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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatttatttatttatttatttgaatcattattatttagcaatttagggttattattcatctctggcttactccaatattttgtcttaatttctcaaaaagGCTGAGATGCCTGCGGATAGTGGCTATCCTGCTTATTTGGCAGCACGTTTAGCCTCTTTCTATGAGCGCGCTGGCAAAGTGAAATGTCTGGGTGGACCAG

Basic information

species Vitis vinifera
transcript Vv09s0054g00890.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 12
--tatttatttatttatttatttgaatcattattatttagcaatttagggttattattcatctctggctt--actccaatattttgtcttaatttctcaaaaagGCTGAGATGCCTGCGGATAGTGGCTATCCTGCTTATTTGGCAGCACGTTTAGCCTCTTTCTATGAGCGCGCTGGCAAAGTGAAATGTCTGGGTGGACCAG
  ||   | ||||||    | | |||       |   |||| | |||  | | ||| ||  | ||    |  | |  ||  |  ||  || ||   |    | |||||| ||||||||||||||||| || ||||| |||||||| |||||||| || || || || || || ||||| || ||||||||||| ||  | ||||
actaggaaattatttgg--agtcgaaagtgctctcgctagctagttactgct-ttactctgcactaatatgaatttgaaactgatgatttgatcaatttcca-gGCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTGGCATCCTTTTACGAACGTGCTGGTAAGGTGAAATGTCTCGGCAGTCCAG

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 12
tatttatttatttatttatttgaatcattattatttagcaatttagggttatt----attcatctctggct--tactccaat--attttgtcttaatttc-tcaaaaagGCTGAGATGCCTGCGGATAGTGGCTATCCTGCTTATTTGGCAGCACGTTTAGCCTCTTTCTATGAGCGCGCTGGCAAAGTGAAATGTCTGGGTGGACCAG
         | |||    ||   ||  |||| | | |    | | |  || ||    ||  || |   | |  || || |||      || |  | |||  | |   ||||||| |||||||| |||||||| || |||||||||||||| ||| |  | || ||||||||||| || ||||| ||||| |  ||||| ||  | ||| 
---------acttaaaagttaagattgttataactcattcgtgttgattttttgaatatctattttatgttaatattctaatgggcaatgccacatttttgttatccagGCTGAAATGCCTGCAGATAGTGGTTACCCTGCTTATTTGGCTGCAAGACTGGCATCTTTCTATGAACGTGCTGGTAAAGTAAGGTGTCTTGGAAGTCCAA

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 12
---tatttatttatttatttatttgaatcattattatttagcaatttagggttattattcatct-ctggcttactccaatattt-tgtcttaatttctcaaaaagGCTGAGATGCCTGCGGATAGTGGCTATCCTGCTTATTTGGCAGCACGTTTAGCCTCTTTCTATGAGCGCGCTGGCAAAGTGAAATGTCTGGGTGGACCAG
   |||  | |  |||     | ||  |  || |  || | || |||    | |   |   ||| ||||  | | | | || |  ||   |  |||||     ||||||| |||||||| |||||||| || || ||||| ||||| |||||||| || || || ||||| || ||||| || || |||||||||||  | ||||
taatatgaaatactttgaacttctgttttgttgt-gttgatcatttt----tcacattctgtctgctggacttcacaactaatggtgcacttttttctggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTGGCATCCTTTTATGAACGTGCTGGTAAGGTAAAATGTCTGGGAAGTCCAG

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 13
---------------------------------------------------------------------tatttatttatttatttatttgaatcattattatttagcaatttagggttattattcatctctggcttactcca-atattttg----tcttaatttctcaaaaagGCTGAGATGCCTGCGGATAGTGGCTATCCTGCTTATTTGGCAGCACGTTTAGCCTCTTTCTATGAGCGCGCTGGCAAAGTGAAATGTCTGGGTGGACCAG
                                                                     | ||| || | |  ||||  |  |  |||  |||      |   | |      ||     |     ||  || |  |||||||    | ||  | |||   | |||| || |||||||| |||||||| |||||||| ||  | || ||||||||||||||||||||||| || ||||| || || |||||||| || || || |
gtgagaaagatttattttttgtgcttaaaatacatatattttgtagccttactttatgatattgaactttctttcttgactagtttaactagacaatttatataccattaggcatgagacacatgggaatggacattgatcaatgtattttgatgatattgttgtcttccacagGCAGAAATGCCTGCAGATAGTGGATATCCTGCATACCTTGCTGCACGTTTAGCCTCTTTCTATGAACGTGCTGGGAAGGTAAAATGTCTAGGAGGCCCTG

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 13
tatttatttatttatttatttgaatcat-tattatttagcaatttagggttattattcatctctggcttactccaatattttgtcttaatttctcaaaaagGCTGAGATGCCTGCGGATAGTGGCTATCCTGCTTATTTGGCAGCACGTTTAGCCTCTTTCTATGAGCGCGCTGGCAAAGTGAAATGTCTGGGTGGACCAG
  || | |  | ||  ||    | | || ||  ||| | ||    |    |   | |   |  ||    |      |   |  |  |  | |||   | |||| || |||||||| |||||||| |||||||| ||  | || |||||||||||||| |||||||| || ||||| || || |||||||| || || || |
-cttgactagtgtaactagacaatttatataccattaaccatgagacacatgggaatggacattgatcaatgtattttgatgatgctgttgtcttccacagGCAGAAATGCCTGCAGATAGTGGATATCCTGCATACCTTGCTGCACGTTTAGCCTCGTTCTATGAACGTGCTGGGAAGGTAAAATGTCTTGGAGGCCCTG

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 13
---tatttatttatttatttatttgaatcattattatttagcaatttagggttattattcatctctggcttactccaatat--tttgtcttaatttctcaaaaagGCTGAGATGCCTGCGGATAGTGGCTATCCTGCTTATTTGGCAGCACGTTTAGCCTCTTTCTATGAGCGCGCTGGCAAAGTGAAATGTCTGGGTGGACCAG
      ||||   |||   | ||||    ||   | ||  |   | |     | | | |  ||| |  || | |  | |      | | ||  ||| |   | ||||||| |||||||| || ||||| ||||| || ||| | |||||||||||||| ||||||||||| || ||||| ||||| |||||||| ||||||||||
gtaatcttatgcgtttcact-tttgctatatggatgttc-gtgttgtcctcatctcacttttctttttctcagtttattgacacctattttgctttgttttatagGCTGAAATGCCTGCTGACAGTGGATATCCAGCCTATCTAGCAGCACGTTTAGCATCTTTCTATGAACGTGCTGGTAAAGTAAAATGTCTTGGTGGACCAG

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: PP1S10_201V6.1 (Physcomitrella patens), 3'ss of exon 13
----tatttatttatttatttatttgaatcattattatttagcaatttagggttattattcatctctggcttactccaatattttgtcttaatttctcaaaaagGCTGAGATGCCTGCGGATAGTGGCTATCCTGCTTATTTGGCAGCACGTTTAGCCTCTTTCTATGAGCGCGCTGGCAAAGTGAAATGTCTGGGTGGACCAG
     || | |  |  |||||  |     |||    |     ||||| ||   |  || |  ||      ||   | ||||| |  ||     |        |||||||||||||||| || ||||| ||||| |||||  | || ||| | ||||| |||||||||||  | || || |||||||| ||||||||  | ||  
tcataatatttaaaaatatttgctcagggcatagcca---gacaattcagaaatgctactt-tccagatattttgctaatatgtgatcacttgtggggcttcagGCTGAGATGCCTGCTGACAGTGGTTATCCAGCTTACCTTGCTGCAAGATTAGCTTCTTTCTATGAAAGAGCCGGGAAAGTGAAGTGTCTGGGAAGCCCGA

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|110720887|gb|EE097200.1|EE097200
EST:     ATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGGACGGCTG                         GCTGAGATGCCTGCGGATAGTGGATATCCTGCTTATTTGGCAGCACGTTTA
genomic: ATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGGACGGCTGgtaagtcctt ... tctcaaaaagGCTGAGATGCCTGCGGATAGTGGCTATCCTGCTTATTTGGCAGCACGTTTA
EST: gi|110715176|gb|EE092929.1|EE092929
EST:     ATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGGACGGCTG                         GCTGAGATGCCTGCGGATAGTGGATATCCTGCTTATTTGGCAGCACGTTTA
genomic: ATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGGACGGCTGgtaagtcctt ... tctcaaaaagGCTGAGATGCCTGCGGATAGTGGCTATCCTGCTTATTTGGCAGCACGTTTA
EST: gi|110707093|gb|EE083190.1|EE083190
EST:     ATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGGACGGCTG                         GCTGAGATGCCTGCGGATAGTGGATATCCTGCTTATTTGGCAGCACGTTTA
genomic: ATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGGACGGCTGgtaagtcctt ... tctcaaaaagGCTGAGATGCCTGCGGATAGTGGCTATCCTGCTTATTTGGCAGCACGTTTA
EST: gi|37189190|gb|CF608539.1|CF608539
EST:     ATTC-ACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGGACGGCTG                         GCTGAGATGCCTGCGGATAGTGGCTATCCTGCTTATTTGGCAGCACGTTTA
genomic: ATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGGACGGCTGgtaagtcctt ... tctcaaaaagGCTGAGATGCCTGCGGATAGTGGCTATCCTGCTTATTTGGCAGCACGTTTA
EST: gi|110692053|gb|EE070859.1|EE070859
EST:     ATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGGACGGCTG                         GCTGAGATGCCTGCGGATAATGGATATCCTGCTTATTTGGCAGCACGTTTA
genomic: ATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGGACGGCTGgtaagtcctt ... tctcaaaaagGCTGAGATGCCTGCGGATAGTGGCTATCCTGCTTATTTGGCAGCACGTTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggttattattcatctctggcttactccaatattttgtcttaatttctcaaaaagGCTGAGATGCCTGCGGATAGTGGCTATCCTGCTTATTTGGCAGCACGTTTAGCCTCTTTCTATGAGCGCGCTGGCAAAGTGAAATGTCTGGGTGGACCAG
                                     tcttaat  putative branch site (score: 3)
                                           tttctc  CT-rich tract
                            aatattttgtcttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatttatttatttatttatttgaatcattattatttagcaatttagggttattattcatctctggcttactccaatattttgtcttaatttctcaaaaagGCTGAGATGCCTGCGGATAGTGGCTATCCTGCTTATTTGGCAGCACGTTTAGCCTCTTTCTATGAGCGCGCTGGCAAAGTGAAATGTCTGGGTGGACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actccaa