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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGAACCCAACAAGGGTGTGAACCCAGATGAGGCTGTTGCCTTTGGTGCTGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAGgtatcatttccattctctatcaatgaccgatagatggttgtgcatcgagtgttgatgaatggtagacatttgatatgatatttgttccatgcag

Basic information

species Vitis vinifera
transcript Vv02s0025g02140.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g02140.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 5
AAGGAACCCAACAAGGGTGTGAACCCAGATGAGGCTGTTGCCTTTGGTGCTGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAGgtatcatttccattctctatcaatgaccgatagatggttgtgcatcgagtgttgatgaatggtagacatttgatatgatat--ttgttccatgcag
||||| |||||||||||||| ||||| |||||||||||||||| ||||||||| || || ||||||||| | || || ||||| ||||| || |||||||||   |  |  ||    || ||  | ||  | | | | |    |  | |      ||  | | | | | ||    || | |  || |   | ||||
AAGGAGCCCAACAAGGGTGTCAACCCTGATGAGGCTGTTGCCTATGGTGCTGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCGGTGACGAAACCAAAGgttcgaccttgatcacata-catagtcctttgggttggtaacaactgcgatcatctgtcttgcatatacttatcgtgctttgattttggtacgcag

upper sequence: Vv02s0025g02140.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 5
AAGGAACCCAACAAGGGTGTGAACCCAGATGAGGCTGTTGCCTTTGGTGCTGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAGgtatcatttccattctctat---caatgaccgatagatggt-tgtgcatcgagtgttgatgaatg-gtagacatttgatatgatatttgttcc-atgcag
||||| |||||||||||||| ||||| ||||||||||||||||||||||| ||||| || |||||||| ||||| || ||||||||||| ||||||||||||     |    || | | |   |  |  ||  | |  ||| | |   | |     |||| | |  |   ||||  | | |||| ||||     ||||||
AAGGAGCCCAACAAGGGTGTCAACCCTGATGAGGCTGTTGCCTTTGGTGCCGCTGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACCAAAGgttcggctcatgttttttgtgctcttttgccactggtaggtgttttttttggtaagtgatcattctgcttacataag-tgtgatttttgccttgatgcag

upper sequence: Vv02s0025g02140.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 5
AAGGAACCCAACAAGGGTGTGAACCCAGATGAGGCTGTTGCCTTTGGTGCTGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAGgtatcatttccattctctatcaatgaccgatagatggttgtgcatcgagtgttgatgaatggtagacatttga-tatgatatttgttccatgcag
||||| |||||||||||||||||||| ||||||||||||||||||||||| || || || |||||||| ||||| || ||||||||||| ||||| ||||||    |   | ||| |||    | |  | | | || || |   ||  ||        ||  |    |  | | | |||| ||   |  ||||||
AAGGAGCCCAACAAGGGTGTGAACCCTGATGAGGCTGTTGCCTTTGGTGCCGCGGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACAAAAGgttcggtgctctttcactagtgct-atagctgggtgtttttttttcttgtaagtggtcatcctgcttacataagtgtgattttgccttgatgcag

upper sequence: Vv02s0025g02140.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA08G02960.1 (Glycine max), 5'ss of exon 5
AAGGAACCCAACAAGGGTGTGAACCCAGATGAGGCTGTTGCCTTTGGTGCTGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAGgtatcatt-tccattctcta-----tcaatgaccgatagatggttgtgcatcgagtgttgatgaatggtagacatttgatatgatat-ttgttccat-gcag-------------------
||||| || ||||||||||| ||||| ||||| || ||||||| ||||||||| || |||||||||||||||||||||||||||||||| || ||||||||||   |  ||  |  ||||     ||||| ||   |  |    |    |   | | || ||| |  |||||  | ||| |   ||   |||  ||| |  |                   
AAGGAGCCAAACAAGGGTGTCAACCCTGATGAAGCAGTTGCCTATGGTGCTGCAGTGCAAGGAAGCATTTTGAGTGGAGAGGGTGGTGAGGAAACCAAAGgtactgtagtctgtaatctaacttctcaattacttgtccagaaat-cataaatattatttatgca-agtagat-tgtgacacattacgctgtctcattgttgtgtggctctctggatccag

upper sequence: Vv02s0025g02140.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA05G36600.1 (Glycine max), 5'ss of exon 5
AAGGAACCCAACAAGGGTGTGAACCCAGATGAGGCTGTTGCCTTTGGTGCTGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAGgtatcatt-tccattctcta-----tcaatgaccgatagatggttgtgcatcgagtgttgatgaatggtagacatttgatatgatatttgttccatgcag-------------------
||||| || ||||||||||| ||||| ||||| || ||||||| ||||||||| || |||||||||||||||||||||||||||||||| || ||||||||||  |   ||  |  ||||     ||| |    |        |  |  ||  | | || ||| | |             || | | ||  ||  ||  |                   
AAGGAGCCAAACAAGGGTGTCAACCCTGATGAAGCAGTTGCCTATGGTGCTGCAGTGCAAGGAAGCATTTTGAGTGGAGAGGGTGGTGAAGAAACCAAAGgtactacagtctgtaatctaacttctcattacttgtccagaaatcctaaat--attatttatgcaagtagattgccacgcattacactttctcattgttgtgtggctctctggatccag

upper sequence: Vv02s0025g02140.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA05G36620.1 (Glycine max), 5'ss of exon 5
AAGGAACCCAACAAGGGTGTGAACCCAGATGAGGCTGTTGCCTTTGGTGCTGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAGgtatcatt-tccattctctatc-----aatgacc-gatagatggttgtgcatcgagtgt---tgat--gaatggtagacatttgatatgatatttgttccatg-cag-----------
||||| || ||||||||||| ||||| ||||| || ||||||| ||||||||| || |||||||||||||||||||||||||||||||| || |||||||||| | |  ||  |  | || |     ||| ||  |       ||  |  ||    | |     ||  || || ||  |||   |  |  || | |||   || ||            
AAGGAGCCAAACAAGGGTGTCAACCCTGATGAAGCAGTTGCCTATGGTGCTGCAGTGCAAGGAAGCATTTTGAGTGGAGAGGGTGGTGAAGAAACCAAAGgtaccgtagtctgtaatgtagcttttaaattacttgtcccgaagtcataaatattatttacgcaattagattgctaagcataacactttctaatcgttgtgtggcaatatctatccag

upper sequence: Vv02s0025g02140.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA08G02940.1 (Glycine max), 5'ss of exon 5
AAGGAACCCAACAAGGGTGTGAACCCAGATGAGGCTGTTGCCTTTGGTGCTGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAGgtatcatttccattctctatcaatgaccga--tagatggttgtgcatcgagtgttgatgaatggtagacatttgatatgatatttgttccatgcag
||||| || |||||||| || ||||| ||||| || ||||||| ||||||||| || |||||||||||||||||||||||||||||||| || |||||||||| |||   |  |   ||| | | |  ||  ||||| | |  ||||      ||    ||| || |     ||     || | | | |       
AAGGAGCCAAACAAGGGGGTCAACCCTGATGAAGCAGTTGCCTATGGTGCTGCAGTGCAAGGAAGCATTTTGAGTGGAGAGGGTGGTGAAGAAACCAAAGgtaccatagtctgtaaatattatttatggaagtagattgctaagcattacacttt--ctaattgttg-----tgtggcaatctctatccag-----

upper sequence: Vv02s0025g02140.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: EFJ17607 (Selaginella moellendorffii), 5'ss of exon 5
AAGGAACCCAACAAGGGTGTGAACCCAGATGAGGCTGTTGCCTTTGGTGCTGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAGgta--tcatttccattctctatcaatgaccgatagatggttgtgcatcgagtgttgatgaatggtagacatttgatatgatatttgttccatgcag
||||| || ||||||||||||||||| || |||||||| || |||||||||||||| || ||  | || ||||| || || || || || ||    |||||||    | | |   |||   |   | |   ||   || |   ||  ||    ||||                                       
AAGGAGCCGAACAAGGGTGTGAACCCCGACGAGGCTGTGGCTTTTGGTGCTGCTGTCCAGGGCGGTATCTTGAGCGGTGAAGGCGGCGACGATGTTAAAGgtaagcaaatacttgtcttcttttgtaattcatctgtgctaacgcg-cgtccattgacag------------------------------------

upper sequence: Vv02s0025g02140.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: EFJ29073 (Selaginella moellendorffii), 5'ss of exon 5
AAGGAACCCAACAAGGGTGTGAACCCAGATGAGGCTGTTGCCTTTGGTGCTGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAGgta--tcatttccattctctatcaatgaccgatagatggttgtgcatcgagtgttgatgaatggtagacatttgatatgatatttgttccatgcag
||||| || ||||||||||||||||| || |||||||| || |||||||||||||| || ||  | || ||||| || || || || || ||    |||||||    |   |   |||   |   | | | ||   || |   ||  ||    | ||                                       
AAGGAGCCGAACAAGGGTGTGAACCCCGACGAGGCTGTGGCTTTTGGTGCTGCTGTCCAGGGCGGTATCTTGAGCGGTGAAGGCGGCGACGATGTTAAAGgtaagcaaagacttgtcttcttttgtaatccatctgtgctaacgcg-cgtccatcgacag------------------------------------

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|26262286|gb|CA813349.1|CA813349
EST:     TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAG                         ATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAATCGTTG
genomic: TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAGgtatcatttc ... ttccatgcagATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG
EST: gi|110708297|gb|EE085674.1|EE085674
EST:     TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAG                         ATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG
genomic: TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAGgtatcatttc ... ttccatgcagATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG
EST: gi|351048169|gb|FQ442139.1|FQ442139
EST:     TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAG                         ATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG
genomic: TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAGgtatcatttc ... ttccatgcagATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG
EST: gi|110379529|gb|EC944729.1|EC944729
EST:     TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAG                         ATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG
genomic: TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAGgtatcatttc ... ttccatgcagATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG
EST: gi|352799018|gb|FQ480867.1|FQ480867
EST:     TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAG                         ATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG
genomic: TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAGgtatcatttc ... ttccatgcagATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG
EST: gi|33404779|gb|CF210406.1|CF210406
EST:     TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAG                         ATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG
genomic: TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAGgtatcatttc ... ttccatgcagATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG
EST: gi|351026509|gb|FQ428521.1|FQ428521
EST:     TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAG                         ATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG
genomic: TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAGgtatcatttc ... ttccatgcagATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG
EST: gi|110690615|gb|EE067868.1|EE067868
EST:     TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAAACCAAAG                         ATATTCTTCTCTTGGATGTGGCTCCGCTCACTNCTTGGAATTGAA-CCGTT
genomic: TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAGgtatcatttc ... ttccatgcagATATTCTTCTCTTGGATGTGGCTCCGCTCACT-CTTGGAATTGAAACCGTT
EST: gi|30296634|gb|CB973428.1|CB973428
EST:     TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGANGTGATGAGACCAAAG                         ATATTCTTCTCTTGGATGTGGCTCCGCTCACTC
genomic: TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAGgtatcatttc ... ttccatgcagATATTCTTCTCTTGGATGTGGCTCCGCTCACTC
EST: gi|352794236|gb|FQ479478.1|FQ479478
EST:     TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAG                         ATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG
genomic: TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAGgtatcatttc ... ttccatgcagATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG
EST: gi|110700835|gb|EE077835.1|EE077835
EST:     TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAG                         ATATTCTTCTCTTGGATGTGGCTCCGCTTACTCTTGGAATTGAAACCGTTG
genomic: TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAGgtatcatttc ... ttccatgcagATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG
EST: gi|351033837|gb|FQ447875.1|FQ447875
EST:     TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAG                         ATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG
genomic: TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAGgtatcatttc ... ttccatgcagATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG
EST: gi|351044960|gb|FQ449214.1|FQ449214
EST:     TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAG                         ATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG
genomic: TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAGgtatcatttc ... ttccatgcagATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG
EST: gi|110719342|gb|EE097207.1|EE097207
EST:     GGAGAGGGTGGTGATGAGACCAAAG                         ATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG
genomic: GGAGAGGGTGGTGATGAGACCAAAGgtatcatttc ... ttccatgcagATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG
EST: gi|110702839|gb|EE079171.1|EE079171
EST:     AAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAG                         ATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG
genomic: AAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAGgtatcatttc ... ttccatgcagATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG
EST: gi|28968374|gb|CB347407.1|CB347407
EST:     TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAG                         ATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG
genomic: TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAGgtatcatttc ... ttccatgcagATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG
EST: gi|349825531|gb|FQ419448.1|FQ419448
EST:     TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAG                         ATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG
genomic: TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAGgtatcatttc ... ttccatgcagATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG
EST: gi|352790752|gb|FQ478300.1|FQ478300
EST:     TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAG                         ATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG
genomic: TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAGgtatcatttc ... ttccatgcagATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG
EST: gi|351055860|gb|FQ452325.1|FQ452325
EST:     TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAG                         ATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG
genomic: TGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAGgtatcatttc ... ttccatgcagATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGGAACCCAACAAGGGTGTGAACCCAGATGAGGCTGTTGCCTTTGGTGCTGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAGgtatcatttccattctctatcaatgaccgatagatggttgtgcatcgagtgttgatgaatggtagacatttgatatgatatttgttccatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG