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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGGAAATAAGAACAAATGCTTTAAAGCTTTTGGTGACACTTCGAAGACCTCTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGTTAAACATCTGGCAGgtacaatggatagcaagaaaataacgattttatatcactgtttttatctgagtgaattgagtgatttctttcttctgtgtttcag

Basic information

species Arabidopsis thaliana
transcript AT1G73020.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G73020.2 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: Vv09s0002g02590.t01 (Vitis vinifera), 5'ss of exon 14
AATGGAAATAAGAACAAATGCTTTAAAGCTTTTGGTGACACTTCGAAGACCTCTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGTTAAACATCTGGCAGgta-----caatggat---agcaagaaaa-taacgattttatatcact-gtttttatctgagtgaattgagtgatttctt----tcttctgtgtttcag-
||  ||||| ||| || ||||  | |||||  | |  |   |    || ||  |||||||||||||||||||||||||||||||| | |||||||  ||||||     |  | | |    ||  ||||| ||  |   | |  ||||| | || ||  |    |  |  | || | | ||    | ||    ||  ||  
AACAGAAATCAGAGCAGATGCGCTGAAGCTGCTTGCCATGTTGAAGAGGCCAGTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGCTTAACATCTTTCAGgtatttgtcttttgttttgggcttgaaaagtattgtcatcaattcacttggttataattactagtttccaatggtgttttaacatgtttcccgtgccacc
















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|116436487|gb|EG479079.1|EG479079
EST:     CTCTTCCCCGTGCTGCTGCAACAATTGGAGCTTGGTTAAACATCTGGCAG                         TTTCTAGTAGTTATGTCCATATGCACAAACTCGGCACTCTTGGTATGCTTA
genomic: CTCTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGTTAAACATCTGGCAGgtacaatgga ... tgtgtttcagTTTCTAGTAGTTATGTCCATATGCACAAACTCGGCACTCTTGGTATGCTTA
EST: gi|86080135|gb|DR375892.1|DR375892
EST:     CTCTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGTTAAACATCTGGCAG                         TTTCTAGTAGTTATGTCCATATGCACAAACTCGGCACTCTTGGTATGCTTA
genomic: CTCTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGTTAAACATCTGGCAGgtacaatgga ... tgtgtttcagTTTCTAGTAGTTATGTCCATATGCACAAACTCGGCACTCTTGGTATGCTTA
EST: gi|116436490|gb|EG479082.1|EG479082
EST:     CTCTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGTTAAACATCTGGCAG                         TTTCTAGTAGTTATGTCCATATGCACAAACTCGGCACTCTTGGTATGCTTA
genomic: CTCTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGTTAAACATCTGGCAGgtacaatgga ... tgtgtttcagTTTCTAGTAGTTATGTCCATATGCACAAACTCGGCACTCTTGGTATGCTTA
EST: gi|116436480|gb|EG479072.1|EG479072
EST:     CTCTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGTTAAACATCTGGCAG                         TTTCTAGTAGTTATGTCCATATG
genomic: CTCTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGTTAAACATCTGGCAGgtacaatgga ... tgtgtttcagTTTCTAGTAGTTATGTCCATATG
EST: gi|116436489|gb|EG479081.1|EG479081
EST:     CTCTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGTTAAACATCTGGCAG                         TTTCTAGTAGTTATGTCCATATGCACAAACTCGGCACTCTTGGTATGCTTA
genomic: CTCTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGTTAAACATCTGGCAGgtacaatgga ... tgtgtttcagTTTCTAGTAGTTATGTCCATATGCACAAACTCGGCACTCTTGGTATGCTTA
EST: gi|116436474|gb|EG479066.1|EG479066
EST:     CTCTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGTTAAACATCTGGCAG                         TTTCTAGTAGTTATGTCCATATGCACAAACTCGGCACTCTTGGTATGCTTA
genomic: CTCTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGTTAAACATCTGGCAGgtacaatgga ... tgtgtttcagTTTCTAGTAGTTATGTCCATATGCACAAACTCGGCACTCTTGGTATGCTTA
EST: gi|116436481|gb|EG479073.1|EG479073
EST:     CTCTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGTTAAACATCTGGCAG                         TTTCTAGTAGTTATGTCCATATGCACAAACTCGGCACTCTTGGTATGCTTA
genomic: CTCTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGTTAAACATCTGGCAGgtacaatgga ... tgtgtttcagTTTCTAGTAGTTATGTCCATATGCACAAACTCGGCACTCTTGGTATGCTTA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGGAAATAAGAACAAATGCTTTAAAGCTTTTGGTGACACTTCGAAGACCTCTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGTTAAACATCTGGCAGgtacaatggatagcaagaaaataacgattttatatcactgtttttatctgagtgaattgagtgatttctttcttctgtgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT