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

gtattttctcaggaaactgatgcttatactgtttatgacattgtagaaatccatgcttttaacactacctacttgcttttcagCCAAGGAGCATGTTGTAGGTTGGTACAGCACAGGCCCTAAACTTCGAGAGAATGATTTGGATGTTCACGCGTTGTTCAATGG

Basic information

species Arabidopsis thaliana
transcript AT5G05780.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os04g56646.1 (Oryza sativa), 3'ss of exon 2
gtattttctcaggaaa-ctgatgcttatactgtttatgacattgtagaaatccatgcttttaacactacctacttgcttttcagCCAAGGAGCATGTTGTAGGTTGGTACAGCACAGGCCCTAAACTTCGAGAGAATGATTTGGATGTTCACGCGTTGTTCAATGG
||||    |  | ||  ||     || |      |      | |||        || | |    || | ||  |     |  |||||||||||||||||| || ||||||||||| || || |||||  | ||||| || |||||| | |||||  | ||||||  
gtatgcagtttgcaagtcttccatttgtttgacctgccctgt-gtaactgattgtgttgtactgacgagctgttcttcgtgtagCCAAGGAGCATGTTGTTGGCTGGTACAGCACCGGTCCAAAACTCAGGGAGAACGACTTGGATATACACGCACTATTCAATAA

upper sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G368908_T02 (Zea mays), 3'ss of exon 2
--gtattttctcaggaaact-gatgcttatactgtttatgacattgta-gaaatccatgctttt----aacactacctacttgcttttcagCCAAGGAGCATGTTGTAGGTTGGTACAGCACAGGCCCTAAACTTCGAGAGAATGATTTGGATGTTCACGCGTTGTTCAATGG
   |  | | |||  |  || | ||| | |   |  |      |  || | | ||  |  |  |    | ||  | ||  |||   | ||||||||||||||||||| || ||||||||||| ||||| |||||  | |||||||| |||||||| || || ||||||||  |
gtatgctgtatcaaaattctcggtgcctgttgggcctgctctgtgctatggattctgttgtcctgatgagcatgagctgtttgtggtgcagCCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAG

upper sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G061745_T03 (Zea mays), 3'ss of exon 2
--gtattttctcagga-----aactgatgcttatactg-tttatgacattgtagaaatccatgcttttaacactacctacttgcttttcagCCAAGGAGCATGTTGTAGGTTGGTACAGCACAGGCCCTAAACTTCGAGAGAATGATTTGGATGTTCACGCGTTGTTCAATGG
   |  | | |||  |     || |  || |    ||| |   ||  ||||      |        | | |||   ||  |||   | ||||||||||||||||||| || ||||||||||| ||||| |||||  | ||||| || |||||||| || || || |||||  |
gtatgctctatcaaaatcctcaaattttgttgggcctgatccgtgctattgcttcttttgtcctgatgagcacgggctgtttgtggtgcagCCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGAACGACTTGGATGTCCATGCATTATTCAACAG

upper sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv02s0025g01490.t01 (Vitis vinifera), 3'ss of exon 2
gtattttctcaggaaactgatgcttatactgtttatgacattgtagaaatccatgcttttaacactacctacttgcttttcagCCAAGGAGCATGTTGTAGGTTGGTACAGCACAGGCCCTAAACTTCGAGAGAATGATTTGGATGTTCACGCGTTGTTCAATGG
||||| |     | || |||||    ||   ||||  |  ||   | |     |  | |    | |  | |      |||||||||||||||||||||| |||||||| |||||||| || ||||| || ||||||||| | ||| |||||    | ||| ||| 
gtattattggttgtaagtgatgag-gtatcttttacaatttttatggacaatgttttatgggaatttacaataattgtttcagCCAAGGAGCATGTTGTTGGTTGGTATAGCACAGGACCAAAACTGCGGGAGAATGATCTAGATATTCACAGACTATTCCATGA

upper sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0007g01980.t01 (Vitis vinifera), 3'ss of exon 2
gtattttctcaggaaactgatgcttatactgtttatgacattgtagaaatccatgcttttaacactacctacttgcttttcagCCAAGGAGCATGTTGTAGGTTGGTACAGCACAGGCCCTAAACTTCGAGAGAATGATTTGGATGTTCACGCGTTGTTCAATGG
||||| | |   | || |||||    |   | |||  |  || ||        | ||| |   | |   |  ||   |||||||||||||||| || || || |||||||||||||| || ||||| || ||||||||  | ||| ||||||   ||||| ||| 
gtattatttttcgtaaatgatgag-gtctcgcttacaat-ttttatgggcgatttcttatgggaatttatgatt-tgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA

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|164159164|gb|ES140153.1|ES140153
EST:     TTCAAGAGAATTAATG                         CCAAGGAGCATGTTGTAGGTTGGTACAGCACAGGCCCTAAACTTCGAGAGA
genomic: TTCAAGAGAATTAATGgtattttctc ... tgcttttcagCCAAGGAGCATGTTGTAGGTTGGTACAGCACAGGCCCTAAACTTCGAGAGA
EST: gi|125149571|gb|EL182665.1|EL182665
EST:     TGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATG                         CCAAGGAGCATGTTGTAGGTTGGTACAGCACA
genomic: TGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATGgtattttctc ... tgcttttcagCCAAGGAGCATGTTGTAGGTTGGTACAGCACA
EST: gi|164132756|gb|ES021857.1|ES021857
EST:     CACAACTATCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATG                         CCAAGGAGCATGTTGTAGGTTGGTACAGCACAGGCCCTAAAC
genomic: CACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATGgtattttctc ... tgcttttcagCCAAGGAGCATGTTGTAGGTTGGTACAGCACAGGCCCTAAAC
EST: gi|124722174|gb|EH813576.1|EH813576
EST:     AGTCAATGTTCCACATGTTCAAGAGAATTAATG                         CCAAGGAGCATGTTGTAGGTTGGTACAGCACAGGCCCTAAACTTCGAGAGA
genomic: AGTCAATGTTCCACATGTTCAAGAGAATTAATGgtattttctc ... tgcttttcagCCAAGGAGCATGTTGTAGGTTGGTACAGCACAGGCCCTAAACTTCGAGAGA
EST: gi|163984651|gb|ES199362.1|ES199362
EST:     CAATGTTCCACATGTTCAAGAGAATTAATG                         CCAAGGAGCATGTTGTAGGTTGGTACAGCACAGGCCCTAAACTTCGAGAGA
genomic: CAATGTTCCACATGTTCAAGAGAATTAATGgtattttctc ... tgcttttcagCCAAGGAGCATGTTGTAGGTTGGTACAGCACAGGCCCTAAACTTCGAGAGA
EST: gi|125124900|gb|EL170608.1|EL170608
EST:     CTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATG                         CCAAGGAGCATGTTGTAGGTTGGTACAGCACAGGCCCTAAACTTCGAGAGA
genomic: CTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATGgtattttctc ... tgcttttcagCCAAGGAGCATGTTGTAGGTTGGTACAGCACAGGCCCTAAACTTCGAGAGA
EST: gi|47831858|gb|CK121542.1|CK121542
EST:     TGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATG                         CCAAGGAGCATGTTGTAGGTTGGTACAGCACAGGCCCTAAACTTCGAGAGA
genomic: TGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATGgtattttctc ... tgcttttcagCCAAGGAGCATGTTGTAGGTTGGTACAGCACAGGCCCTAAACTTCGAGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtttatgacattgtagaaatccatgcttttaacactacctacttgcttttcagCCAAGGAGCATGTTGTAGGTTGGTACAGCACAGGCCCTAAACTTCGAGAGAATGATTTGGATGTTCACGCGTTGTTCAATGG
                            ttttaac  putative branch site (score: 2)
                                       cctacttgcttttc  putative PPT
                            ttttaaca  TA-rich tract