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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGAGGGAAAGGGAACCAGTACTTTAAGAGTGCATTTTTGGGATATACAACCGGTTTGGTTGTAACAATTGTTGTCATGAACTGGTTTCAAGCTGCACAGgtgactactacaaaatccatttctctatcctatatgactgatacgtgtggagatatagttccctttgttgaatttcattcagtatctagctggctttaactgtttaagaccagtggaagttagagtatttccatgtgtgagttttctcgtgttattcactacttggtcctaactgttattctaacttcactttcag

Basic information

species Vitis vinifera
transcript Vv06s0009g03520.t01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: LOC_Os02g02530.2 (Oryza sativa), 5'ss of exon 10
CAGAGGGAAAGGGAACCAGTACTTTAAGAGTGCATTTTTGGGATATACAACCGGTTTGGTTGTAACAATTGTTGTCATGAACTGGTTTCAAGCTGCACAGgtgactactacaaaatccatttctctatcctatatgactgatacgtgtggagatatagttccctttgttgaatttcattcagtatctagctggctttaactgtttaagaccagtggaagttagagtatttccatgtgtgagttttctcgtgttattcactacttggtcctaactgttattctaacttcactttcag
 ||||| |    |||||  ||||| || |||||||||||||| |||||    ||||||   || || ||  |||| ||||||||||||||||| |||||||||| |  |   |  |    ||||       || |  |    ||   |     |  |   | | |  |   | |   || |||   ||| |   || |||                                                                                                
AAGAGGAATTAAGAACCGCTACTTCAATAGTGCATTTTTGGGTTATACGGTGGGTTTGACCGTGACGATAATTGTGATGAACTGGTTTCAAGCCGCACAGgtgagtcatgttacttgggattcttgccatcatgtttcctccactcatt----ttcaaggcacatcataagagtgagtttagttcgtagattatttaaacaaaa--------------------------------------------------------------------------------------------

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GRMZM2G150251_T02 (Zea mays), 5'ss of exon 10
CAGAGGGAAAGGGAACCAGTACTTTAAGAGTGCATTTTTGGGATATACAACCGGTTTGGTTGTAACAATTGTTGTCATGAACTGGTTTCAAGCTGCACAGgtgactactacaaaatccatttctctatcctatatgactgatacgtgtggagatatagttccctttgttgaatttcattcagtatctagctggctttaactgtttaagaccagtggaagttagagtatttccatgtgtgagttttctcgtgttattcactacttggtcctaactgttattctaacttcactttcag
 ||||| |    ||| |  ||||| || || ||||||| ||||||  |    ||| |||  || || ||  |||| |||||||||||||||||||||||||||| |         ||  || |||     ||||||       | |||          ||||| |||||    |    || ||          || |   | |||  |    | ||  | | |  |||| |                                                                 
AAGAGGTATCAAGAAGCGTTACTTCAACAGCGCATTTTCGGGATACGCCGTGGGTATGGCGGTGACCATCATTGTAATGAACTGGTTTCAAGCTGCACAGgtgagt---------tctgttgctcaggtttatatggt-----cctgt----------ttccccttgtttctgtcacctctgtgatattaatactatggttatttgggg--gggggggggtggcttattgcag---------------------------------------------------------------

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GRMZM2G044348_T03 (Zea mays), 5'ss of exon 9
CAGAGGGAAAGGGAACCAGTACTTTAAGAGTGCATTTTTGGGATATACAACCGGTTTGGTTGTAACAATTGTTGTCATGAACTGGTTTCAAGCTGCACAGgtgactactacaaaatccatttctctatcctatatgactgatacgtgtggagatatagttccctttgttgaatttcattcagtatctagctggctttaactgtttaagaccagtggaagttagagtatttccatgtgtgagttttctcgtgttattcactacttggtcctaactgttattctaacttcactttcag
 ||||| |    ||| |  ||||| || |||||||||||||||||  |    ||| ||   || || || ||||| ||||||||||||||||| |||||||||  | ||   |    ||  | | |||  | | |   |  | | |||     |    | ||  |  |   | | |  | | | | | |  ||  || | ||                                                                                              
AAGAGGTACCAAGAAGCGTTACTTCAACAGTGCATTTTTGGGATACGCTGTGGGTATGACGGTGACCATCGTTGTAATGAACTGGTTTCAAGCGGCACAGgtgtgttctgtta--ctcaggtttatatt-tgtctagtttctccttgtttc--tgccatccctgtaatattaatactatgattgttttggcggggtttattgcag-------------------------------------------------------------------------------------------

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA06G08620.3 (Glycine max), 5'ss of exon 10
CAGAGGGAAAGGGAACCAGTACTTTAAGAGTGCATTTTTGGGATATACAACCGGTTTGGTTGTAACAATTGTTGTCATGAACTGGTTTCAAGCTGCACAGgtgactactacaaaatccatttctctatcctatatgactgatacgtgtggagatatagttccctttgttgaatttcattcagtatctagctggctttaactgtttaagaccagtggaagttagagtatttccatgtgtgagttttctcgtgttattcactacttggtcctaactgttattctaacttcactttcag
|||||| |||  |  |||||| || |||||||||||| | ||||| ||    || |||||  | ||||||||||| |||||||||||||| ||||||||||| |||              || |  | |    |||      |  | ||| |||  |     || | ||   |||||  || | ||||  ||  |||   |    |                                                                                          
CAGAGGAAAACAGCCCCAGTATTTCAAGAGTGCATTTGTAGGATACACTGTTGGCTTGGTCCTTACAATTGTTGTGATGAACTGGTTTCAGGCTGCACAGgtaactgtggtgtgg---ggttgtgaaactatcatgg-----atttttggtgat-caaccttctctattatttttca--cactttctaattgtatttcttttgccag-----------------------------------------------------------------------------------------

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA06G08620.2 (Glycine max), 5'ss of exon 10
CAGAGGGAAAGGGAACCAGTACTTTAAGAGTGCATTTTTGGGATATACAACCGGTTTGGTTGTAACAATTGTTGTCATGAACTGGTTTCAAGCTGCACAGgtgactactacaaaatccatttctctatcctatatgactgatacgtgtggagatatagttccctttgttgaatttcattcagtatctagctggctttaactgtttaagaccagtggaagttagagtatttccatgtgtgagttttctcgtgttattcactacttggtcctaactgttattctaacttcactttcag
|||||| |||  |  |||||| || |||||||||||| | ||||| ||    || |||||  | ||||||||||| |||||||||||||| ||||||||||| |||              || |  | |    |||      |  | ||| |||  |     || | ||   |||||  || | ||||  ||  |||  || ||     || |                                                                                   
CAGAGGAAAACAGCCCCAGTATTTCAAGAGTGCATTTGTAGGATACACTGTTGGCTTGGTCCTTACAATTGTTGTGATGAACTGGTTTCAGGCTGCACAGgtaactgtggtgtgg---ggttgtgaaactatcatgg-----atttttggtgat-caaccttctctattatttttca--cactttctaattgtattt--cttttgccagccgg-----------------------------------------------------------------------------------

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA04G08510.1 (Glycine max), 5'ss of exon 10
CAGAGGGAAAGGGAACCAGTACTTTAAGAGTGCATTTTTGGGATATACAACCGGTTTGGTTGTAACAATTGTTGTCATGAACTGGTTTCAAGCTGCACAGgtgactactacaaaatccatttctctatcctatatgactgatacgtgtggagatatagttccctttgttgaatttcattcagtatctagctggctttaactgtttaagaccagtggaagttagagtatttccatgtgtgagttttctcgtgttattcactacttggtcctaactgttattctaacttcactttcag
 ||||| |||  |  |||||| || |||||||||||| | ||||| ||    || |||||  | ||||||||||| |||||||||||||| ||||||||||| |||  |          ||| | | | || | | |  |||  |||||| | | | |  |  |   |||| |||   | |  |     ||  || | | | || |    || |   | ||   |||||||  | ||  ||                                                       
TAGAGGAAAACAGCCCCAGTATTTCAAGAGTGCATTTGTAGGATACACTGTTGGCTTGGTCCTTACAATTGTTGTGATGAACTGGTTTCAGGCTGCACAGgtaactgatctgtttcatcttttttttttct-tgttagggatg-gtgtggggttgtggaactatc-attgatttttggtgatcaatctact--ctattatttttca----cacttctaatt---gtatttcttt-tgccag-------------------------------------------------------

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: AT2G03120.1 (Arabidopsis thaliana), 5'ss of exon 9
CAGAGGGAAAGGGAACCAGTACTTTAAGAGTGCATTTTTGGGATATACAACCGGTTTGGTTGTAACAATTGTTGTCATGAACTGGTTTCAAGCTGCACAGgtgactactacaaaatccatttctctatcctatatgactgatacgtgtggagatatagttccctttgttgaatttcattcagtatctagctggctttaactgtttaagaccagtggaagttagagtatttccatgtgtgagttttctcgtgttattcactacttggtcctaactgttattctaacttcactttcag
 ||| | | |      || ||||| |  ||||||||| | |||||  |    ||| || |  | || ||||| |||||||||||||||||||| |||||||| | |  |      |  |||  | |   |||| |     |  | | |   |  ||  ||| || || |   |||      || | |   | || ||   ||||| ||                                                                                        
AAGACGTAGACAACCACAATACTTCACAAGTGCATTTATCGGATACGCTGTTGGTGTGATCCTCACGATTGTAGTCATGAACTGGTTTCAAGCAGCACAGgtcagtttttgtgtcttaattgttgtcatctatttattgcaaccttattttgggat--ttctctctgataggttttt----gtttttgttttgcctt---tgtttcag----------------------------------------------------------------------------------------

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|27579299|gb|CB001994.1|CB001994
EST:     CCGGTTTGGTTGTAACAATTGTTGTCATGAACTGGTTTCAAGCTGCACAG                         CCTGCACTTCTTTATATTGTACCAGCAGTTATTGGATTTATGGCTGCTCAT
genomic: CCGGTTTGGTTGTAACAATTGTTGTCATGAACTGGTTTCAAGCTGCACAGgtgactacta ... tcactttcagCCTGCACTTCTTTATATTGTACCAGCAGTTATTGGATTTATGGCTGCTCAT
EST: gi|22012962|gb|BQ797996.1|BQ797996
EST:     CCGGTTTGGTTGTAACAATTGTTGTCATGAACTGGTTTCAAGCTGCACAG                         CCTGCACTTCTTTATATTGTACCAGCAGTTATTGGATTTATGGCTGCTCAT
genomic: CCGGTTTGGTTGTAACAATTGTTGTCATGAACTGGTTTCAAGCTGCACAGgtgactacta ... tcactttcagCCTGCACTTCTTTATATTGTACCAGCAGTTATTGGATTTATGGCTGCTCAT
EST: gi|110391760|gb|EC956760.1|EC956760
EST:     CCGGTTTGGTTGTAACAATTGTTGTCATGAACTGGTTTCAAGCTGCACAG                         CCTGCACTTCTTTATATTGTACCAGCAGTTATTGGATTTATGGCTGCTCAT
genomic: CCGGTTTGGTTGTAACAATTGTTGTCATGAACTGGTTTCAAGCTGCACAGgtgactacta ... tcactttcagCCTGCACTTCTTTATATTGTACCAGCAGTTATTGGATTTATGGCTGCTCAT
EST: gi|27580263|gb|CB002958.1|CB002958
EST:     ATGAACTGGTTTCAAGCTGCACAG                         CCTGCACTTCTTTATATTGTACCAGCAGTTATTGGATTTATGGCTGCTCAT
genomic: ATGAACTGGTTTCAAGCTGCACAGgtgactacta ... tcactttcagCCTGCACTTCTTTATATTGTACCAGCAGTTATTGGATTTATGGCTGCTCAT
EST: gi|32246622|gb|CD712441.1|CD712441
EST:     CCGGTTTGGTTGTAACAATTGTTGTCATGAACTGGTTTCAAGCTGCACAG                         CCTGCACTTCTTTATATTGTACCAGCAGTTATTGGATTTATGGCTGCTCAT
genomic: CCGGTTTGGTTGTAACAATTGTTGTCATGAACTGGTTTCAAGCTGCACAGgtgactacta ... tcactttcagCCTGCACTTCTTTATATTGTACCAGCAGTTATTGGATTTATGGCTGCTCAT
EST: gi|34364249|gb|CF405834.1|CF405834
EST:     CCGGTTTGGTTGTAACAATTGTTGTCATGAACTGGTTTCAAGCTGCACAG                         CCTGCACTTCTTTATATTGTACCAGCAGTTATTGGATTTATGGCTGCTCAT
genomic: CCGGTTTGGTTGTAACAATTGTTGTCATGAACTGGTTTCAAGCTGCACAGgtgactacta ... tcactttcagCCTGCACTTCTTTATATTGTACCAGCAGTTATTGGATTTATGGCTGCTCAT
EST: gi|110691134|gb|EE068892.1|EE068892
EST:     CCGGTTTGGTTGTAACAATTGTTGTCATGAACTGGTTTCAAGCTGCACAG                         CCTGCACTTCTTTATATTGTACCAGCAGTTATTGGATTTATGGCTGCTCAT
genomic: CCGGTTTGGTTGTAACAATTGTTGTCATGAACTGGTTTCAAGCTGCACAGgtgactacta ... tcactttcagCCTGCACTTCTTTATATTGTACCAGCAGTTATTGGATTTATGGCTGCTCAT
EST: gi|110361505|gb|EC924984.1|EC924984
EST:     CCGGTTTGGTTGTAACAATTGTTGTCATGAACTGGTTTCAAGCTGCACAG                         CCTGCACTTCTTTATATTGTACCAGCAGTTATTGGATTTATGGCTGCTCAT
genomic: CCGGTTTGGTTGTAACAATTGTTGTCATGAACTGGTTTCAAGCTGCACAGgtgactacta ... tcactttcagCCTGCACTTCTTTATATTGTACCAGCAGTTATTGGATTTATGGCTGCTCAT
EST: gi|110376904|gb|EC941978.1|EC941978
EST:     CCGGTTTGGTTGTAACAATTGTTGTCATGAACTGGTTTCAAGCTGCACAG                         CCTGCACTTCTTTATATTGTACCAGCAGTTATTGGATTTATGGCTGCTCAT
genomic: CCGGTTTGGTTGTAACAATTGTTGTCATGAACTGGTTTCAAGCTGCACAGgtgactacta ... tcactttcagCCTGCACTTCTTTATATTGTACCAGCAGTTATTGGATTTATGGCTGCTCAT
EST: gi|110383384|gb|EC947755.1|EC947755
EST:     CATGAACTGGTTTCAAGCTGCACAG                         CCTGCACTTCTTTATATTGTACCAGCAGTTATTGGATTTATGGCTGCTCAT
genomic: CATGAACTGGTTTCAAGCTGCACAGgtgactacta ... tcactttcagCCTGCACTTCTTTATATTGTACCAGCAGTTATTGGATTTATGGCTGCTCAT
EST: gi|27582830|gb|CB005525.1|CB005525
EST:     CCGGTTTGGTTGTAACAATTGTTGTCATGAACTGGTTTCAAGCTGCACAG                         CCTGCACTTCTTTATATTGTACCAGCAGTTATTGGATTTATGGCTGCTCAT
genomic: CCGGTTTGGTTGTAACAATTGTTGTCATGAACTGGTTTCAAGCTGCACAGgtgactacta ... tcactttcagCCTGCACTTCTTTATATTGTACCAGCAGTTATTGGATTTATGGCTGCTCAT
EST: gi|110730433|gb|EE107509.1|EE107509
EST:     CCGGTTTGGTTGTAACAATTGTTGTCATGAACTGGTTTCAAGCTGCACAG                         CCTGCACTTCTTTATATTGTACCAGCAGTTATTGGATTTATGGCTGCTCAT
genomic: CCGGTTTGGTTGTAACAATTGTTGTCATGAACTGGTTTCAAGCTGCACAGgtgactacta ... tcactttcagCCTGCACTTCTTTATATTGTACCAGCAGTTATTGGATTTATGGCTGCTCAT
EST: gi|110374870|gb|EC939811.1|EC939811
EST:     CTGGTTTCAAGCTGCACAG                         CCTGCACTTCTTTATATTGTACCAGCAGTTATTGGATTTATGGCTGCTCAT
genomic: CTGGTTTCAAGCTGCACAGgtgactacta ... tcactttcagCCTGCACTTCTTTATATTGTACCAGCAGTTATTGGATTTATGGCTGCTCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGAGGGAAAGGGAACCAGTACTTTAAGAGTGCATTTTTGGGATATACAACCGGTTTGGTTGTAACAATTGTTGTCATGAACTGGTTTCAAGCTGCACAGgtgactactacaaaatccatttctctatcctatatgactgatacgtgtggagatatagttccctttgttgaatttcattcagtatctagctggctttaactgtttaagaccagtggaagttagagtatttccatgtgtgagttttctcgtgttattcactacttggtcctaactgttattctaacttcactttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC