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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccttagatatgcaaacatgttttaggatgtctcagttttctgtatctttattagtctcctcaaagtaaagcattgaaaggctgtgtttccgtaactgtataaattagATATGATATCATAGTCGATGCGACTGATAATCCTCCAAGCCGTTACATGATCAGTGATTGTTGTGTCTTGTTAGGAAAG

Basic information

species Arabidopsis thaliana
transcript AT5G55130.1
intron # 5
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G55130.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G46300.1 (Glycine max), 3'ss of exon 5
--gtatccttagatatgcaaacatgttttaggatgtctcag------ttttctgtatctttattagtctc-ctcaaagtaaagcattgaaa--ggctgtgtttccgt-----aactgtataaatt----agATATGATATCATAGTCGATGCGACTGATAATCCTCCAAGCCGTTACATGATCAGTGATTGTTGTGTCTTGTTAGGAAAG
   ||   |||   |    |      |||    |  ||||       |||  | |||  |||    | ||  |  || |  || |||   |  | || | |||||       || | | | ||||    ||||||||||| ||||| ||||| || |||||| |||| | ||| ||| ||||||||||||| |||||  |  | ||||||
gtataattttaataacaagattgatctttctttttgctcaaggcctctttcttctatgcttacctttttcatttcaatttgagtattaccactgactttttttccccttctgaattatgtgaatttggtagATATGATATAATAGTAGATGCAACAGATAATGCTCCTACCCGGTACTTGATCAGTGATTGCTGTGTGGTCCTTGGAAAG

upper sequence: AT5G55130.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA14G02410.1 (Glycine max), 3'ss of exon 4
---------gtatccttagatatgcaaacatgttt-taggatgtctcagttttctgtat----ctttattagtctcctcaaagtaaagcattgaaaggctgtgtttccgtaactgtataaatt----agATATGATATCATAGTCGATGCGACTGATAATCCTCCAAGCCGTTACATGATCAGTGATTGTTGTGTCTTGTTAGGAAAG
          |||  | ||||         | |||    || | |||  | |||| ||     | || ||  | || |     || |  |        |  | |||   ||| | | | ||||    ||||||||||| ||||| ||||| || |||||| |||| | ||| ||| ||||||||||||| |||||  |  ||||||||
gtataatttctattataagattgatttttctttttgcttgaggcctctttcttctatacttaacctttttcatttcattttt-tatattaccactgaccattttttttataattatgtgaatttggtagATATGATATAATAGTAGATGCAACAGATAATGCTCCTACCCGATACTTGATCAGTGATTGCTGTGTGGTTCTAGGAAAG
















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|164180680|gb|ES118056.1|ES118056
EST:     GGAAATCCTCAGCCA                         ATATGATATCATAGTCGATGCGACTGATAATCCTCCAAGCCGTTACATGAT
genomic: GGAAATCCTCAGCCAgtatccttag ... tataaattagATATGATATCATAGTCGATGCGACTGATAATCCTCCAAGCCGTTACATGAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtctcctcaaagtaaagcattgaaaggctgtgtttccgtaactgtataaattagATATGATATCATAGTCGATGCGACTGATAATCCTCCAAGCCGTTACATGATCAGTGATTGTTGTGTCTTGTTAGGAAAG
 ttccgtaac  putative branch site 
                                       taactgtataaatta  TA-rich tract