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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcattattattttttcattttccttatttttttaattcttccctttccttccttttttttcctttccgtgactcaacattgtcacttgtcacttatgtagATAGTAAACTGGAGAACTCATCTAAAATTTCCAGAAGAAGCAAAGTTATCTCCAGAAGCAAAGGACCTTATTAGTAAGCTCTTATGTAATGTTGACCAGA

Basic information

species Vitis vinifera
transcript Vv05s0049g01220.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 7
--gcatt-attattttttcattttccttatttttttaattcttccctttccttccttttttttcctttccgtgactcaacat-tgtcacttgtcacttatgtagATAGTAAACTGGAGAACTCATCTAAAATTTCCAGAAGAAGCAAAGTTATCTCCAGAAGCAAAGGACCTTATTAGTAAGCTCTTATGTAATGTTGACCAGA
  |  |  || ||  || | |||   |  ||  ||||   ||    |||| ||  | ||| |   ||    | |      || ||  || | |||    || |||||||||| ||||||| | || ||||||||||||||||||  ||  | ||  ||||||||||||| ||||||||||  ||| |||||||||| |||||||
aagtgtccatcatgattccctttatgtctttccttta---ctgtattttcttttatctttatcaattatgatcatattgtatctgatacct-tcaaacttgcagATAGTAAATTGGAGAAGTTATTTAAAATTTCCAGAAGAAGTTAAACTTTCGGCAGAAGCAAAGGATCTTATTAGTAGACTCCTATGTAATGTGGACCAGA

upper sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 7
------gcattattattttttcattttccttatttttttaattcttccctttccttccttttttttcctttccgtgactcaacattgtcacttgtcacttatgtagATAGTAAACTGGAGAACTCATCTAAAATTTCCAGAAGAAGCAAAGTTATCTCCAGAAGCAAAGGACCTTATTAGTAAGCTCTTATGTAATGTTGACCAGA
       ||| || |||   |   | || ||  |||  |   | |||  ||  |||| |   || |  | |   ||  ||     ||  || | | | || || |||||||||| ||||||| | || ||||||||||||||||||  ||  | ||  ||||||||||||| ||||||||||  ||| |||||||||| || ||||
acatatccatcatgattccctttatgtctttcctttactgtattttcttttatcttcatcaattatgatcttattgtatc-----tgatacctttaaatt-tgcagATAGTAAATTGGAGAAATTATTTAAAATTTCCAGAAGAAGTTAAAATTTCGGCAGAAGCAAAGGATCTTATTAGTAGACTCCTATGTAATGTGGATCAGA

upper sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 7
gcattattattttttcattttccttattttttta-attcttccctttccttccttttttttcctttccg----tgactcaacattgtcacttgtcacttatgtagATAGTAAACTGGAGAACTCATCTAAAATTTCCAGAAGAAGCAAAGTTATCTCCAGAAGCAAAGGACCTTATTAGTAAGCTCTTATGTAATGTTGACCAGA
     || || | | ||| ||  ||  |||  |  |||| |    ||   || |||||| || |   |     |||    |  ||    |   |    || | ||||||||||||||||||||  | |||| |||||||||||||| ||  | ||  |||| |||||||| |||||| |||  ||| |||||||||| || ||||
-----ataatgtgtccatgttgattgctttaatggattccttttattgtatcattttttgtcttcatcaattatgatcttattttacttcaccttcaatacgcagATAGTAAACTGGAGAACTACTTTAAAGTTTCCAGAAGAAGCTAAACTTTCAGCAGAGGCAAAGGATCTTATTTGTAGACTCCTATGTAATGTGGAGCAGA

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|71879891|gb|DT028946.1|DT028946
EST:     TGGGATATCCACCTTTTTATTCAGATGAACCTATGACAACTTGTAGGAAG                         ATAGTAAACTGGAGAACTCATCTAAAATTTCCAGAAGAAGCAAAGTTATCT
genomic: TGGGATATCCACCTTTTTATTCAGATGAACCTATGACAACTTGTAGGAAGgtagttcttg ... acttatgtagATAGTAAACTGGAGAACTCATCTAAAATTTCCAGAAGAAGCAAAGTTATCT
EST: gi|71878386|gb|DT027441.1|DT027441
EST:     TGGGATATCCACCTTTTTATTCAGATGAACCTATGACAACTTGTAGGAAG                         ATAGTAAACTGGAGAACTCATCTAAAATTTCCAGAAGAAGCAAAGTTATCT
genomic: TGGGATATCCACCTTTTTATTCAGATGAACCTATGACAACTTGTAGGAAGgtagttcttg ... acttatgtagATAGTAAACTGGAGAACTCATCTAAAATTTCCAGAAGAAGCAAAGTTATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccttccttttttttcctttccgtgactcaacattgtcacttgtcacttatgtagATAGTAAACTGGAGAACTCATCTAAAATTTCCAGAAGAAGCAAAGTTATCTCCAGAAGCAAAGGACCTTATTAGTAAGCTCTTATGTAATGTTGACCAGA
       tttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcattattattttttcattttccttatttttttaattcttccctttccttccttttttttcctttccgtgactcaacattgtcacttgtcacttatgtagATAGTAAACTGGAGAACTCATCTAAAATTTCCAGAAGAAGCAAAGTTATCTCCAGAAGCAAAGGACCTTATTAGTAAGCTCTTATGTAATGTTGACCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacttgt