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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataaagccattactcaaaactcaaacctttcattggttttgtccagtttctaatcatatcttctcatatatgtagGATTTCATCTACGAGGAAGAGCTCCAGCGATTTGTTGAGAGTGGTGCTCTCGCAGAGCTAAGTGTCGCCTTCTCTCGTGAAGGACCCACCAAAGAATACG

Basic information

species Arabidopsis thaliana
transcript AT4G30210.2
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G30210.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv11s0052g00880.t01 (Vitis vinifera), 3'ss of exon 15
gtaataaagccattactcaaaact-----caaacctttcattggttt-tgtccagt------ttctaatcatatcttctcatatat--gtagGATTTCATCTACGAGGAAGAGCTCCAGCGATTTGTTGAGAGTGGTGCTCTCGCAGAGCTAAGTGTCGCCTTCTCTCGTGAAGGACCCACCAAAGAATACG
||||   || |  || || |   |     ||||  |  |  |  ||| |||| | |       | ||||  | | | ||  ||| |  | |||| | ||| || || || |||||  |  | ||||||||   |||||| ||| ||||||| | ||| || ||||| ||||||||||||||||| ||||| |
gtaagtcagaccctaatctattttatgaacaaatgtggctatattttgtgtcaaatgtgaaactttaattttgtgtgcttctatctttgcagGACTACATTTATGAAGATGAGCTGAATGGCTTTGTTGAATCTGGTGCGCTCTCAGAGCTGATTGTTGCTTTCTCACGTGAAGGACCCACCAAGGAATATG
















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|86044357|gb|DR340112.1|DR340112
EST:     TTGAACTTGGGCCATCAGTTTTGTTCTTTGGATGCAGAAACCGTAGAATG                         GATTTCATCTACGAGGAAGAGCTCCAGCGATTTTGGTGAGAGTGGTGCTCT
genomic: TTGAACTTGGGCCATCAGTTTTGTTCTTTGGATGCAGAAACCGTAGAATGgtaataaagc ... atatatgtagGATTTCATCTACGAGGAAGAGCTCCAGCGATTT-GTTGAGAGTGGTGCTCT
EST: gi|116436419|gb|EG479011.1|EG479011
EST:     TTGAACTTGGGCCATCAGTTTTGTTCTTTGGATGCAGAAACCGTAGAATG                         GATTTCATCTACGAGGAAGAGCTCCAGCGATTTGTTGAGAGTGGTGCTCTC
genomic: TTGAACTTGGGCCATCAGTTTTGTTCTTTGGATGCAGAAACCGTAGAATGgtaataaagc ... atatatgtagGATTTCATCTACGAGGAAGAGCTCCAGCGATTTGTTGAGAGTGGTGCTCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaacctttcattggttttgtccagtttctaatcatatcttctcatatatgtagGATTTCATCTACGAGGAAGAGCTCCAGCGATTTGTTGAGAGTGGTGCTCTCGCAGAGCTAAGTGTCGCCTTCTCTCGTGAAGGACCCACCAAAGAATACG
                           ttctaat  putative branch site (score: 2)
                                      tcttctcat  putative PPT
                              taatcatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataaagccattactcaaaactcaaacctttcattggttttgtccagtttctaatcatatcttctcatatatgtagGATTTCATCTACGAGGAAGAGCTCCAGCGATTTGTTGAGAGTGGTGCTCTCGCAGAGCTAAGTGTCGCCTTCTCTCGTGAAGGACCCACCAAAGAATACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA