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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcataaattcaaaagataattttatttccttctctctggcttctaagaaaagttaaatcgaccatctgagtgtttccatgtttggttttctaattgcagCTAGTAAAGCTGAATCTACACCCTGATGCAAAAGGCTCATATGTAGAAGTCTTGGAAAGGTATATCAACTTGGGGCCTATTGTCGACTTTTGTGTAGTTG

Basic information

species Arabidopsis thaliana
transcript AT4G05420.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G13680.1 (Glycine max), 3'ss of exon 11
-agcataaattcaaaagataattttatttccttctctctggcttctaagaaaagttaaatcgaccatctgagtgtttccatgtttggttttctaattgcagCTAGTAAAGCTGAATCTACACCCTGATGCAAAAGGCTCATATGTAGAAGTCTTGGAAAGGTATATCAACTTGGGGCCTATTGTCGACTTTTGTGTAGTTG
    | |  ||  ||   || | |    |     |  |||  | || |         | ||   |||   |   |  | || | || |  |  ||| ||||||| |||| || |||||||| |||||||||||||| || ||||| ||||| |||||||||||| |||| |||||||||||||| ||||| ||||| || |
ttaaagactttggaagtgtagtatggcatatccatagctgaatacttatgcttacatattcagacataacatattgacaatctctgatggtaaaat-gcagCTAATAAAACTAAATCTACAGCCTGATGCAAAAGGTTCTTATGTGGAAGTATTGGAAAGGTATGTCAATTTGGGGCCTATTGTTGACTTCTGTGTGGTAG

upper sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 11
-agcataaattcaaaagataattttatttccttctctctggcttctaagaaaagttaaatcgaccatctgagtgtttccatgtttggttttctaattgcagCTAGTAAAGCTGAATCTACACCCTGATGCAAAAGGCTCATATGTAGAAGTCTTGGAAAGGTATATCAACTTGGGGCCTATTGTCGACTTTTGTGTAGTTG
    |    ||  ||   || | |    |     |  |||  | || |         | ||   |||   |   |  | || | || | ||  ||| ||||||| |||| || |||||||| |||||||||||||| || ||||||||||   ||||||||||| | || |||||||||||||| ||||| ||||| || |
ttaaagtctttggaagtgtagtatggcatatccattgctgaatacttatgcttacatattcagacataacatattgacaatctctgatgttaaaat-gcagCTAATAAAACTAAATCTACAGCCTGATGCAAAAGGTTCTTATGTAGAAGGACTGGAAAGGTATGTAAATTTGGGGCCTATTGTTGACTTCTGTGTGGTAG
















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|116456285|gb|EG498877.1|EG498877
EST:     ACCTTGACAATGCCGTTGTCTTTGTCGGCTCAAGCTATGGTGATTCACAG                         CTAGTAAAGCTGAATCTACACCCTGATGCAAAAGGCTCATATGTAGAAGTC
genomic: ACCTTGACAATGCCGTTGTCTTTGTCGGCTCAAGCTATGGTGATTCACAGgtatgctaga ... ctaattgcagCTAGTAAAGCTGAATCTACACCCTGATGCAAAAGGCTCATATGTAGAAGTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaaaagttaaatcgaccatctgagtgtttccatgtttggttttctaattgcagCTAGTAAAGCTGAATCTACACCCTGATGCAAAAGGCTCATATGTAGAAGTCTTGGAAAGGTATATCAACTTGGGGCCTATTGTCGACTTTTGTGTAGTTG
                                           ttctaat  putative branch site (score: 2)
                                         ttttct  CT-rich tract
                                         ttttctaatt  TA-rich tract