Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgttaaacttccttacattgtctcaaaacccgggtttatccatcggttctgaactaaacatcactcaaactgtgttttcttttgcattgcagCCGAGAGAGATTCGGGGAGATGCACGCGAGATTATGGTGGGAAGAGAACAGGGCAAGGATACATGAACAATACTTGTGATCATAAATCTAAGAGTTTTGT

Basic information

species Arabidopsis thaliana
transcript AT5G20540.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G20540.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os08g36020.1 (Oryza sativa), 3'ss of exon 4
------gtactgttaaacttc--cttacattgtctcaaaacccgggtttatccatcggttctgaactaaacatcactcaaactgtgttttcttttgcat-tgcagCCGAGAGAGATTCGGGGAGATGCACGCGAGATTATGGTGGGAAGAGAACAGGGCAAGGATACATGAACAATACTTGTGATCATAAATCTAAGAGTTTTGT
        | |  | | | ||  || |  | || ||  ||  |    |||    ||| | ||  |   |||||   |  | |||| ||  || ||     |||||||| |||| |||| | ||||||||||| ||  ||||||||||||||||| |||||||||||||||| || ||  | |||  | | ||   |    | | |
tggcagagattcatgagcatctgctcatttggtttcgcaataca--ctta---gtcgttcctctaaagaacatgtatttatctgttttggctgttctgcgtgcagCCGGGAGAAATTCAGCGAGATGCACGCCAGGCTATGGTGGGAAGAGAACCGGGCAAGGATACATGATCAGTATCTCTGAGAAGACATGCTAATCATGTAT

upper sequence: AT5G20540.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os09g27230.1 (Oryza sativa), 3'ss of exon 4
gtactgttaaacttccttacattgtctcaaaacccggg-----tttatccatcggttctgaactaaacatcactcaaactg-------tgttttcttttgcattgcagCCGAGAGAGATTCGGGGAGATGCACGCGAGATTATGGTGGGAAGAGAACAGGGCAAGGATACATGAACAATACTTGTGATCATAAATCTAAGAGTTTTGT
    || |  | |  |   |||  ||  | ||   ||       | |       | |   | |  |  ||||   |||  |       | || ||| |||| ||||||||||||||| ||| | |||||||| || ||  ||||||||||||| ||| | || |||||||||||||| ||  | |||                     
----tgcttgaatctc---catgatcgaagaatttggaagcaactgaattgctagctactagcagatgatcatggaaagagacttaattattctctcttgc-ttgcagCCGAGAGAGGTTCAGCGAGATGCATGCCAGGCTATGGTGGGAAGAAAACCGAGCGAGGATACATGAACAGTATCTCTGA---------------------

upper sequence: AT5G20540.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G429658_T01 (Zea mays), 3'ss of exon 5
-----------------------------------------------------gtactgttaaacttccttacattgtctcaaaacccgggt--ttatccatcggttctgaactaaacatcact--------caaactgtgtttt------cttttgca-ttgcagCCGAGAGAGATTCGGGGAGATGCACGCGAGATTATGGTGGGAAGAGAACAGGGCAAGGATACATGAACAATACTTGTGATCATAAATCTAAGAGTTTTGT
                                                         || ||    |      ||   || |||| | | |    || ||| |      ||| || |||  | |         | ||  |  |||      |  |||   ||||||||| ||||  ||| | |||| ||| || ||| ||||||||||||||||| | || |||||||| ||||||||| | |||  | |||     |||      
gtttgtgacccatgatgcttcagagccctttccactagcttgctcttagaataaacttgctatgtataacatgatcaacttaaaatcagagaagctagccacctacatagaattatacaagattgcagtagatacacgattgtttacatggcccttgtgcttgcagCCGGGAGAAGTTCAGCGAGAGGCATGCCAGACTATGGTGGGAAGAGAACCGAGCGAGGATACACGAACAATACCTCTGAGAAGAAACGCCCGAGACCATC

upper sequence: AT5G20540.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G037941_T01 (Zea mays), 3'ss of exon 4
gtactgttaaacttccttacattg--tctcaaaacccgggtttatccatcggttctgaactaaacatcactcaaactgtgtttt--cttttgcat-tgcagCCGAGAGAGATTCGGGGAGATGCACGCGAGATTATGGTGGGAAGAGAACAGGGCAAGGATACATGAACAATACTTGTGATCATAAATCTAAGAGTTTTGT
 |||  |||||    | |   |||  | | ||| |  |    | ||| |   || ||   |    |     |  ||||| || |  || ||   | |||||||| ||||||||| | |||||||| || || |||||||||||||| |||   || || ||| |||| || ||  | |||    | |  |   || |   |
-tacctttaaaaacacattggttgattataaaatcaagaacctctcccttttttttggtatggttagagaacttactgttttatggctattctttgtgcagCCGGGAGAGATTCAGTGAGATGCATGCCAGGTTATGGTGGGAAGAAAACCAAGCGAGAATATATGAGCAGTATCTCTGAGAGAAGACGTGTTAGCTACAT

upper sequence: AT5G20540.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G16800.1 (Glycine max), 3'ss of exon 5
-gtactgttaaacttccttacattgtctcaaaacccgggtttatccatcggttctgaactaaacatcactcaaact---gtgttttcttttgcattgcagCCGAGAGAGATTCGGGGAGATGCACGCGAGATTATGGTGGGAAGAGAACAGGGCAAGGATACATGAACAATACTTGTGA-TCAT-AAATCTAAGAGTTTTGT
  |||    | ||     || || ||         |  | |      | | |   ||| | ||    | | |       ||||| || | ||     ||||||||| | ||| ||||||||||| || ||||||||||||||||||||| | || || ||||||||||||||||||||| |  | | || | | |       
gatacacacacacacatatatatagtgcttgttttcatggtagaattttgatgtagaagtcaatggaatttatttcttggtgttctcatgtgttacacagCCGAGAAAAATTTGGGGAGATGCATGCTAGATTATGGTGGGAAGAGAACCGTGCCAGAATACATGAACAATACTTGTGAGTTGTGAGATTTTACAAAGGG--

upper sequence: AT5G20540.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G05900.1 (Glycine max), 3'ss of exon 4
gtactgttaaacttccttacattgt-ctcaaaacccgggtttatccatcggttctgaactaaacatcactcaaact---gtgttttcttttgcattgcagCCGAGAGAGATTCGGGGAGATGCACGCGAGATTATGGTGGGAAGAGAACAGGGCAAGGATACATGAACAATACTTGTGATCATAAATCTAAGAGTTTTGT
 |||    | |      |||||||| ||       |  | ||     | | |   ||| |  |    | | |       ||||| || | ||      |||||||| |  || ||||||||||| || ||||||||||||||||||||| | || || |||||||||||||||||||||                     
atacatacataaacatatacattgtgcttgtttttcatggttgaattttgatgtagaagtctatggaatttatttcttggtgttctcatgtgttacatagCCGAGAAAAGTTTGGGGAGATGCATGCTAGATTATGGTGGGAAGAGAACCGTGCCAGAATACATGAACAATACTTGTGA---------------------

upper sequence: AT5G20540.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G18980.1 (Glycine max), 3'ss of exon 3
--gtactgttaaacttccttac----attgtctca-aaacccgggtttatccatcggttctgaactaaacatcactcaaactgtgttttcttttgcattgcagCCGAGAGAGATTCGGGGAGATGCACGCGAGATTATGGTGGGAAGAGAACAGGGCAAGGATACATGAACAATACTTGTGATCATAAATCTAAGAGTTTTGT
   |  | | ||| || |  ||    ||||   |  | |   | ||||||   | |   ||| | |    ||  ||     ||| |  || | |    ||||| ||||| |  || ||||||||||| || ||| ||||||||||||||||| | || || ||||||||||||||||||||| |   |  |  ||| || |  
gcatgttat-aaatttacgaacggggattgatgcgcatatttgagtttattt-ttgtgactgtatttt-tatttcttttggtgtttcctcgtatttggtgcagTCGAGAAAAGTTTGGGGAGATGCATGCTAGACTATGGTGGGAAGAGAACCGTGCCAGAATACATGAACAATACTTGTGAGCTAGATGCCTAGATTTATCA

upper sequence: AT5G20540.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G07930.1 (Glycine max), 3'ss of exon 3
gtactgttaaac-ttccttacattgtctcaaaacccgggtttatccatcggtt----ctgaactaaacatcactcaaactgtgttttcttttgcat--tgcagCCGAGAGAGATTCGGGGAGATGCACGCGAGATTATGGTGGGAAGAGAACAGGGCAAGGATACATGAACAATACTTGTGATCATAAATCTAAGAGTTTTGT-
   ||||||  | |||    |    | |||  | |  | | ||    ||   |    ||| |  |||  |   ||     |||||| ||  |   |  ||||| ||||| |  || || |||||||| || ||| | ||||||||||||||| | || || |||||||||||||||||||||  ||   || ||| | |   | 
---ctgttagccattctgctctcaatttcattagcatgttataattctcatgtagaactgtatgaaatttatttcttttggtgtttcctcatatttgatgcagTCGAGAAAAGTTTGGTGAGATGCATGCTAGACTGTGGTGGGAAGAGAACCGTGCCAGAATACATGAACAATACTTGTGAGAATTC-TCAAAGGGGTGGCTG

upper sequence: AT5G20540.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv11s0016g01460.t01 (Vitis vinifera), 3'ss of exon 5
--gtactgttaaacttc---cttacattgtctcaaaacccgggtttatccatcggttctgaactaaacatc--actcaaactgtgttttcttttgcattgcagCCGAGAGAGATTCGGGGAGATGCACGCGAGATTATGGTGGGAAGAGAACAGGGCAAGGATACATGAACAATACTTGTGATCATAA-ATCTAAGAGTTTTGT
  | |    | || | |   |||  |   | || ||    ||  |||  ||| |  | ||| || |||  |    ||    | | | | | |||    |||||||||||  | || || |||||||| || ||| | |||||||| |||||| ||||||| ||||||||||| |||||||||       | | | |  |  |  
cagcatatctcaattcctgccttttaccatttccaa-tagggaatta--catggactttgagctgaaccccctgttcttgttttatatgcatttttggtgcagCCGAGAACGGTTTGGAGAGATGCATGCTAGACTTTGGTGGGAGGAGAACCGGGCAAGAATACATGAACAGTACTTGTGAAGGAGCTAACCAGGGATCATC-

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|86088309|gb|DR384068.1|DR384068
EST:     ATTAAAGTTTTACCAGGTGGGAAAAGAGAGCTTCGAAGAGTCAGATTCAG                         CCGAGAGAGATTCGGGGAGATGCACGCGAGATTATGGTGGGAAGAGAACAG
genomic: ATTAAAGTTTTACCAGGTGGGAAAAGAGAGCTTCGAAGAGTCAGATTCAGgtactgttaa ... tgcattgcagCCGAGAGAGATTCGGGGAGATGCACGCGAGATTATGGTGGGAAGAGAACAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atccatcggttctgaactaaacatcactcaaactgtgttttcttttgcattgcagCCGAGAGAGATTCGGGGAGATGCACGCGAGATTATGGTGGGAAGAGAACAGGGCAAGGATACATGAACAATACTTGTGATCATAAATCTAAGAGTTTTGT
              aactaaa  putative branch site (score: 2)
                                ctgtgttttctttt  putative PPT
                                     ttttctttt  TA-rich tract