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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcttcttcattttctgggatttgattgaatcaatttgtaggattcgagttttgaaagttagtattcattttcgtttgtgggcagCTTGTGGAGTTTGCCACTCTGATCTTCATGTGATGAAAGGAGAGATACCGTTCGCTAGTCCTTGTGTTATTGGTCATGAGATTACTGGTGAAGTTGTTGA

Basic information

species Arabidopsis thaliana
transcript AT5G63620.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G63620.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os08g01760.1 (Oryza sativa), 3'ss of exon 1
--------------gttcttcttcattttctg-----ggatttgattgaatcaatttgtaggat---tcgagttttgaaagttagtattcattttcgtttgtgggcagCTTGTGGAGTTTGCCACTCTGATCTTCATGTGATGAAAGGAGAGATACCGTTCGCTAGTCCTTGTGTTATTGGTCATGAGATTACTGGTGAAGTTGTTGA
              |   |   || | | |||     |  |||  |||  ||  |||||  | |   |||| || |  | | |     |        | ||||  |||||||||||||||||||||| ||||| |||||  | || || ||| | || ||| | || || || ||| |||| |||||||| ||||| || ||||||||
gtcgcatcattgcagccatctatcgtctgctgctcctgcgtttctttgtttc--tttgtttgtttcctcgaattattgaggctgacgctggccca-atctgtg--cagCTTGTGGAGTTTGCCACTCCGATCTCCATGTTCTCAAGGGTGAGCTCCCATTCTCCAGCCCCTGCGTTGTTGGGCATGAGATCACTGGGGAGGTTGTTGA

upper sequence: AT5G63620.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G00740.2 (Glycine max), 3'ss of exon 2
--------------gttcttcttcattttctg-ggatttgattgaatcaatttgtaggattcgagttttgaaagttagtattcattttcgtttgtgggcagCTTGTGGAGTTTGCCACTCTGATCTTCATGTGATGAAAGGAGAGATACCGTTCGCTAGTCCTTGTGTTATTGGTCATGAGATTACTGGTGAAGTTGTTGA
                   || |  | |||   |||    ||   ||   ||| | |||   |  || | |   ||   ||  | ||  |||   | | ||| |||||||| |||||||||||||| ||||| |||||||| || || |||||  | |||||||||||| | || ||||||||||| ||||| ||||||||
agagggggctggggaagaatcatagtgttcaatggagggaatgagatgtgtttttgggaagaggtttcttattattga-atctaattgtgttatggtgtagCCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGTTTACCAGTCCTTGTGTTGTGGGGCATGAGATTACCGGTGAGGTTGTTGA

upper sequence: AT5G63620.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G33140.1 (Glycine max), 3'ss of exon 1
-----------gttcttcttcattttctgggatttgattgaatcaatttgtaggattcgag---ttttgaaagttagtattcattttcgtttgtgggcagCTTGTGGAGTTTGCCACTCTGATCTTCATGTGATGAAAGGAGAGATACCGTTCGCTAGTCCTTGTGTTATTGGTCATGAGATTACTGGTGAAGTTGTTGA
                || |  | | | | |    || |||      || |   |||  ||   |||   |   | | ||  | ||  ||||  | | ||| |||||||| |||||||||||||| ||||| |||||||| || || |||||  | |||||||||||| | || ||||||||||| ||||| ||||||||
gggggctggggaaggatcctagtgtccagtggagggaatgagatgtgtttttttattgaagaggtttcttatcattgaatctaattgtgttttggtgtagCCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGTTTTCCAGTCCTTGTGTTGTGGGGCATGAGATTACCGGTGAGGTTGTTGA

upper sequence: AT5G63620.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ12439 (Selaginella moellendorffii), 3'ss of exon 1
gttcttcttcattttctgggatttgattgaatcaatttgtaggattcgagttttgaaag-ttagtattcattttcgtttgt-gggcagCTTGTGGAGTTTGCCACTCTGATCTTCATGTGATGAAAGGAGAGATACCGTTCGCTAGTCCTTGTGTTATTGGTCATGAGATTACTGGTGAAGTTGTTGA
                                   | ||| |||||   |||| ||  | |   | |  |||| | |   | ||||||||||||||||||||||||| ||| | ||  | || ||    ||    |||||| |    ||    ||| | || || ||  | ||||| ||  | || ||
----------------------------------gtatgt-ggatt---gtttggatcgatcgatctaaatttccatggatcgggcagCTTGTGGAGTTTGCCACTCGGATTTGCACATCATCAAGAAGGATCAGCCGTTCCCCTTGCCAGTAGTTCTCGGCCACGAAGTGACTGGAGAGATCGTGGA

upper sequence: AT5G63620.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ34092 (Selaginella moellendorffii), 3'ss of exon 1
gttcttcttcattttctgggatttgattgaatcaatttgtaggattcgagttttgaaag-ttagtattcattttcgtttgt-gggcagCTTGTGGAGTTTGCCACTCTGATCTTCATGTGATGAAAGGAGAGATACCGTTCGCTAGTCCTTGTGTTATTGGTCATGAGATTACTGGTGAAGTTGTTGA
                                   | ||| |||||   |||| ||  | |   | |  |||| | |   | ||||||||||||||||||||||||| ||| | ||  | || ||    ||    |||||| |    ||    ||| | || |||||  | ||||| ||  |  | ||
----------------------------------gtatgt-ggatt---gtttggatcgatcgatctaaatttccatggatcgggcagCTTGTGGAGTTTGCCACTCGGATTTGCACATCATCAAGAAGGATCAGCCGTTCCCCTTGCCAGTAGTTCTCGGCCATGAAGTGACTGGAGAGATCATGGA

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|301502831|gb|HO208371.1|HO208371
EST:     ATTTCATATTCCCCGCCCCAAATCCAATGAAATTCTCATCAAAACCAAAG                         CTTGTGGAGTTTGCCACTCTGATCTTCATGTGATGAAAGGAGAGATACCGT
genomic: ATTTCATATTCCCCGCCCCAAATCCAATGAAATTCTCATCAAAACCAAAGgttcttcttc ... ttgtgggcagCTTGTGGAGTTTGCCACTCTGATCTTCATGTGATGAAAGGAGAGATACCGT
EST: gi|152038511|gb|AV826144.2|AV826144
EST:     ATTTCATATTCCCCGCCCCAAATCCAATGAAATTCTCATCAAAACCAAAG                         CTTGTGGAGTTTGCCACTCTGATCTTCATGTGATGAAAGGAGAGATACCGT
genomic: ATTTCATATTCCCCGCCCCAAATCCAATGAAATTCTCATCAAAACCAAAGgttcttcttc ... ttgtgggcagCTTGTGGAGTTTGCCACTCTGATCTTCATGTGATGAAAGGAGAGATACCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaatttgtaggattcgagttttgaaagttagtattcattttcgtttgtgggcagCTTGTGGAGTTTGCCACTCTGATCTTCATGTGATGAAAGGAGAGATACCGTTCGCTAGTCCTTGTGTTATTGGTCATGAGATTACTGGTGAAGTTGTTGA
                                      ttttcgttt  CT-rich tract
                            ttagtattcatttt  TA-rich tract