Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgtttcgttatggtcatcgatatcttttgtgatggtcatttgctaaaatatgatactgctatgtgtgcagGATGAAGTTGAAGTTTTTATATATGTTTGCTGCTGGATTCTACACGTACTCTATATTCGCGTTGGTGTTTTGGGAAACAAGACGGTCTGATTTCGGAGTT

Basic information

species Arabidopsis thaliana
transcript AT3G25540.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G25540.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g37080.2 (Oryza sativa), 3'ss of exon 2
-----gtaagttgtttcgttatggtcatcgatatcttttgtgatggtca--tttgctaaaatatgatactg----ctatgtgtgcagGATGAAGTTGAAGTTTTTATATATGTTTGCTGCTGGATTCTACACGTACTCTATATTCGCGTTGGTGTTTTGGGAAACAAGACGGTCTGATTTCGGAGTT
        | ||| | | |||| |   |  || |  ||  |  |  |||   | |   | || | | | |     |  | | | |||   |||  | |||  | | ||||||| |||||||||||||||||| || || ||||| ||  |  |||||||||||||||| || || ||||| || || 
gtaatacgaattggtcctttattgc--ttcatgttcttactagttctcaggctggtgtatatctaacaattttccccttatctacagATGGAAACTTAAGGCTGTCTATATGTATGCTGCTGGATTCTACACATATTCCATATTTGCACTTATGTTTTGGGAAACAAGGCGTTCAGATTTTGGCGTG

upper sequence: AT3G25540.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G170868_T01 (Zea mays), 3'ss of exon 2
-----gtaagttgtttcgttatggtcatcgata----tcttttgtgatggtca-tttgcta-aaatatgatactgcta----tgtgtgcagGATGAAGTTGAAGTTTTTATATATGTTTGCTGCTGGATTCTACACGTACTCTATATTCGCGTTGGTGTTTTGGGAAACAAGACGGTCTGATTTCGGAGTT
          |  || |  | |  |  |  |||    |  |   || |  ||| | ||||  | || | ||  |  |     |     |||  ||||  | |||  | ||||||||| |||||||||||||||||| || || ||||| ||  |  |||||||||||||||| || || || || ||||| 
gtaattctgatccttccactgtactttttaataaaaattctcactggttttcaatctgctctagatctaatggttgtgcccttactctcagATTGAAACTTAAGGCTGTATATATGTATGCTGCTGGATTCTACACATATTCCATATTTGCACTTATGTTTTGGGAAACAAGGCGTTCAGACTTTGGAGTG

upper sequence: AT3G25540.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G444643_T01 (Zea mays), 3'ss of exon 3
gtaa-----gttgtttcgttatggtcatcgata----tcttttgtgatggtca--tttgctaaaatatgata----ctgctatgtgtgcagGATGAAGTTGAAGTTTTTATATATGTTTGCTGCTGGATTCTACACGTACTCTATATTCGCGTTGGTGTTTTGGGAAACAAGACGGTCTGATTTCGGAGTT
||||      |  || |  | |  |  | ||||    |  ||  || |  |||   | |   |||| | ||     |  |  |     |||  ||||  | |||  | ||||||||| |||||||||||||||||| || || ||||| ||  |  |||||||||||||||| || || || || ||||| 
gtaattcttatccttccactgtactttttgatagaaattcttaatgcttctcaggctggtataaatctaatggttgcacccttactctcagATTGAAACTTAAGGCTGTATATATGTATGCTGCTGGATTCTACACATATTCCATATTTGCACTTATGTTTTGGGAAACAAGGCGTTCAGACTTTGGAGTG

upper sequence: AT3G25540.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv01s0010g01110.t01 (Vitis vinifera), 3'ss of exon 2
----------------------------------------------------------------gtaagttgtttcgtta--tggtcatcga-tatcttttgtgatggtcatttgctaaaatatgatactgctatgtgtgcagGATGAAGTTGAAGTTTTTATATATGTTTGCTGCTGGATTCTACACGTACTCTATATTCGCGTTGGTGTTTTGGGAAACAAGACGGTCTGATTTCGGAGTT
                                                                 ||| || || | |||  ||  | | || || ||      |||    |  | | |   |||||| |  |     | |||| |||| ||||||  ||| ||||||| |  || |||||||||||| ||||| ||||| || ||| | |||||||||||||| ||||||||||| ||||| 
gtaaggttttcacaagccatacattaaaagcttatggttgttaaattctggcttttgtgttagcttaactttttcctttagctgtgctttgaatagctcagcctatgaa-gtcagttgagtgatgata-tattgcaaattcagGTTGAAATTGAAGGGTTTGTATATGTATTGTGGTGGATTCTACACATACTCCATATTTGCTTTGATTTTTTGGGAAACAAGGCGGTCTGATTTTGGAGTG

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|116454729|gb|EG497321.1|EG497321
EST:     TACTTTTGGATTGGTCCTGGAGATCAGATTTGGCCTGATCAACCAATGAA                         GATGAAGTTGAAGTTTTTATATATGTTTGCTGCTGGATTCTACACGTACTC
genomic: TACTTTTGGATTGGTCCTGGAGATCAGATTTGGCCTGATCAACCAATGAAgtaagttgtt ... atgtgtgcagGATGAAGTTGAAGTTTTTATATATGTTTGCTGCTGGATTCTACACGTACTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcgatatcttttgtgatggtcatttgctaaaatatgatactgctatgtgtgcagGATGAAGTTGAAGTTTTTATATATGTTTGCTGCTGGATTCTACACGTACTCTATATTCGCGTTGGTGTTTTGGGAAACAAGACGGTCTGATTTCGGAGTT
                         tgctaaa  putative branch site (score: 2)
                      atttgctaaaatat  TA-rich tract