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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaaattttcaaatactcacggagaaagtgtctttcccagtctacctatgtagtccattcctatagaaattctgatttgaactaccacgtggcttcttatctcacctgaatcctgagatgtcttattacaaagccttgttgagtttttaaattattattttttctattcttgcagTGATCATGTTCTTGATATCTTGGTCATTCACTGTGGTTGCCATTGCACTTGCAAGTCTTATATACAAATACGTTGGCCTAAAAGGAAAGGCTGGGGACTG

Basic information

species Arabidopsis thaliana
transcript AT1G30450.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G30450.3 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA15G22520.1 (Glycine max), 3'ss of exon 10
gtatgaaattttcaaatactcacggagaaagtgtctttcccagtctacctatgtagtccattcctatagaaattctgatttga-actaccacgtggcttcttatctcacctgaatcctgagatgtcttattacaaagccttgttgagtttttaaattattattttttctattcttgcagTGATCATGTTCTTGATATCTTGGTCATTCACTGTGGTTGCCATTGCACTTGCAAGTCTTATATACAAATACGTTGGCCTAAAAGGAAAGGCTGGGGACTG
                                                                           |  ||||  | ||     | | | |||| |  ||     | |||     |  | |   |  |     ||||   || |   | |  |  |   ||    |||||||||||||||| | || |||||||||||||| |||||  |  |    |||||||| || ||||| || |||||  || | ||||||||||||||||||||
-------------------------------------------------------------------------catagtttgctattattcattaggtgcttacc--actgtggtactgc----tgctgtgtgagtgttacattgaaacttgattctgtggtgatccttacctatgcagTGATCATGTTCCTAATCTCTTGGTCATTCACCGTGGTGTCTTTGCTCCTTGCAAGCCTCATATATAAGTACGTGAGCATTAAAGGAAAGGCTGGGGACTG

upper sequence: AT1G30450.3 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv10s0003g04530.t01 (Vitis vinifera), 3'ss of exon 11
gtatgaaattttcaaatactcacggagaaagtgtctttcccagtctacctatgtagtccattcctatagaaattctgatttgaactaccacgtg-gcttcttatctcacctgaatcctgagatgtcttattacaaagccttgttgagtttttaaattattattttttctattct-tgcagTGATCATGTTCTTGATATCTTGGTCATTCACTGTGGTTGCCATTGCACTTGCAAGTCTTATATACAAATACGTTGGCCTAAAAGGAAAGGCTGGGGACTG
                                                                  | ||   ||   |  |  |     | || |  | |||   ||| || ||       | | || ||  |    | | || |        |    |  || || | || | ||||||||||||||||||||||||||||||||| ||||||||  || | || ||||||||||| |||||  | || ||  || | ||||| ||||||||||||||
------------------------------------------------------------------tggatggtcgtgtacgtgcatgtgcatgtgtgtattactccacatgcat------gtatttttttttaggatcatattta--------acagctgcttcttgtgttttgtgcagTGATCATGTTCTTGATATCTTGGTCATTTACTGTGGTGTCCCTAGCCCTTGCAAGTCTCATATATTATTATGTATGCATCAAAGGGAAGGCTGGGGACTG
















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|47829383|gb|CK119067.1|CK119067
EST:     GAAATATCATCATTGGAGCCTTTCCTTTGTTGGAGCCTCACTTTGCATAG                         TGATCATGTTCTTGATATCTTGGTCATTCACTGTGGTTGCCATTGCACTTG
genomic: GAAATATCATCATTGGAGCCTTTCCTTTGTTGGAGCCTCACTTTGCATAGgtatgaaatt ... attcttgcagTGATCATGTTCTTGATATCTTGGTCATTCACTGTGGTTGCCATTGCACTTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttattacaaagccttgttgagtttttaaattattattttttctattcttgcagTGATCATGTTCTTGATATCTTGGTCATTCACTGTGGTTGCCATTGCACTTGCAAGTCTTATATACAAATACGTTGGCCTAAAAGGAAAGGCTGGGGACTG
                                  ttattttttctattct  CT-rich tract
               ttgttgagtttttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaaattttcaaatactcacggagaaagtgtctttcccagtctacctatgtagtccattcctatagaaattctgatttgaactaccacgtggcttcttatctcacctgaatcctgagatgtcttattacaaagccttgttgagtttttaaattattattttttctattcttgcagTGATCATGTTCTTGATATCTTGGTCATTCACTGTGGTTGCCATTGCACTTGCAAGTCTTATATACAAATACGTTGGCCTAAAAGGAAAGGCTGGGGACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA