Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcatttttatgcatacctctcaattttgggagtgccgtgattcaattttattggtttgatcagaaatatttatttctattatttctgtttgctatcagGGTTTTGTTTCAGCTGTCAGTCACATGCGTTCATTTGTTCCAGCTGTTTATGATGTAACAGTGGCAATTCCCAAAACTCAGCCTTCACCAACAATGCTCA

Basic information

species Vitis vinifera
transcript Vv08s0007g08110.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g08110.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA02G31320.1 (Glycine max), 3'ss of exon 7
---------cttcatttttatgcatacctctcaattttgggagtgccgtgattcaattttattggtttgatcagaaatatttatttctattatttctgtttgctatcagGGTTTTGTTTCAGCTGTCAGTCACATGCGTTCATTTGTTCCAGCTGTTTATGATGTAACAGTGGCAATTCCCAAAACTCAGCCTTCACCAACAATGCTCA
          ||   |  || |||   ||  | || || ||  |    |  |||  || |  || |||| || |||||||||| | ||  ||| |     |||| |||||||||||||||||| || |  || ||||| || |||||||| ||  ||||||||||||| |||||||||||||| | |   ||| | || |||||||| |
cttacatatattacctaataggcagtgctaaccatattagg--ttttattgttcttttctgatg-tttgctctgaaatatttact-ctgctatgt-----tgctttcagGGTTTTGTTTCAGCAGTAAACCATATGCGCTCGTTTGTTCCTGCCATTTATGATGTAACTGTGGCAATTCCCAAGAGTTCACCTGCTCCTACAATGCTAA

upper sequence: Vv08s0007g08110.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA10G12560.2 (Glycine max), 3'ss of exon 6
------cttcatttttatgca-tacctctcaattttgggagtgccgtgattcaattttattggtttgatcagaaatatttatttctattatttctgtttgctatcagGGTTTTGTTTCAGCTGTCAGTCACATGCGTTCATTTGTTCCAGCTGTTTATGATGTAACAGTGGCAATTCCCAAAACTCAGCCTTCACCAACAATGCTCA
       ||   |  || ||| | |    || | |     ||    |  |||  || | |||||| | || |||||||||| | |   ||| |     |||| |||||||||||||||||| || |  || ||||| || |||||||| ||  ||||||||||||| |||||||||||||| | |   ||| | || |||||||| |
acatatattacctaataggcagtgctaaccattatattaggttttattgttcttttctgttggtt-gctctgaaatatttactcc-gctatgt-----tgctttcagGGTTTTGTTTCAGCAGTAAACCATATGCGCTCTTTTGTTCCTGCCATTTATGATGTAACTGTGGCAATTCCCAAGAGTTCACCTGCTCCTACAATGCTAA

upper sequence: Vv08s0007g08110.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA03G29600.1 (Glycine max), 3'ss of exon 7
cttcatttttatgcatacctctcaattttgggagtgccgtgattcaattttattggtttgatcagaaatatttatt-tctattattt-ctgtt----tgctatcagGGTTTTGTTTCAGCTGTCAGTCACATGCGTTCATTTGTTCCAGCTGTTTATGATGTAACAGTGGCAATTCCCAAAACTCAGCCTTCACCAACAATGCTCA
  |||||| |   | ||     ||   |          |  |   |||| ||||  |||  ||   |||||||||  | || ||||| |||||    | || ||||||||||||||| || || ||||| ||||| ||||||||||| ||  |||||||||||||||| || || || || | |   ||| | || |||||||| |
--tcatttattaacttatgctacatgctacaagaattaggaaagtaattctatt--tttactct--aatatttatcatgtaatatttactgttgtgtttctttcagGGTTTTGTTTCTGCAGTAAGTCATATGCGCTCATTTGTTCCTGCCATTTATGATGTAACAGTAGCCATCCCTAAGAGTTCCCCTGCTCCTACAATGCTAA

upper sequence: Vv08s0007g08110.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA19G32420.1 (Glycine max), 3'ss of exon 7
cttcatttttatgcatacctctcaattttgggagtgccgtgattcaattttattggtttgatcagaaatatttatt-tctattattt-ctgtt----tgctatcagGGTTTTGTTTCAGCTGTCAGTCACATGCGTTCATTTGTTCCAGCTGTTTATGATGTAACAGTGGCAATTCCCAAAACTCAGCCTTCACCAACAATGCTCA
      | | ||| ||     |    |    || |   |  | | |||| ||||  |||  || | |||||||||  | || ||||| |||||    | || ||||||||||||||| || || ||||| ||||| ||||||||||| ||  |||||||| ||||||| || || || || | |   ||| | || |||||||| |
---agctctcatgtattaacttatgctacaagaattaggaaagt-aattctatt--tttactctgtaatatttatagtgtaatatttactgttgtgtttctttcagGGTTTTGTTTCTGCAGTAAGTCATATGCGCTCATTTGTTCCTGCCATTTATGATATAACAGTAGCTATCCCTAAGAGTTCCCCTGCTCCTACAATGCTAA

upper sequence: Vv08s0007g08110.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT3G57650.1 (Arabidopsis thaliana), 3'ss of exon 7
cttcatttttatgcatacctctcaattttgggagtgccgtgattcaattttattggtttgatcagaaatatttatttctattatttctgtttgc-tatcagGGTTTTGTTTCAGCTGTCAGTCACATGCGTTCATTTGTTCCAGCTGTTTATGATGTAACAGTGGCAATTCCCAAAACTCAGCCTTCACCAACAATGCTCA
  |   |    |  |||| | ||| |||    ||  |          || |  | ||    || |   || ||| |    ||  || | |||   | ||||||||| || |||||||| ||| | |||||||||||||| |||||  |||||||| | |||||| | ||||| |||||    ||  |||| || ||||| |
-atgggtagcctttatacgtttcattttcatcagatcgacttggtggttgttattgtgatttctgccctaattactagacttgcttgtatttttgtttcagGGTTTCGTGTCAGCTGTTAGTAATATGCGTTCATTTGTCCCAGCAATTTATGATATGACAGTGACTATTCCAAAAACCTCTCCACCACCCACGATGCTAA

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|110685332|gb|EE063631.1|EE063631
EST:     CTGCATCGGGGTTGCCTGTTCCTAGAAATGTTCTGATTCCCCGTACTAAG                         GGTTTTGTTTCAACTGTCAGTCACATGCGTTCATTTGTTCCAGCTGTTTAT
genomic: CTGCATCGGGGTTGCCTGTTCCTAGAAATGTTCTGATTCCCCGTACTAAGgttaaatttt ... ttgctatcagGGTTTTGTTTCAGCTGTCAGTCACATGCGTTCATTTGTTCCAGCTGTTTAT
EST: gi|71862495|gb|DT011550.1|DT011550
EST:     CTGCATCGGGGTTGCCTGTTCCTAGAAATGTTCTGATTCCCCGTACTAAG                         GGTTTTGTTTCAGCTGTCAGTCACATGCGTTCATTTGTTCCAGCTGTTTAT
genomic: CTGCATCGGGGTTGCCTGTTCCTAGAAATGTTCTGATTCCCCGTACTAAGgttaaatttt ... ttgctatcagGGTTTTGTTTCAGCTGTCAGTCACATGCGTTCATTTGTTCCAGCTGTTTAT
EST: gi|110703094|gb|EE079637.1|EE079637
EST:     CTGCATCGGGGTTGCCTGTTCCTAGAAATGTTCTGATTCCCCGTACTAAG                         GGTTTTGTTTCAGCTGTCAGTCACATGCGTTCATTTGTTCCAGCTGTTTAT
genomic: CTGCATCGGGGTTGCCTGTTCCTAGAAATGTTCTGATTCCCCGTACTAAGgttaaatttt ... ttgctatcagGGTTTTGTTTCAGCTGTCAGTCACATGCGTTCATTTGTTCCAGCTGTTTAT
EST: gi|110688154|gb|EE066378.1|EE066378
EST:     CTGCATCGGGGTTGCCTGTTCCTAGAAATGTTCTGATTCCCCGTACTAAG                         GGTTTTGTTTCAGCTGTCAGTCACATGCGTTCATTTGTTCCAGCTGTTTAT
genomic: CTGCATCGGGGTTGCCTGTTCCTAGAAATGTTCTGATTCCCCGTACTAAGgttaaatttt ... ttgctatcagGGTTTTGTTTCAGCTGTCAGTCACATGCGTTCATTTGTTCCAGCTGTTTAT
EST: gi|161717359|gb|FC065274.1|FC065274
EST:     CTGCATCGGGGTTGCCTGTTCCTAGAAATGTTCTGATTCCC-GTACTAAG                         G-TTTTGTTTCAGCTGTCAGTCACATGCGTTCATTTGTTC-AGCTGTT-AT
genomic: CTGCATCGGGGTTGCCTGTTCCTAGAAATGTTCTGATTCCCCGTACTAAGgttaaatttt ... ttgctatcagGGTTTTGTTTCAGCTGTCAGTCACATGCGTTCATTTGTTCCAGCTGTTTAT
EST: gi|33405255|gb|CF210882.1|CF210882
EST:     TGCATCGGGGTTGCCTGTTCCTAGAAAATGTTCTGATTCCCCGTACTAAG                         GGTTTTTGTTTCAGCTGTCAGTCACATGCG
genomic: TGCATCGGGGTTGCCTGTTCCTAGAAA-TGTTCTGATTCCCCGTACTAAGgttaaatttt ... ttgctatcagGGTTTT-GTTTCAGCTGTCAGTCACATGCG
EST: gi|110696361|gb|EE072411.1|EE072411
EST:     CTGCAACGGGGTTGCCTGTTCCTAGAAATGTTCTGATTCCCCGTACTAAG                         GGTTTTGTTTCAGCTGTCAGTCACATGCGTTCATTTGTTCCAGCTGTTTAT
genomic: CTGCATCGGGGTTGCCTGTTCCTAGAAATGTTCTGATTCCCCGTACTAAGgttaaatttt ... ttgctatcagGGTTTTGTTTCAGCTGTCAGTCACATGCGTTCATTTGTTCCAGCTGTTTAT
EST: gi|110708022|gb|EE085087.1|EE085087
EST:     CTGCATCGGGGTTGCCTGTTCCTAGAAATGTTCTGATTCCCCGTACTAAG                         GGTTTTGTTTCAGCTGTCAGTCACATGCGTTCATTTGTTCCAGCTGTTTAT
genomic: CTGCATCGGGGTTGCCTGTTCCTAGAAATGTTCTGATTCCCCGTACTAAGgttaaatttt ... ttgctatcagGGTTTTGTTTCAGCTGTCAGTCACATGCGTTCATTTGTTCCAGCTGTTTAT
EST: gi|161715416|gb|FC068047.1|FC068047
EST:     CTGCATCGGGGTTGCCTGTTCCTAGAAATGTTCTGATTCCCCGTACTAAG                         GGTTTTGTTTCAGCTGTCAGTCACATGCGTTCATTTGTTCCAGCT
genomic: CTGCATCGGGGTTGCCTGTTCCTAGAAATGTTCTGATTCCCCGTACTAAGgttaaatttt ... ttgctatcagGGTTTTGTTTCAGCTGTCAGTCACATGCGTTCATTTGTTCCAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattttattggtttgatcagaaatatttatttctattatttctgtttgctatcagGGTTTTGTTTCAGCTGTCAGTCACATGCGTTCATTTGTTCCAGCTGTTTATGATGTAACAGTGGCAATTCCCAAAACTCAGCCTTCACCAACAATGCTCA
          gtttgat  putative branch site (score: 5)
                                      tttctgttt  putative PPT
           tttgatcagaaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttcatttttatgcatacctctcaattttgggagtgccgtgattcaattttattggtttgatcagaaatatttatttctattatttctgtttgctatcagGGTTTTGTTTCAGCTGTCAGTCACATGCGTTCATTTGTTCCAGCTGTTTATGATGTAACAGTGGCAATTCCCAAAACTCAGCCTTCACCAACAATGCTCA

- - - - -tatgcat
- - - - - - - - -cctctca
- - - - - - - - - - - - - - -gggagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - -tggtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaaata