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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATTACTTGAAGTGGTGTAAGCCCAAGAAGATCATGAACAGTGCAGAAAATTTAGGAGAGGTTCTCCGAGGTGATCGCATTGAGAATTCCATTTATACTgtgagtgttttctagaaaaagaagataaaaaaaggtctttattagatgttaccattttttatgttactgaatttatgcatatctaagtctatgaattttttcccag

Basic information

species Vitis vinifera
transcript Vv09s0002g02140.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g02140.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA08G20640.1 (Glycine max), 5'ss of exon 2
CTATTACTTGAAGTGGTGTAAGCCCAAGAAGATCATGAACAGTGCAGAAAATTTAGGAGAGGTTCTCCGAGGTGATCGCATTGAGAATTCCATTTATACTgtgagtgttttcta------------------gaaaaagaagataaaaaaaggtctttattagatgttaccattttttatgttactgaatttatgcatatctaagtctatgaattttttcccag
||| | ||||||||  || || ||||| | |||  |||||| |||||||||||| |||||||||||  |||||||||| |||||||||||  | ||||| |||||  | |  |                   | | |||| ||| |  |||  ||  |  ||  ||||  | | |||  |  |    | |  | |  | | |   | |     | |||| ||||
CTACTTCTTGAAGTATTGCAAACCCAAAACGATATTGAACAATGCAGAAAATTTGGGAGAGGTTCTTAGAGGTGATCGTATTGAGAATTCAGTATATACAgtgagcatctgttgcctcatcctttgacatttggataagatgatgatgaaat-tcagtgataattgttttcttgtttagttgtgtcaactcaaagtttttttttttttccttttctttttccag

upper sequence: Vv09s0002g02140.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA07G01240.1 (Glycine max), 5'ss of exon 2
CTATTACTTGAAGTGGTGTAAGCCCAAGAAGATCATGAACAGTGCAGAAAATTTAGGAGAGGTTCTCCGAGGTGATCGCATTGAGAATTCCATTTATACTgtgagtgttttctagaaaaa-----gaagataaaaaaaggtctttattagat---gttaccattttttatgttactgaatttatgcatatctaagtctatgaattttttcccag-----------
||| | ||||||||  || || ||||| |||||  ||||||  || |||||||| |||||||||||  ||||||||||||||||||||||  | ||||| |||||  | |  |     |      ||   |   | ||| |  | || | ||   || | ||||  ||   |   |   | | |  |  |  | || | |   | ||||||              
CTACTTCTTGAAGTATTGCAAACCCAAAAAGATATTGAACAACGCCGAAAATTTGGGAGAGGTTCTTAGAGGTGATCGCATTGAGAATTCAGTATATACAgtgagcatctgttgcttcatcctttgacatttggataagatgatgatgaaatttggtgatcattgctttcttgtttagttgtgtcaacttaaaggtttttttttcttttccttttctctttccag

upper sequence: Vv09s0002g02140.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT3G13772.1 (Arabidopsis thaliana), 5'ss of exon 2
CTATTACTTGAAGTGGTGTAAGCCCAAGAAGATCATGAACAGTGCAGAAAATTTAGGAGAGGTTCTCCGAGGTGATCGCATTGAGAATTCCATTTATACTgtgagtgttttctagaaaaagaagataaaaaaaggtctttattagatgttaccattttttatgttactgaatttatgcatatctaagtctatgaattttttcccag
||| ||| |||| |  ||||||||    |||||| |||||| ||| || |||||||| ||||||||| ||||||| ||||||||||||||| |||||||||| ||  ||  |   |         | | |     ||   || |||||||  | ||| | |    |   |||||  |                             
CTACTACCTGAATTACTGTAAGCCTCCTAAGATCTTGAACAATGCTGAGAATTTAGGGGAGGTTCTCAGAGGTGACCGCATTGAGAATTCCGTTTATACTgtaagcattaccccaattcttctacttacacctcttcaccatgagatgttgacttttctgaaacaaaaaaatttcag-----------------------------

upper sequence: Vv09s0002g02140.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT1G55130.1 (Arabidopsis thaliana), 5'ss of exon 2
CTATTACTTGAAGTGGTGTAAGCCCAAGAAGATCATGAACAGTGCAGAAAATTTAGGAGAGGTTCTCCGAGGTGATCGCATTGAGAATTCCATTTATACTgtgagtgttttctagaaaaagaagataaaaaaaggtctttattagatgttaccattttttatgttactgaatttatgcatatctaagtctatgaattttttcccag
||| ||| |||| |  ||||||||   ||||||| |||| |  |  |||||||| || ||||||||| |||| |||||||||||||||||  |||||||||| ||                       ||||   | |  |||  || ||   |  ||      |  | |  | |||      | || || || ||| | |  |||
CTACTACCTGAATTACTGTAAGCCTCCGAAGATCTTGAATACCGGCGAAAATTTGGGGGAGGTTCTCAGAGGAGATCGCATTGAGAATTCGGTTTATACTgtaagc----------------------aaaactctgtccatttcatctttgtaccttaatctctcatcatctgatgt-----tgagactttggattctgtttcag

upper sequence: Vv09s0002g02140.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: PP1S140_64V6.1 (Physcomitrella patens), 5'ss of exon 2
CTATTACTTGAAGTGGTGTAAGCCCAA---GAAGATCATGAACAGTGCAGAAAATTTAGGAGAGGTTCTCCGAGGTGATCGCATTGAGAATTCCATTTATACTgtgagtgttttctagaaaaagaa---gataaaaaaaggtctttatta-gatgttaccat--tttttatgttactgaatttatgcatatctaagtctatgaattttttcccag
   |  |||||  |  || ||||| |       |||  |||||||||| || || || ||||||||||| |||||||||||||||||||| ||   |||   |||  ||  | |||     ||      | |  | | |  |||||      ||||||  ||     ||  |||   |  |||||     | || || |||  || |        
--CTCGCTTGAC-TACTGCAAGCCAAGTTCAGGGATTGTGAACAGTGCCGAGAACTTGGGAGAGGTTCTTCGAGGTGATCGCATTGAGAACTCACCTTACGTTgtacgtaatctctgagccaaagtcttggtgcacataattcttttcagcaatgttagtataccccttgagttgaaggctttatat---tgtacgt-tatacatct--------

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|110691298|gb|EE069240.1|EE069240
EST:     ATTTAGGAGAGGTTCTCCGAGGTGATCGCATTGAGAATTCCATTTATACT                         TTCCAAATGAGGGAAGGGCAGCCATGCAAAGTGGCTTGTCGAATGCATCTT
genomic: ATTTAGGAGAGGTTCTCCGAGGTGATCGCATTGAGAATTCCATTTATACTgtgagtgttt ... tttttcccagTTCCAAATGAGGGAAGGGCAGCCATGCAAAGTGGCTTGTCGAATGCATCTT
EST: gi|71862773|gb|DT011828.1|DT011828
EST:     ATTTAGGAGAGGTTCTCCGAGGTGATCGCATTGAGAATTCCATTTATACT                         TTCCAAATGAGGGAAGGGCAGCCATGCAAAGTGGCTTGTCGAATGCATCTT
genomic: ATTTAGGAGAGGTTCTCCGAGGTGATCGCATTGAGAATTCCATTTATACTgtgagtgttt ... tttttcccagTTCCAAATGAGGGAAGGGCAGCCATGCAAAGTGGCTTGTCGAATGCATCTT
EST: gi|351033128|gb|FQ446481.1|FQ446481
EST:     ATTTAGGAGAGGTTCTCCGAGGTGATCGCATTGAGAATTCCATTTATACT                         TTCCAAATGAGGGAAGGGCAGCCATGCAAAGTGGCTTGTCGAATGCATCTT
genomic: ATTTAGGAGAGGTTCTCCGAGGTGATCGCATTGAGAATTCCATTTATACTgtgagtgttt ... tttttcccagTTCCAAATGAGGGAAGGGCAGCCATGCAAAGTGGCTTGTCGAATGCATCTT
EST: gi|71865270|gb|DT014325.1|DT014325
EST:     ATTTAGGAGAGGTTCTCCGAGGTGATCGCATTGAGAATTCCATTTATACT                         TTCCAAATGAGGGAAGGGCAGCCATGCAAAGTGGCTTGTCGAATGCATCTT
genomic: ATTTAGGAGAGGTTCTCCGAGGTGATCGCATTGAGAATTCCATTTATACTgtgagtgttt ... tttttcccagTTCCAAATGAGGGAAGGGCAGCCATGCAAAGTGGCTTGTCGAATGCATCTT
EST: gi|351030399|gb|FQ432337.1|FQ432337
EST:     ATTTAGGAGAGGTTCTCCGAGGTGATCGCATTGAGAATTCCATTTATACT                         TTCCAAATGAGGGAAGGGCAGCCATGCAAAGTGGCTTGTCGAATGCATCTT
genomic: ATTTAGGAGAGGTTCTCCGAGGTGATCGCATTGAGAATTCCATTTATACTgtgagtgttt ... tttttcccagTTCCAAATGAGGGAAGGGCAGCCATGCAAAGTGGCTTGTCGAATGCATCTT
EST: gi|349833072|gb|FQ416450.1|FQ416450
EST:     ATTTAGGAGAGGTTCTCCGAGGTGATCGCATTGAGAATTCCATTTATACT                         TTCCAAATGAGGGAAGGGCAGCCATGCAAAGTGGCTTGTCGAATGCATCTT
genomic: ATTTAGGAGAGGTTCTCCGAGGTGATCGCATTGAGAATTCCATTTATACTgtgagtgttt ... tttttcccagTTCCAAATGAGGGAAGGGCAGCCATGCAAAGTGGCTTGTCGAATGCATCTT
EST: gi|34546863|gb|CF515095.1|CF515095
EST:     ATTTGGGAGAGGTTCTCCGAGGTGATCGCATTGAGAATTCCATTTATACT                         TTCCAAATGAGGGAAGGGCAGCCATGCAAAGTGGCTTGTCGAATGCATCTT
genomic: ATTTAGGAGAGGTTCTCCGAGGTGATCGCATTGAGAATTCCATTTATACTgtgagtgttt ... tttttcccagTTCCAAATGAGGGAAGGGCAGCCATGCAAAGTGGCTTGTCGAATGCATCTT
EST: gi|161713929|gb|FC062883.1|FC062883
EST:     ATTTAGGAGAGGTTCTCCGAGGTGATCGCATTGAGAATTCCATTTATACT                         TTCCAAATGAGGGAAGGGCAGCCATGCAAAGTGGCTTGTCGAATGCATCTT
genomic: ATTTAGGAGAGGTTCTCCGAGGTGATCGCATTGAGAATTCCATTTATACTgtgagtgttt ... tttttcccagTTCCAAATGAGGGAAGGGCAGCCATGCAAAGTGGCTTGTCGAATGCATCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATTACTTGAAGTGGTGTAAGCCCAAGAAGATCATGAACAGTGCAGAAAATTTAGGAGAGGTTCTCCGAGGTGATCGCATTGAGAATTCCATTTATACTgtgagtgttttctagaaaaagaagataaaaaaaggtctttattagatgttaccattttttatgttactgaatttatgcatatctaagtctatgaattttttcccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG