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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtctctctatactctctgcttcgcagaaaattggaaaagtcattttcaaaagattttaaagctcttacttttgaatgactagGGAGAGGATCTGATACGCGACAGCGGGATTCCATTTGCAATTGTACGGCCATGTGCTTTAACAGAAGAGCCTGCCGGAGCTGATCTCATTTTCGAACAAG

Basic information

species Arabidopsis thaliana
transcript AT4G18810.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G18810.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv10s0003g01640.t01 (Vitis vinifera), 3'ss of exon 13
----gtttgtctctctat--actctctgcttcgcagaaaattggaaaagtcattttcaaaagattttaaagctcttacttttgaatgact--------agGGAGAGGATCTGATACGCGACAGCGGGATTCCATTTGCAATTGTACGGCCATGTGCTTTAACAGAAGAGCCTGCCGGAGCTGATCTCATTTTCGAACAAG
     |||||    | |    ||  ||     |   ||| |       |    | |  |   |||||     | ||  |      | |||        ||||||||||| ||||||| || || ||  | || | |||||||||  |||| ||||| ||||| || |||||||| ||||||||||||||||| || ||||
tgtcttttgttggccaactagctaactaggaagtgaaaactccatgtggcagctctttatttattttttcatttttcttagccggtcacttttacaacagGGAGAGGATTTGATACGGGAAAGTGGAGTGCCTTATGCAATTGTGAGGCCTTGTGCATTAACTGAGGAGCCTGCTGGAGCTGATCTCATTTTTGATCAAG
















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|124981233|gb|EL054115.1|EL054115
EST:     CCGTGAGATTAAACAAAGAGCTTGATTTCATTCTCACTTACAAGTTAAAG                         GGAGAGGATCTGATACGCGACAGCGGGATTCCA
genomic: CCGTGAGATTAAACAAAGAGCTTGATTTCATTCTCACTTACAAGTTAAAGgtttgtctct ... gaatgactagGGAGAGGATCTGATACGCGACAGCGGGATTCCA
EST: gi|125294284|gb|EL308369.1|EL308369
EST:     AGCTTGATTTCATTCTCACTTACAAGTTAAAG                         GGAGAGGATCTGATACGCGACAGCGGGATTCCATTTGCAATTGTACGGCCA
genomic: AGCTTGATTTCATTCTCACTTACAAGTTAAAGgtttgtctct ... gaatgactagGGAGAGGATCTGATACGCGACAGCGGGATTCCATTTGCAATTGTACGGCCA
EST: gi|124959116|gb|EL033820.1|EL033820
EST:     CCGTGAGATTAAACAAAGAGCTTGATTTCATTCTCACTTACAAGTTAAAG                         GGAGAGGATCTGATACGCGACAGCGGGATTCCATTTGCAATTGTACGGCCA
genomic: CCGTGAGATTAAACAAAGAGCTTGATTTCATTCTCACTTACAAGTTAAAGgtttgtctct ... gaatgactagGGAGAGGATCTGATACGCGACAGCGGGATTCCATTTGCAATTGTACGGCCA
EST: gi|116396417|gb|EG439009.1|EG439009
EST:     CCGTGAGATTAAACAAAGAGCTTGATTTCATTCTCACTTACAAGTTAAAG                         GGAGAGGATTTGATACGCGACAGCGGGATTCCATTTGCAATTGTACGGCCA
genomic: CCGTGAGATTAAACAAAGAGCTTGATTTCATTCTCACTTACAAGTTAAAGgtttgtctct ... gaatgactagGGAGAGGATCTGATACGCGACAGCGGGATTCCATTTGCAATTGTACGGCCA
EST: gi|125188883|gb|EL203837.1|EL203837
EST:     CACTTACAAGTTAAAG                         GGAGAGGATCTGATACGCGACAGCGGGATTCCATTTGCAATTGTACGGCCA
genomic: CACTTACAAGTTAAAGgtttgtctct ... gaatgactagGGAGAGGATCTGATACGCGACAGCGGGATTCCATTTGCAATTGTACGGCCA
EST: gi|116396418|gb|EG439010.1|EG439010
EST:     CCGTGAGATTAAACAAAGAGCTTGATTTCATTCTCACTTACAAGTTAAAG                         GGAGAGGATCTGATACGCGACAGCGGGATTCCATTTGCAATTGTACGGCCA
genomic: CCGTGAGATTAAACAAAGAGCTTGATTTCATTCTCACTTACAAGTTAAAGgtttgtctct ... gaatgactagGGAGAGGATCTGATACGCGACAGCGGGATTCCATTTGCAATTGTACGGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattggaaaagtcattttcaaaagattttaaagctcttacttttgaatgactagGGAGAGGATCTGATACGCGACAGCGGGATTCCATTTGCAATTGTACGGCCATGTGCTTTAACAGAAGAGCCTGCCGGAGCTGATCTCATTTTCGAACAAG
                                  ctcttac  putative branch site (score: 3)
            tcattttcaaaagatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtctctctatactctctgcttcgcagaaaattggaaaagtcattttcaaaagattttaaagctcttacttttgaatgactagGGAGAGGATCTGATACGCGACAGCGGGATTCCATTTGCAATTGTACGGCCATGTGCTTTAACAGAAGAGCCTGCCGGAGCTGATCTCATTTTCGAACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT