataacgtgtg-ttata-tatatacccataagatg--------caatggtggtcacatatttgcggatgactgatgcactgaactggtcatacttgattgactgcagATCTGGAGAGTTGCTCCTGCCCCACAGGGCGACAAGTATCAGTACACACACTTCGCACACAAAATAAACAGCTTCGACACGGCACCTAAGAAGCTGTTGG

upper sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G114126_T01 (Zea mays), 3'ss of exon 8
gtatgtcgtttcttttccgttttacatttttactggcctttgctagggttctgtgtgat-tatactttgcaaccttgggttattgttgaccaacattgtttgactttttagcggttgcttatgcttgtcgttggtttttcttgttttcttcagGTGTGGCATTTGGCTGATGTCCCCAAAAACGACAACTTTCAGTACACTCACTTTGCTCACAAGATAAACAGCTTCGACACAGCGCCTGCTAAGCTCTTGG
                  |||   |||  || ||  |  || ||     |  |  | |  | |  |||  |  |     | | ||   |      |    |   |      | | || |    |    || | ||  ||     || || ||| | |||    | ||   || |||  | ||||||   | ||||||||| |||||||| ||||| ||||||||||||  ||| || |||   ||||| ||||
------------------gttggtcatacttccttccactttctgtaactacggataacctctgttttata--cacacatgaatgaaaatgctggtcacatagttgccggacagctgatgtaccgaaccgctcgtactta--acttgctgcagATCTGGAGAGTCGCCCCTGCCCCACAGAACGACGGGTATCAGTACACACACTTTGCGCACAAAATAAACAGCTTCAGCACGGCACCTAAGAAGCTGTTGG

upper sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA11G14770.1 (Glycine max), 3'ss of exon 8
gtatgtcgtttcttttccgttttacatttttactggcctttgctagggttctgtgtgattatactttgcaaccttgggttattgttgaccaacattgtttgactttttagcggttgcttatgcttgtcgttggtttttcttgttttcttcagGTGTGGCATTTGGCTGATGTCCCCAAAAACGACAACTTTCAGTACACTCACTTTGCTCACAAGATAAACAGCTTCGACACAGCGCCTGCTAAGCTCTTGG
                                             |   |   | |  |||||||||||     |   | | || |||| |||| |  |  || ||  ||   || |||||  ||||| ||   | |  || | |||| ||||| |||||| | |||||||| ||| | || ||||| |||||||| || || |||||||| || ||||||||||| ||||| || |||   ||| | ||||
---------------------------------------------gaagtaatttttcttatactttgctgatatat-taactggtgac-aacactagt--accttaaag---ttccttatcattgtcatttcctctgattttattctgcagGTTTGGCATGTTGCTGATGTTCCCCAGAATGACAAATTTCAGTATACACATTTTGCTCATAAAATAAACAGCTTTGACACTGCCCCTAAAAAGTTGTTGG

upper sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA12G06690.1 (Glycine max), 3'ss of exon 8
gtatgtcgtttcttttccgttttacatttttactggcctttgctagggtt-ctgtgtgattatactttgcaaccttgggttattgttgaccaacattgtttgactttttagcggttgcttatgcttgtcgttggtttttcttgttttcttcagGTGTGGCATTTGGCTGATGTCCCCAAAAACGACAACTTTCAGTACACTCACTTTGCTCACAAGATAAACAGCTTCGACACAGCGCCTGCTAAGCTCTTGG
                                           ||  ||   | |    |||||||||||     ||   ||||| |||       |   | |    |||   ||| |||||  ||||| ||   | |  || | || | ||||| |||||| | |||||||| ||| | || ||||| |||||||| || || |||||||| || ||||||||||| ||||| || |||   ||| | ||||
-----------------------------------------aataaagtaatttttctcttatactttgc-----tgatatattggtga-----ggtcactaataccttaa-agttccttatcattgtcatttcctctgatt-tattatgcagGTTTGGCATGTTGCTGATGTTCCCCAGAATGACAAATTTCAGTATACACATTTTGCTCATAAAATAAACAGCTTTGACACTGCCCCTAGAAAGTTGTTGG

upper sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 8
gtatgtcgtttcttttccgttttacatttttactggcctttgctagggttctgtgtgattatactttgcaaccttgggttattgttgaccaacattgtttgactttttagcggttgcttatgcttgtcgttggtttttcttgttttcttcagGTGTGGCATTTGGCTGATGTCCCCAAAAACGACAACTTTCAGTACACTCACTTTGCTCACAAGATAAACAGCTTCGACACAGCGCCTGCTAAGCTCTTGG
                                                     ||| ||||     ||||    ||   || |   |    | |  |  |   |  | |    |||   ||   |  |   | | || ||| | |  | ||||| |||||| | |||||||| ||  |   |||||| |||||||||||||| ||||| || || ||||||||||| |||||||| |||   ||| | ||||
--------------------------------------------------acttgtcattagcacatgcattgctga--tacttgagctgtaaaaagactatgtgctgataaattgtcaattgatcactgcgttattgcttttctgttgcagGTTTGGCATGTTGCTGATGTTCCTGAGGGCGACAAATTTCAGTACACTCATTTTGCACATAAAATAAACAGCTTTGACACAGCTCCTAGGAAGTTGTTGG

upper sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ19778 (Selaginella moellendorffii), 3'ss of exon 8
gtatgtcgtttcttttccgttttacatttttactggcctttgctagggttctgtgtgattatactttgcaaccttgggttattgttgaccaacattgtttgactttttagcggttgcttatgcttgtcgttggtttttcttgttttcttcagGTGTGGCATTTGGCTGATGTCCCCAAAAACGACAACTTTCAGTACACTCACTTTGCTCACAAGATAAACAGCTTCGACACAGCGCCTGCTAAGCTCTTGG
                                                                                     ||  | | || |     | || ||  ||   |||   | ||  ||||        |  ||  | |||||||||    | || || || ||||| ||||| || || |||||||| || |||||||||||||| |||||||||||||| |||||      |||  |  
------------------------------------------------------------------------------------gtgggcgatatggagaatcgttatatagggatctttgacctg--gttg--------taattgatgcagGTGTGGAGAGTAGCGGACGTTCCCAAGAACGATAAGTTCCAGTACACGCATTTTGCTCACAAGATTAACAGCTTCGACACGGCGCCAAACGGGCTACTTC

upper sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ08612 (Selaginella moellendorffii), 3'ss of exon 8
gtatgtcgtttcttttccgttttacatttttactggcctttgctagggttctgtgtgattatactttgcaaccttgggttattgttgaccaacattgtttgactttttagcggttgcttatgcttgtcgttggtttttcttgttttcttcagGTGTGGCATTTGGCTGATGTCCCCAAAAACGACAACTTTCAGTACACTCACTTTGCTCACAAGATAAACAGCTTCGACACAGCGCCTGCTAAGCTCTTGG
                                                                                     ||| | | || |     | || ||  ||   ||| | | ||  ||||        |  ||  | |||||||||    | || || || ||||| ||||| || || |||||||| || |||||||||||||| |||||||||||||| |||||      |||  |  
------------------------------------------------------------------------------------gtgagcgatatggagaatcgttatatagggatcttttacctg--gttg--------taattgatgcagGTGTGGAGAGTAGCGGACGTTCCCAAGAACGATAAGTTCCAGTACACGCATTTTGCTCACAAGATTAACAGCTTCGACACGGCGCCAAACGGGCTACTTC

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|124986711|gb|EL059212.1|EL059212
EST:     CCGAAGGGGAACCCCTTCCAGGAACAGAGCTGAAAGAG                         GTGTGGCATTTGGCTGATGTCCCCAAAAACGACAACTTTCAGTACACTCAC
genomic: CCGAAGGGGAACCCCTTCCAGGAACAGAGCTGAAAGAGgtatgtcgtt ... ttttcttcagGTGTGGCATTTGGCTGATGTCCCCAAAAACGACAACTTTCAGTACACTCAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgactttttagcggttgcttatgcttgtcgttggtttttcttgttttcttcagGTGTGGCATTTGGCTGATGTCCCCAAAAACGACAACTTTCAGTACACTCACTTTGCTCACAAGATAAACAGCTTCGACACAGCGCCTGCTAAGCTCTTGG
 gtttgac  putative branch site (score: 4)
                                ttggtttttcttgttt  putative PPT
                                    tttttctt  TA-rich tract