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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACACTGTGCAGGTGAAAAATGTGACTCTTCCGAAGGGAACATATGTAAAACTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCATgtgagttgttgctaataatctttattgctaggagaaggtaggtaaggtgtctcttgatgttcatcaatattttatgctgttgcaagagaggggaatcctg...

Basic information

species Vitis vinifera
transcript Vv03s0038g00750.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g00750.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: LOC_Os02g08480.1 (Oryza sativa), 5'ss of exon 7
ACACTGTGCAGGTGAAAAATGTGACTCTTCCGAAGGGAACATATGTAAAACTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCATgtgagt--tgtt--gctaataatctttattgctaggagaaggtaggtaaggtgtctcttgatgttcatcaatatttt------atgctgttgcaaga--gaggggaatcctg------------------------------------
| |  |||    | |||||||  | ||| || || ||||||||||| || || ||||| || |||||||||||||| || ||||||||||||||||| |||| |||  ||||  |  ||| || ||   | ||        |     |     | |||| || | |     | || |      ||  | | |   ||   | | ||  ||||                                    
ATATGGTGTTCATAAAAAATGCCAATCTCCCTAAAGGAACATATGTGAAGCTGCAGCCTCACACAACAGACTTCTTAGACATTTCAAACCCAAAAGCAATgttagtattgtttggtaaattattttctgttcttttcttttgctatcacttcatgtcttcatatactattgtgttgtgattggatcttatggtttgactaatgagatccctgaagaacagtaacaagccatttatgccattcttgcag

upper sequence: Vv03s0038g00750.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G114220_T01 (Zea mays), 5'ss of exon 7
ACACTGTGCAGGTGAAAAATGTGACTCTTCCGAAGGGAACATATGTAAAACTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCATgtgagttgttgctaataatctttattgctagga----gaaggtaggtaaggtgtctcttgatgttcatcaatattttatgctgttgcaagagaggggaatcctg--
||||||| || || ||||||| ||||||||| ||||| |||||||| ||| | || || || ||||| || ||  |||||||||||||||| |||||||||| ||       | | |||  |   |   | ||    |||  |        | |||||||   ||   |  |||  | |    || |  |       | |      
ACACTGTCCATGTAAAAAATGCGACTCTTCCCAAGGGCACATATGTGAAATTGCAACCTCACACAACTGATTTTCTGGATATTTCAAACCCGAAAGCCATgtaaggaaacctttaaaattgtc-ctataatgatcttgaaaattctcttcatttctcttggcattaggcgttatcat-tctcattacttgctgttaaattttccag

upper sequence: Vv03s0038g00750.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G037185_T01 (Zea mays), 5'ss of exon 6
ACACTGTGCAGGTGAAAAATGTGACTCTTCCGAAGGGAACATATGTAAAACTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCATgtgagttgttgctaat--aatctttattg-ctaggagaaggtaggtaaggtgtctcttgatgttcatcaatattttatgctgttgcaagag----aggggaatcctg----------------------------------------------------
| |  |||    | |||||||  |  || || ||||| |||||||| ||  | ||||| ||||||||||||||  | |||||||||||||| ||||| |||| |||  ||  | ||  ||| ||| ||  |   | |||   |  |    |  | |||    |||    ||| ||| |  | |  | || |    | || | |  |                                                     
ATATGGTGTTCATAAAAAATGCCAACCTCCCCAAGGGCACATATGTGAAGTTGCAGCCTCATACAACAGACTTTCTAGATATTTCAAACCCCAAAGCAATgttagtaatttttcattaaatatttcttatcctagtgaaaaca--tccttttacccttccccttcccatatagtttgtattctgactagggttacatggtattagtagcgttttgaatccctcaaaacactaatgaccctgtttgtgttattcttgcag

upper sequence: Vv03s0038g00750.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA05G34630.2 (Glycine max), 5'ss of exon 7
ACACTGTGCAGGTGAAAAATGTGACTCTTCCGAAGGGAACATATGTAAAACTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCATgtgagttgttgctaataatctttattgctaggagaaggtaggtaaggtgtctcttgatgttcatcaatatttta--tgctgttgcaagagaggggaatcctg
||| |||  | |||||||||||||| ||||| ||||| |||||||| ||  |||||||||| |||| |||||| ||||||||||| || |||||||| ||||||||||    | || |  ||||  | | |   ||| || |  |  |  ||    |||    ||  |  |  |  |||  ||     |       ||  | 
ACATTGTCAAAGTGAAAAATGTGACACTTCCAAAGGGGACATATGTTAAGTTACAGCCCCACACAAAAGACTTTTTGGATATTTCCAATCCAAAAGCTATgtgagttgacatttattaagttta--gtttgataaagctatgatatttacctaccaatgagtttctcttgtaaaagtgcaattctgtcactcaaatatgttt

upper sequence: Vv03s0038g00750.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA08G05030.1 (Glycine max), 5'ss of exon 7
ACACTGTGCAGGTGAAAAATGTGACTCTTCCGAAGGGAACATATGTAAAACTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCATgtgagttgttgctaataatctttattgctaggagaaggtaggta-aggtgtctcttgatg-----ttcatcaatattt-----tatgctgttgcaagagaggggaatcctg------------------
||| |||  | |||||||||||||| ||||| ||||| |||||||| ||  ||||||| || |||| |||||||||||||||||| || |||||||| ||||||||||    | || |  |||| |   |  |     |   || |  |  ||    |||      || | | |||||      |  |  |  |  |||   |  ||                      
ACATTGTTAAAGTGAAAAATGTGACACTTCCAAAGGGGACATATGTTAAGTTACAGCCTCACACAAAAGACTTCTTGGATATTTCCAATCCAAAAGCTATgtgagttgacatttattaagtttagtttgataaatctatgattatatttccctaccaatgagtttctcttgagtatttacattcacacactgacttgagttagttatttgattgtgcttttttatgcag

upper sequence: Vv03s0038g00750.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA04G00980.1 (Glycine max), 5'ss of exon 6
ACACTGTGCAGGTGAAAAATGTGACTCTTCCGAAGGGAACATATGTAAAACTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCATgtgagttgttgctaataatctttat-tgctaggagaaggtaggtaa--ggtgtctcttgatgttcatcaatattttatgctgttgcaagagaggggaatcctg-
|||  ||    ||||||   ||  | ||||| |||||||||||||| ||| ||||||| || ||||  ||||| || |||||||| || |||||||| |||||||||||    | | ||| | || |  | |  |||  || | ||  | | |         |  |||||||||   | |    |||       |   || || 
ACATCGTAAGAGTGAAATTCGTATCACTTCCAAAGGGAACATATGTTAAATTACAGCCACACACAAAGGACTTTTTTGATATTTCCAATCCAAAAGCTATgtgagttgtc---agtgatcgtaatatattggatgaaaataagaaatagttattgaacatgataaatcaatattcctt-caaaagcatatccttgttttcatgc

upper sequence: Vv03s0038g00750.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT2G21270.3 (Arabidopsis thaliana), 5'ss of exon 7
ACACTGTGCAGGTGAAAAATGTGACTCTTCCGAAGGGAACATATGTAAAACTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCATgtgagttg---ttgctaataatctttattgctaggagaaggtaggtaaggtgtctcttgatgttcatcaatatttt-atgctgttgcaagagaggggaatcctg--------------------------------------------------------------------------------------
||| ||||   || | |||||| |||||||| |||||||| || || |||||||||||||| |||||||||||| ||||||| || ||||| ||||||||||||||     ||  |  ||  || |  |  | | ||     |  ||   |  | | | |||||  | | |  ||  |   |||   |  | |    | | ||                                                                                       
ACATTGTGAGAGTTAGAAATGTCACTCTTCCAAAGGGAACTTACGTTAAACTACAGCCCCACACAACAGACTTCCTGGATATATCCAACCCGAAAGCCATgtgagtccgacttatttctaccctcttgtatttg-agccctcatatactttcccacatcatgttgtttattgcttagagaatgtattattatatctaagttcttcccgttttctggctcgtagttgtttgatgtcactctttttatcttgttcccaatattctttactgataattgagtgaacgttgcag

upper sequence: Vv03s0038g00750.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT4G38930.1 (Arabidopsis thaliana), 5'ss of exon 7
ACACTGTGCAGGTGAAAAATGTGACTCTTCCGAAGGGAACATATGTAAAACTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCATgtgagttgttgctaataatctttattgctaggagaaggtaggtaaggtgtctcttgatg-ttcatcaatattttatgctgttgcaagagaggggaatcctg--------------
|||  |||   || | |||||| |||||||| |||||||| || || ||||| || ||||| |||||||||||  | |||||  | ||||| |||||||||| | ||    || |          |  |        ||    |    | || |  ||  ||    ||||   ||  ||||    |  ||   |  |||||              
ACATGGTGAGAGTTAGAAATGTCACTCTTCCAAAGGGAACCTACGTGAAACTGCAACCCCACACAACAGACTTTCTCGATATAGCTAACCCGAAAGCCATgtaa-ttccgacttactcctccccctcttgtatttttgtctccatctagactttgaattctttgcgaataccgtactctgtgtatattgaaccggttcctgtgtttctgctgcag

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|110687487|gb|EE064951.1|EE064951
EST:     CTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCAT                         CTTGGAGACAACACTAAGGAACTTTTCCTGCTTAACCACTGGAGATAGTAT
genomic: CTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCATgtgagttgtt ... tataatgcagCTTGGAGACAACACTAAGGAACTTTTCCTGCTTAACCACTGGAGATAGTAT
EST: gi|30126806|gb|CB912145.1|CB912145
EST:     CTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCAT                         CTTGGAGACAACACTAAGGAACTTTTCCTGCTTAACCACTGGAGATAGTAT
genomic: CTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCATgtgagttgtt ... tataatgcagCTTGGAGACAACACTAAGGAACTTTTCCTGCTTAACCACTGGAGATAGTAT
EST: gi|110416730|gb|EC982730.1|EC982730
EST:     CTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCAT                         CTTGGAGACAACACTAAGGAACTTTTCCTGCTTAACCACTGGAGATAGTAT
genomic: CTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCATgtgagttgtt ... tataatgcagCTTGGAGACAACACTAAGGAACTTTTCCTGCTTAACCACTGGAGATAGTAT
EST: gi|110698550|gb|EE076176.1|EE076176
EST:     CTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCAT                         CTTGGAGACAACACTAAGGAACTTTTCCTGCTTAACCACTGGAGATAGTAT
genomic: CTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCATgtgagttgtt ... tataatgcagCTTGGAGACAACACTAAGGAACTTTTCCTGCTTAACCACTGGAGATAGTAT
EST: gi|26262376|gb|CA813439.1|CA813439
EST:     CTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCAT                         CTTGGAGACAACACTAAGGAACTT
genomic: CTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCATgtgagttgtt ... tataatgcagCTTGGAGACAACACTAAGGAACTT
EST: gi|26262164|gb|CA813227.1|CA813227
EST:     CTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCAT                         CTTGGAGACAACACTAAGGAACTTTTCCTGCTTAACCACTGGAGATAGTAT
genomic: CTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCATgtgagttgtt ... tataatgcagCTTGGAGACAACACTAAGGAACTTTTCCTGCTTAACCACTGGAGATAGTAT
EST: gi|71856948|gb|DT006003.1|DT006003
EST:     CTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCAT                         CTTGGAGACAACACTAAGGAACTTTTCCTGCTTAACCACTGGAGATAGTAT
genomic: CTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCATgtgagttgtt ... tataatgcagCTTGGAGACAACACTAAGGAACTTTTCCTGCTTAACCACTGGAGATAGTAT
EST: gi|110724233|gb|EE099882.1|EE099882
EST:     CTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCAT                         CTTGGAGACAACACTAAGGAACTTTTCCTGCTTAACCACTGGAGATAGTAT
genomic: CTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCATgtgagttgtt ... tataatgcagCTTGGAGACAACACTAAGGAACTTTTCCTGCTTAACCACTGGAGATAGTAT
EST: gi|110723124|gb|EE100074.1|EE100074
EST:     CTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCAT                         CTTGGAGACAACACTAAGGAACTTTTCCTGCTTAACCACTGGAGATAGTAT
genomic: CTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCATgtgagttgtt ... tataatgcagCTTGGAGACAACACTAAGGAACTTTTCCTGCTTAACCACTGGAGATAGTAT
EST: gi|294966730|gb|GW837749.1|GW837749
EST:     CTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCAT                         CTTGGAGACAACACTAAGGAACTTTTCCTGCTTAACCACTGGAGATAGTAT
genomic: CTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCATgtgagttgtt ... tataatgcagCTTGGAGACAACACTAAGGAACTTTTCCTGCTTAACCACTGGAGATAGTAT
EST: gi|110401031|gb|EC967624.1|EC967624
EST:     TACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCAT                         CTTGGAGACAACACTAAGGAACTTTTCCTGCTTAACCACTGGAGATAGTAT
genomic: TACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCATgtgagttgtt ... tataatgcagCTTGGAGACAACACTAAGGAACTTTTCCTGCTTAACCACTGGAGATAGTAT
EST: gi|71868328|gb|DT017383.1|DT017383
EST:     CTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCAT                         CTTGGAGACAACACTAAGGAACTTTTCCTGCTTAACCACTGGAGATAGTAT
genomic: CTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCATgtgagttgtt ... tataatgcagCTTGGAGACAACACTAAGGAACTTTTCCTGCTTAACCACTGGAGATAGTAT
EST: gi|110391465|gb|EC956442.1|EC956442
EST:     CTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCAT                         CTTGGAGACAACACTAAGGAACTTTTCCTGCTTAACCACTGGAGATAGTAT
genomic: CTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCATgtgagttgtt ... tataatgcagCTTGGAGACAACACTAAGGAACTTTTCCTGCTTAACCACTGGAGATAGTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACACTGTGCAGGTGAAAAATGTGACTCTTCCGAAGGGAACATATGTAAAACTACAGCCCCATACAACAGACTTCTTGGATATTTCAAACCCAAAAGCCATgtgagttgttgctaataatctttattgctaggagaaggtaggtaaggtgtctcttgatgttcatcaatattttatgctgttgcaagagaggggaatcctg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aggagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaagaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggggaat