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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taacccggaggaaagcctgatatggtgaagtcttccacattaaataatcttcttttttctgagacatggttaaagctctgggggtgtattgtgaatgcagGCCCATATTGCACAAATATGCCAATGAAGATGTGTCTCTTGGTTCGTGGTTTATCGGTCTTGAAGTTGAGCACATTGATGAACGCAATATGTGCTGTGGG

Basic information

species Vitis vinifera
transcript Vv18s0001g04150.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g04150.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os09g27950.1 (Oryza sativa), 3'ss of exon 9
--taacccggaggaaagcctgatatggtgaagtcttccacattaaataatcttcttttttctgagacatggttaaagctctgggggtgtattgtg-aatgcagGCCCATATTGCACAAATATGCCAATGAAGATGTGTCTCTTGGTTCGTGGTTTATCGGTCTTGAAGTTGAGCACATTGATGAACGCAATATGTGCTGTGGG
   | ||  ||| |  ||   | ||| |       | || |  |||||   ||| |||| ||||    |   | |  |||| | |    |   |  ||  |||||| ||||||||||||||||| || ||||| || || |||||  | |||||||||||| | || || ||||||||||| ||  |  | ||||||||||| 
gtaagcctagagaatggctgcacatgat-----tcttcagacaaaata---ttcattttactgaattgttactgatactcttgtgtcccaccatataacccagGCCTATATTGCACAAATATGCAAACGAAGACGTTTCACTTGGCGCATGGTTTATCGGTTTAGACGTGGAGCACATTGACGACAGAGACATGTGCTGTGGA

upper sequence: Vv18s0001g04150.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G013079_T01 (Zea mays), 3'ss of exon 9
taacccggaggaaagcctgatatggtgaagtcttccacattaaataatcttcttttttctgagacatggttaaagct-ctgggggtgtattgtgaatgcagGCCCATATTGCACAAATATGCCAATGAAGATGTGTCTCTTGGTTCGTGGTTTATCGGTCTTGAAGTTGAGCACATTGATGAACGCAATATGTGCTGTGGG
              |  || |    | | ||     ||||  |  | | |   ||  ||| |        ||| | | |  | | | | || |     |||||| || |||||||||||||| |||||||| ||||| ||||| || ||||| || ||| | |||||| | |||||||||||| | || ||||||||||| 
--------------gtatgtttaattcatgttcatgacatacagaagtgtctgttcatctaaaggggaactaatgatgccagtgatat-ttat-----cagGCCTATCTTGCACAAATATGCAAATGAAGACGTGTCGCTTGGATCATGGTTCATTGGTTTGGAAGTTAATCACATTGATGAAAGGAACATGTGCTGTGGA

upper sequence: Vv18s0001g04150.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G070708_T02 (Zea mays), 3'ss of exon 9
taacccggaggaaagcctgat--atggtgaagtcttccacattaaataatcttcttttttctgagacatggttaaagctctgggggtgtattgtgaatgcagGCCCATATTGCACAAATATGCCAATGAAGATGTGTCTCTTGGTTCGTGGTTTATCGGTCTTGAAGTTGAGCACATTGATGAACGCAATATGTGCTGTGGG
          | | |  | ||   || | | | | | || |        | | | | |    |  |  |   | | |||    | |  |||| |     |||||| || ||||||||||| || || ||||| ||||| ||||| |||||||| |||||| | |||||| | ||||| |||||| | || ||||||||||| 
----------gtatgtttaattcgtgttcacgacatacaaaagggtgcctgtccatctaaagggaaactaactgatgctgcaagcg-atattttt----cagGCCTATCTTGCACAAATACGCAAACGAAGACGTGTCGCTTGGATCGTGGTTCATCGGTTTGGAAGTTAATCACATCGATGAAAGGAACATGTGCTGTGGA

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|110374940|gb|EC939886.1|EC939886
EST:     AGATTTATGCAATCTCAAAGGATCTGGCCACATACATCTCAATCAACCA                         GCCCATATTGCACAAATATGCCAATGAAGATGTGTCTCTTGGTTCGTGGTT
genomic: AGATTTATGCAATCTCAAAAGATCTGGCCACATACATCTCGATCAACCAgtaagaattg ... gtgaatgcagGCCCATATTGCACAAATATGCCAATGAAGATGTGTCTCTTGGTTCGTGGTT
EST: gi|111125070|gb|EE253689.1|EE253689
EST:     CAGATTTATGCAATCTCAAAAGATCTGGCCACATACATCTCGATCAACCA                         GCCCATATTGCACAAATATGCCAATGAAGATGTGTCTCTTGGTTCGTGGTT
genomic: CAGATTTATGCAATCTCAAAAGATCTGGCCACATACATCTCGATCAACCAgtaagaattg ... gtgaatgcagGCCCATATTGCACAAATATGCCAATGAAGATGTGTCTCTTGGTTCGTGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcttcttttttctgagacatggttaaagctctgggggtgtattgtgaatgcagGCCCATATTGCACAAATATGCCAATGAAGATGTGTCTCTTGGTTCGTGGTTTATCGGTCTTGAAGTTGAGCACATTGATGAACGCAATATGTGCTGTGGG
     tctttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taacccggaggaaagcctgatatggtgaagtcttccacattaaataatcttcttttttctgagacatggttaaagctctgggggtgtattgtgaatgcagGCCCATATTGCACAAATATGCCAATGAAGATGTGTCTCTTGGTTCGTGGTTTATCGGTCTTGAAGTTGAGCACATTGATGAACGCAATATGTGCTGTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - -agcctga
- - - - - - - - - - - - - - - -cttccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggggtg