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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtctctatcttcattgcatgatttcatctaatatctatttgcttctttacccttaaaagctttgtgtctattgttttgacagCCTCATGTAGTCCGTTTGGATCGTCACACTCTTAAACTTTTGAAATACTGGACATGGCAATTTGTGGTCATTCGACCCGTGTGCTCCACTTTGATGATAG

Basic information

species Arabidopsis thaliana
transcript AT4G21570.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G21570.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv00s0404g00020.t01 (Vitis vinifera), 3'ss of exon 3
-gttcgtctctatcttcattgcatgatttcatctaata---tctatttgct-tctttacccttaaaag----ctttgtgtctattgttttga------cagCCTCATGTAGTCCGTTTGGATCGTCACACTCTTAAACTTTTGAAATACTGGACATGGCAATTTGTGGTCATTCGACCCGTGTGCTCCACTTTGATGATAG
  ||| | | ||| | ||   ||    || ||   | |   | | |  | | ||  ||    || |||      |      | | ||| | |      |||||||     |||||| ||||||  || || || || ||| | ||||| ||||||||||| ||||| ||||| || || || ||||||| |||||||||| 
gattcatatgtat-tccaaaacacatatttataagacaagctttgtgagttctcgatatggctagaagaatatctgacacttgtggttctaaaaactgcagCCTCGAACCGTCCGTCTGGATCACCATACACTGAAGCTTCTCAAATATTGGACATGGCAGTTTGTTGTCATCCGTCCTGTATGCTCCATTTTGATGATAA

upper sequence: AT4G21570.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ26085 (Selaginella moellendorffii), 3'ss of exon 2
gttcgtctctatcttcattgcatgatttcatctaatatctatttgcttctttacccttaaaagc-tttgtgtctattgttttgacagCCTCATGTAGTCCGTTTGGATCGTCACACTCTTAAACTTTTGAAATACTGGACATGGCAATTTGTGGTCATTCGACCCGTGTGCTCCACTTTGATGATAG
                   | |||  |||  ||  | |||  |   ||    || ||| | ||  ||| | |   ||  ||    ||||||| | ||| |   |  | |  ||||||||||| ||| | |||| ||||||||||||||| ||| ||||||| || |||   ||||   | |||||  
-------------------gtatg--ttcgcct--tctctggtgctttggagactcttgatagtatttcttttctttccttccttagCCTCACGAAGTTCCGCTCAACCAACACACTCTTAAGCTTCTCAAATCCTGGACATGGCAATTCGTGATCATTCGTCCGGTGCTATCCATCCTCATGATCT
















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|301501540|gb|HO207080.1|HO207080
EST:     GAATCAAAGGAAGAGAGATTCACCATTCTTTCCCAATGACTCTTTTTCAG                         CCTCATGTAGTCCGTTTGGATCGTCACACTCTTAAACTTTTGAAATACTGG
genomic: GAATCAAAGGAAGAGAGATTCACCATTCTTTCCCAATGACTCTTTTTCAGgttcgtctct ... gttttgacagCCTCATGTAGTCCGTTTGGATCGTCACACTCTTAAACTTTTGAAATACTGG
EST: gi|125045048|gb|EL117317.1|EL117317
EST:     TCTTTTTCTAG                         CCTCATGTAGTCCGTTTGGATCGTCACACTCTTAAACTTTTGAAATACTG
genomic: TCTTTTTC-AGgttcgtctct ... gttttgacagCCTCATGTAGTCCGTTTGGATCGTCACACTCTTAAACTTTTGAAATACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaatatctatttgcttctttacccttaaaagctttgtgtctattgttttgacagCCTCATGTAGTCCGTTTGGATCGTCACACTCTTAAACTTTTGAAATACTGGACATGGCAATTTGTGGTCATTCGACCCGTGTGCTCCACTTTGATGATAG
 atctaat  putative branch site (score: 3)
                                           ttgtttt  putative PPT
                                         tattgtttt  TA-rich tract