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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatttccttttgattttgtttgtttgccagtctatattaattgatccattgattcatgatattttctacaccaaatttagGGGTCGGAAGAGGGCATGCGTTACTTACTGCATAACTTATATACTGAGCTGCATCACCAAGCATTCTCCTCAGTACAAAATTTTAATGTTGGGACGTATA

Basic information

species Vitis vinifera
transcript Vv02s0025g02420.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os10g37520.1 (Oryza sativa), 3'ss of exon 2
------gtaagatttccttttgattttgtttgtt-tgccagtctatattaattgatccattgattcatgatattttctacaccaaatttagGGGTCGGAAGAGGGCATGCGTTACTTACTGCATAACTTATATACTGAGCTGCATCACCAAGCATTCTCCTCAGTACAAAATTTTAATGTTGGGACGTATA
      ||    | |  |  |  ||   |||||| ||   || |  |||  ||  |  ||    |  ||||  || ||          ||||||  |||||||||| ||| |||| |||||||| |  || || |||||||||||||| ||||| || ||| ||||||| ||  | ||| | || ||  | 
gtgcgtgtcccgtgttttactcgttgattttgttgtgtttgtttggattttttttttgatgaggttgtgatgcttcctggtt--gtcgtagGGGGAGGAAGAGGGCGTGCATTACCTACTGCATCAGCTACATCCTGAGCTGCATCACGAAGCACTCGCCTGAGTACAAGATCCTGATGATTGGGCGCGTG

upper sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G067638_T01 (Zea mays), 3'ss of exon 2
---------------gtaagatttccttttgattttgtttgtttgccagtctatattaattgatccattgattcatgatattttctacaccaaatttagGGGTCGGAAGAGGGCATGCGTTACTTACTGCATAACTTATATACTGAGCTGCATCACCAAGCATTCTCCTCAGTACAAAATTTTAATGTTGGGACGTATA
                |  |  ||     ||| ||   | | ||  |  ||| | ||  | ||| |   ||   | | |  |   |   ||    | ||||| ||||||||||| || || || |||||||| || || || || ||||||||||||||||| ||||| ||||||||| || | ||| | || ||| | 
gtgcgttgcgccctcctccgccttgggggtgaattcagtcgatt-tcgttctgttttggtggatacggcgacg-aggctgatggattttccgtggtcagGGGGCGGAAGAGGGCGTGTGTCACGTACTGCATCACCTACATCCTCAGCTGCATCACCAAGCACTCTCCCCAGTACAAAGTTCTTATGATTGGGCGTGTC

upper sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G41090.1 (Glycine max), 3'ss of exon 2
------------gtaagatttcct-tttgattttgtttgtttgccagtctatattaattgatccattgattcatgatattttctac--acc----aaatttagGGGTCGGAAGAGGGCATGCGTTACTTACTGCATAACTTATATACTGAGCTGCATCACCAAGCATTCTCCTCAGTACAAAATTTTAATGTTGGGACGTATA
             |  | |||| | ||| || ||||| |  | || |||  ||| | ||  | || ||  | ||| |  ||  | |  |||     || | || || ||||||||||| || || |||||||||||||| || ||  |||| ||||||||||||||||||||||| |||||| |  | |||||||| || || 
gtgagacgtctttttcggtttcttgtttcatcttgtt-gcatacctgtc-gtataatttttttcagtgtctaatggtgcttcttgcttaccctgtgaaatcagAGGCCGGAAGAGGGCTTGTGTGACTTACTGCATAACCTACATTTTGAGTTGCATCACCAAGCATTCTCCTCAATACAAAGTCCTGATGTTGGGCCGCATT

upper sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G13760.2 (Glycine max), 3'ss of exon 2
gtaagatttccttttgattttgtttgtttgccagtctatattaattgatccattgattcatgatattttctacaccaaatttagGGGTCGGAAGAGGGCATGCGTTACTTACTGCATAACTTATATACTGAGCTGCATCACCAAGCATTCTCCTCAGTACAAAATTTTAATGTTGGGACGTATA
|| |||| || ||||   |||  ||||||   |      ||  | |  | || ||  |||||||  ||  ||| |  || | || || ||||||||||| || || |||||||||||||| || ||  |||| ||||||||||||||||||||||| |||||| |  | |||||||| ||||| 
gtgagatgtcttttttggttt-cttgtttcataactgtcatagaatttttcagtgtctcatgatgcttcttaccctgaaatcagAGGCCGGAAGAGGGCTTGTGTGACTTACTGCATAACCTACATTTTGAGTTGCATCACCAAGCATTCTCCTCATTACAAAGTCCTGATGTTGGGCCGTATT

upper sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G27720.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaagatttccttttgattttgtttgtttgccagtctatattaattgatccattgattcatgatattttctacaccaaatttagGGGTCGGAAGAGGGCATGCGTTACTTACTGCATAACTTATATACTGAGCTGCATCACCAAGCATTCTCCTCAGTACAAAATTTTAATGTTGGGACGTATA
|| ||  |||  |   ||  | ||   |     |   || |||| |  |  | | ||     ||| |   |   |   ||  |||||||| ||||||||||| ||||| || || || || |||||| |||||||||||||||||||||||||||| || ||  |||| ||| | || ||| | 
gtgagcattctctcgtatgcttttaagtaatatggaaatcttaactcttttagtaatgttgcataatgg-tgttctgtatc-agGGGTCGTAAGAGGGCATGTGTTACCTATTGTATTACCTATATATTGAGCTGCATCACCAAGCATTCTCCTCAATATAAGGTTTTGATGGTAGGCCGTGTC

upper sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G49310.1 (Arabidopsis thaliana), 3'ss of exon 2
----gtaagatttccttttgattttgtttgtt--tgccagtctatattaatt--gatccattgattcatgatattttctacaccaaatttagGGGTCGGAAGAGGGCATGCGTTACTTACTGCATAACTTATATACTGAGCTGCATCACCAAGCATTCTCCTCAGTACAAAATTTTAATGTTGGGACGTATA
    | ||| | ||  | | || || |  ||   ||    |  |    || |  | |      | | ||    || | |       ||| |||||||| ||||||||||| ||||| ||||| |||  ||| ||||| || |||||||||||||| ||||| ||||||||| |||| ||| | || ||||| 
gtgagaaagctctctctcttatgttttaagtccgtgttgttggaggagaactatgtttaggcaactaatatctttgtgtgtgttggattcagGGGTCGAAAGAGGGCATGTGTTACATACTGTATAGTTTACATACTAAGTTGCATCACCAAGCACTCTCCACAGTACAAAGTTTTGATGGTTGGCCGTATC

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|351042244|gb|FQ442711.1|FQ442711
EST:     GGGTCCTCTATGTTGTTTGGGACAATTGTTGGGTCTCTGGCTGATAAACA                         GGGTCAGAAGAGGGCATGTGTTACTTACTGCATAACTTATATACTGAGCTG
genomic: GGGTCCTCTATGTTGTTTGGGACAATTGTTGGGTCTCTGGCTGATAAACAgtaagatttc ... ccaaatttagGGGTCGGAAGAGGGCATGCGTTACTTACTGCATAACTTATATACTGAGCTG
EST: gi|351046994|gb|FQ454604.1|FQ454604
EST:     GGGTCCTCTATGTTGTTTGGGACAATTGTTGGGTCTCTGGCTGATAAACA                         GGGTCGGAAGAGGGCATGTGTTACTTACTGCATAACTTATATACTGAGCTG
genomic: GGGTCCTCTATGTTGTTTGGGACAATTGTTGGGTCTCTGGCTGATAAACAgtaagatttc ... ccaaatttagGGGTCGGAAGAGGGCATGCGTTACTTACTGCATAACTTATATACTGAGCTG
EST: gi|349829349|gb|FQ419881.1|FQ419881
EST:     GGGTCCTCTATGTTGTTTGGGACAATTGTTGGGTCTCTGGCTGATAAACA                         GGGTCGGAAGAGGGCATGTGTTACTTACTGCATAACTTATATACTGAGCTG
genomic: GGGTCCTCTATGTTGTTTGGGACAATTGTTGGGTCTCTGGCTGATAAACAgtaagatttc ... ccaaatttagGGGTCGGAAGAGGGCATGCGTTACTTACTGCATAACTTATATACTGAGCTG
EST: gi|351024947|gb|FQ433364.1|FQ433364
EST:     GGGTCCTCTATGTTGTTTGGGACAATTGTTGGGTCTCTGGCTGATAAACA                         GGGTCGGAAGAGGGCATGTGTTACTTACTGCATAACTTATATACTGAGCTG
genomic: GGGTCCTCTATGTTGTTTGGGACAATTGTTGGGTCTCTGGCTGATAAACAgtaagatttc ... ccaaatttagGGGTCGGAAGAGGGCATGCGTTACTTACTGCATAACTTATATACTGAGCTG
EST: gi|351045803|gb|FQ440988.1|FQ440988
EST:     GGGTCCTCTATGTTGTTTGGGACAATTGTTGGGTCTCTGGCTGATAAACA                         GGGTCGGAAGAGGGCATGTGTTACTTACTGCATAACTTATATACTGAGCTG
genomic: GGGTCCTCTATGTTGTTTGGGACAATTGTTGGGTCTCTGGCTGATAAACAgtaagatttc ... ccaaatttagGGGTCGGAAGAGGGCATGCGTTACTTACTGCATAACTTATATACTGAGCTG
EST: gi|351044296|gb|FQ452848.1|FQ452848
EST:     GGGTCCTCTATGTTGTTTGGGACAATTGTTGGGTCTCTGGCTGATAAACA                         GGGTCGGAAGAGGGCATGTGTTACTTACTGCATAACTTATATACTGAGCTG
genomic: GGGTCCTCTATGTTGTTTGGGACAATTGTTGGGTCTCTGGCTGATAAACAgtaagatttc ... ccaaatttagGGGTCGGAAGAGGGCATGCGTTACTTACTGCATAACTTATATACTGAGCTG
EST: gi|351053919|gb|FQ441685.1|FQ441685
EST:     GGGTCCTCTATGTTGTTTGGGACAATTGTTGGGTCTCTGGCTGATAAACA                         GGGTCGGAAGAGGGCATGTGTTACTTACTGCATAACTTATATACTGAGCTG
genomic: GGGTCCTCTATGTTGTTTGGGACAATTGTTGGGTCTCTGGCTGATAAACAgtaagatttc ... ccaaatttagGGGTCGGAAGAGGGCATGCGTTACTTACTGCATAACTTATATACTGAGCTG
EST: gi|351017775|gb|FQ436128.1|FQ436128
EST:     GGGTCCTCTATGTTGTTTGGGACAATTGTTGGGTCTCTGGCTGATAAACA                         GGGTCGGAAGAGGGCATGTGTTACTTACTGCATAACTTATATACTGAGCTG
genomic: GGGTCCTCTATGTTGTTTGGGACAATTGTTGGGTCTCTGGCTGATAAACAgtaagatttc ... ccaaatttagGGGTCGGAAGAGGGCATGCGTTACTTACTGCATAACTTATATACTGAGCTG
EST: gi|110698059|gb|EE075637.1|EE075637
EST:     GGGTCCTCTATGTTGTTTGGGACAATTGTTGGGTCTCTGGCTGATAAACA                         GGGTCGGAAGAGGGCATGCGTTACTTACTGCATAACTTATATACTGAGCTG
genomic: GGGTCCTCTATGTTGTTTGGGACAATTGTTGGGTCTCTGGCTGATAAACAgtaagatttc ... ccaaatttagGGGTCGGAAGAGGGCATGCGTTACTTACTGCATAACTTATATACTGAGCTG
EST: gi|110708440|gb|EE085985.1|EE085985
EST:     GGGTCCTCTATGTTGTTTGGGACAATTGTTGGGTCTCTGGCTGATAAACA                         GGGTCGGAAGAGGGCATGCGTTACTTACTGCATAACTTATATACTGAGCTG
genomic: GGGTCCTCTATGTTGTTTGGGACAATTGTTGGGTCTCTGGCTGATAAACAgtaagatttc ... ccaaatttagGGGTCGGAAGAGGGCATGCGTTACTTACTGCATAACTTATATACTGAGCTG
EST: gi|351052785|gb|FQ456512.1|FQ456512
EST:     GGGTCCTCTATGTTGTTTGGGACAATTGTTGGGTCTCTGGCTGATAAACA                         GGGTCGGAAGAGGGCATGTGTTACTTACTGCATAACTTATATACTGAGCTG
genomic: GGGTCCTCTATGTTGTTTGGGACAATTGTTGGGTCTCTGGCTGATAAACAgtaagatttc ... ccaaatttagGGGTCGGAAGAGGGCATGCGTTACTTACTGCATAACTTATATACTGAGCTG
EST: gi|349828828|gb|FQ419161.1|FQ419161
EST:     GGGTCCTCTATGTTGTTTGGGACAATTGTTGGGTCTCTGGCTGATAAACA                         GGGTCGGAAGAGGGCATGTGTTACTTACTGCATAACTTATATACTGAGCTG
genomic: GGGTCCTCTATGTTGTTTGGGACAATTGTTGGGTCTCTGGCTGATAAACAgtaagatttc ... ccaaatttagGGGTCGGAAGAGGGCATGCGTTACTTACTGCATAACTTATATACTGAGCTG
EST: gi|349832411|gb|FQ420972.1|FQ420972
EST:     GGGTCCTCTATGTTGTTTGGGACAATTGTTGGGTCTCTGGCTGATAAACA                         GGGTCGGAAGAGGGCATGTGTTACTTACTGCATAACTTATATACTGAGCTG
genomic: GGGTCCTCTATGTTGTTTGGGACAATTGTTGGGTCTCTGGCTGATAAACAgtaagatttc ... ccaaatttagGGGTCGGAAGAGGGCATGCGTTACTTACTGCATAACTTATATACTGAGCTG
EST: gi|351038992|gb|FQ457667.1|FQ457667
EST:     GGGTCCTCTATGTTGTTTGGGACAATTGTTGGGTCTCTGGCTGATAAACA                         GGGTCGGAAGAGGGCATGTGTTACTTACTGCATAACTTATATACTGAGCTG
genomic: GGGTCCTCTATGTTGTTTGGGACAATTGTTGGGTCTCTGGCTGATAAACAgtaagatttc ... ccaaatttagGGGTCGGAAGAGGGCATGCGTTACTTACTGCATAACTTATATACTGAGCTG
EST: gi|351039728|gb|FQ464766.1|FQ464766
EST:     GGGTCCTCTATGTTGTTTGGGACAATTGTTGGGTCTCTGGCTGATAAACA                         GGGTCGGAAGAGGGCATGTGTTACTTACTGCATAACTTATATACTGAGCTG
genomic: GGGTCCTCTATGTTGTTTGGGACAATTGTTGGGTCTCTGGCTGATAAACAgtaagatttc ... ccaaatttagGGGTCGGAAGAGGGCATGCGTTACTTACTGCATAACTTATATACTGAGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccagtctatattaattgatccattgattcatgatattttctacaccaaatttagGGGTCGGAAGAGGGCATGCGTTACTTACTGCATAACTTATATACTGAGCTGCATCACCAAGCATTCTCCTCAGTACAAAATTTTAATGTTGGGACGTATA
     tctatattaattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatttccttttgattttgtttgtttgccagtctatattaattgatccattgattcatgatattttctacaccaaatttagGGGTCGGAAGAGGGCATGCGTTACTTACTGCATAACTTATATACTGAGCTGCATCACCAAGCATTCTCCTCAGTACAAAATTTTAATGTTGGGACGTATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC