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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtcttcttagttaaaaagttgacaactttttgttttgttcttctctttagattattttgttttcttttctctctgcagGTGATTATGGAGATTCCTCTTGAACTGATGATAACCATTAGACAGAAGCACCCTTGGATGTTTTTCCCTGATATTGTACCAATTGGTCATCCTATTTTCG

Basic information

species Arabidopsis thaliana
transcript AT4G20130.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G20130.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G16830.1 (Glycine max), 3'ss of exon 3
-------------gtcagtcttcttagttaaaaagttgacaa----ctttttgttttgttcttctctttagattattttgttt-tcttttctctctgcagGTGATTATGGAGATTCCTCTTGAACTGATGATAACCATTAGACAGAAGCACCCTTGGATGTTTTTCCCTGATATTGTACCAATTGGTCATCCTATTTTCG
                ||| |  |||     |   || |  |    |||  |  ||  |   | ||  | ||| ||||   |  | || |   |  |||||| || ||||| |||||||||||| ||||| ||||||| ||  |||||| ||| ||||||||||||||||||||  | ||  | | |||||| || || |
aatgtaaggggtaaaaagtataattaagcctatgttttattatattcttaattcttaatagctgtccatggatgatttccctaatgttgtacttgggcagGTTATAATGGAAATTCCTCTTGAATTGATGTTAACCATAAGCAAGAAGCTCCCGTGGATGTTTTTCCCTGATATAATTCCCTTGGATCATCCAATATTTG

upper sequence: AT4G20130.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G05510.1 (Glycine max), 3'ss of exon 3
-------------------gtcagtcttcttagttaaaaagttgacaactttttgttttgttcttctctttagattattt-tgttttcttttctctctgcagGTGATTATGGAGATTCCTCTTGAACTGATGATAACCATTAGACAGAAGCACCCTTGGATGTTTTTCCCTGATATTGTACCAATTGGTCATCCTATTTTCG
                    | |  | | |  |||  |   ||     |||  |  ||  |   | ||  | ||| ||||   |  | || |   |  ||||||  | ||||| |||||||||||| ||||| ||||||| ||  |||||| ||| ||||||||||||||||||||  | ||  | | |||||| || || |
gttgggggtataaagtgcaatgaagcctat--gttttatgattatattcttaattcttaatagctgtccatggatgatttgcctaatgttgtacttgggcagGTTGTAATGGAAATTCCTCTTGAATTGATGTTAACCATAAGCAAGAAGCTCCCATGGATGTTTTTCCCTGATATAATTCCCTTGGATCATCCAATATTTG

upper sequence: AT4G20130.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ04899 (Selaginella moellendorffii), 3'ss of exon 1
gtcagtcttcttagttaaaaagttgacaactttttgttttgttcttctctttagattattttgttttcttttctctctgcagGTGATTATGGAGATTCCTCTTGAACTGATGATAACCATTAGACAGAAGCACCCTTGGATGTTTTTCCCTGATATTGTACCAATTGGTCATCCTATTTTCG
||  ||     | | |       ||   || |     | ||  |       |     ||  |  | ||||    |||  ||||| ||  | ||  | ||  | ||  |  |  | ||| | ||    || | |||||||||||| ||||| |||||||||||||| ||||| ||  | || |
gtgggtaagtctggattgctttctgg-gacatgaaactctgaccaaagaacttatccatccttctctctt---cctccacagGTTATACTCGAAGTACCCATGGAGATACTTGTCACCGTGAGCAGCAATCTCCCTTGGATGTTCTTCCCGGATATTGTACCAATCGGTCACCCAGTGTTTG

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|19876170|gb|AU237001.1|AU237001
EST:     GTTTTGGTGTCTATGCTTCTAAGGATATCGAACCTCGCCGTCGAGCTAGA                         GTGATTATGGAGATTCCTCTTGAACTGATGATAACCATTAGACAGAAGCAC
genomic: GTTTTGGTGTCTATGCTTCTAAGGATATCGAACCTCGCCGTCGAGCTAGAgtcagtcttc ... ctctctgcagGTGATTATGGAGATTCCTCTTGAACTGATGATAACCATTAGACAGAAGCAC
EST: gi|124992268|gb|EL064537.1|EL064537
EST:     GTTTTGGTGTCTATGCTTCTAAGGATATCGAACCTCGCCGTCGAGCTAGA                         GTGATTATGGAGATTCCTCTTGAACTGATGATAACCA
genomic: GTTTTGGTGTCTATGCTTCTAAGGATATCGAACCTCGCCGTCGAGCTAGAgtcagtcttc ... ctctctgcagGTGATTATGGAGATTCCTCTTGAACTGATGATAACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactttttgttttgttcttctctttagattattttgttttcttttctctctgcagGTGATTATGGAGATTCCTCTTGAACTGATGATAACCATTAGACAGAAGCACCCTTGGATGTTTTTCCCTGATATTGTACCAATTGGTCATCCTATTTTCG
              ttcttctctttagatt  CT-rich tract
                      tttagattattttgtt  TA-rich tract