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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTCTGATCCTGTGTGGGTGATGAATGTTGTTCCTCCCCGCAAGCCATCAACTCTGGGAGTCATTTATGACAGAGGTCTTATTGGGGTCTACCATGATTGgtgagttactgtgtcatgtgctactcttgtctacggaataaatatgcacctgggttgaaatgaagtgttttagagtcatagattagccaccttcatatcg...

Basic information

species Vitis vinifera
transcript Vv15s0048g01990.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0048g01990.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os04g48140.1 (Oryza sativa), 5'ss of exon 5
CGTCTGATCCTGTGTGGGTGATGAATGTTGTTCCTCCCCGCAAGCCATCAACTCTGGGAGTCATTTATGACAGAGGTCTTATTGGGGTCTACCATGATTGgtgag---ttactgtgtcatgtgctactcttgtctacggaataaatatgcacctgggttgaaatgaagtgttttagagtcatagattagccaccttcatatcg--
  ||||||||||| ||||| ||||||||||||||| | |  || ||||  || || ||||| || |||||||| || |||||||| || || ||||| |||| ||   ||||| |  ||     |     | |||      | | ||||        ||| |||      ||||      ||| | || | |  ||||| |    
TCTCTGATCCTGTATGGGTTATGAATGTTGTTCCTGCTCAAAAACCATTGACACTTGGAGTAATATATGACAGGGGCCTTATTGGAGTTTATCATGACTGgtaaggacttactattacagaaatttgcaatatctttctgctga-tatgtttt---attgtaatcccaacttttctcaatataaacta-ctatgttcatctattt

upper sequence: Vv15s0048g01990.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G076841_T01 (Zea mays), 5'ss of exon 5
CGTCTGATCCTGTGTGGGTGATGAATGTTGTTCCTCCCCGCAAGCCATCAACTCTGGGAGTCATTTATGACAGAGGTCTTATTGGGGTCTACCATGATTGgtgagttactgtgtcatgtgctactcttgtctacggaataaatatgcacctgggttgaaatgaagtgttttagagt-catagattagccaccttcatatcg
  ||||||||||| ||||| |||||||||||||||   |  |||||||  || || ||||| |||||||| || || ||||| ||||| || ||||| ||||  |   ||   ||     | |  |   |        || ||||  |  |         || | | | || || | |||    | |  |  || | ||  
TATCTGATCCTGTATGGGTTATGAATGTTGTTCCTGGTCAGAAGCCATTGACACTTGGAGTTATTTATGATAGGGGCCTTATAGGGGTTTATCATGACTGgtatgaatctaactcgctaccaatgccaatgccacatttagatata-atttcaacctttctgtattttgttggatttcatcttattgataattttacatac

upper sequence: Vv15s0048g01990.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA07G08360.1 (Glycine max), 5'ss of exon 5
CGTCTGATCCTGTGTGGGTGATGAATGTTGTTCCTCCCCGCAAGCCATCAACTCTGGGAGTCATTTATGACAGAGGTCTTATTGGGGTCTACCATGATTGgtgagttactgtgtcatgtgctactcttgtcta-cggaataaatatgcacctgggttgaaatgaagtgttttag--agtcatagattagccaccttcatatcg
  ||||||||||||||||| ||||||||||||||  | | |||||||  |||||| |  |  || | |||||||||||||||||| ||||| |||||||||||||||  | ||        | ||  ||| |  |  || |    |     |    |    ||   ||| |||   | |  || |||       || ||||  
ATTCTGATCCTGTGTGGGTAATGAATGTTGTTCCATCTCACAAGCCAATAACTCTTGATGCAATCTTTGACAGAGGTCTTATTGGAGTCTATCATGATTGgtgagttttt-tgctgaaaatttctagtgtttctcttaaaaggactttttgttatatcttttggcttgtcttaatcaatggtaaattgagtg--ttgatatga

upper sequence: Vv15s0048g01990.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA03G01870.1 (Glycine max), 5'ss of exon 5
CGTCTGATCCTGTGTGGGTGATGAATGTTGTTCCTCCCCGCAAGCCATCAACTCTGGGAGTCATTTATGACAGAGGTCTTATTGGGGTCTACCATGATTGgtgagttactgtgtcatgtgctactcttgtctacggaataaatatgcacctgggttgaa---atgaagtgttttag--agtcatagattagccaccttcatatcg
  ||||||||||||||||| ||||||||||||||  | | |||||||  |||||| |  |  || | |||||||||||||||||| || || |||||||||||||||  | ||        | |   ||| |      ||||   ||   | | || |     ||   ||| |||   | |  || |||         |||    
ATTCTGATCCTGTGTGGGTAATGAATGTTGTTCCATCTCACAAGCCAATAACTCTTGATGCAATCTTTGACAGAGGTCTTATTGGAGTTTATCATGATTGgtgagttttt-tgctgaaaatttcaagtgtttctct--taaaagggctttttgttttatcttttggcttgtcttaatcaatggtaaattgagtgttgacatga--

upper sequence: Vv15s0048g01990.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA09G40110.2 (Glycine max), 5'ss of exon 5
CGTCTGATCCTGTGTGGGTGATGAATGTTGTTCCTCCCCGCAAGCCATCAACTCTGGGAGTCATTTATGACAGAGGTCTTATTGGGGTCTACCATGATTGgtgagttactgtgtcatgtgcta----ctcttgtct--acggaataaatatgcacctgggttgaaatgaagtgttttagagtcatagattagccaccttcatatcg
  |||||||||||||||||||||||||| |||||  | |  |||||| | ||||| |  || || | |||||||||||||||||| || || ||||||||||||| |  |     ||||   |     ||||||||  | ||||| |    | | ||     |   |||  | ||     ||| | ||  |   || |        
AATCTGATCCTGTGTGGGTGATGAATGTAGTTCCAGCACAAAAGCCACCTACTCTTGATGTTATCTTTGACAGAGGTCTTATTGGAGTTTATCATGATTGgtgagctttttctgaatgtttcagtgtttcttgtcttaaaggaattatcccgaatctttcaagctctgatcttttgacacgtcttggaaaataaacttct------

upper sequence: Vv15s0048g01990.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA18G45990.1 (Glycine max), 5'ss of exon 5
CGTCTGATCCTGTGTGGGTGATGAATGTTGTTCCTCCCCGCAAGCCATCAACTCTGGGAGTCATTTATGACAGAGGTCTTATTGGGGTCTACCATGATTGgtgagttactgtgtcatgtgctactcttgtctacggaataaatatgcacctggg---ttgaaatgaagtgttttagagtcatagattagccaccttcatatcg-
  |||||||||||||||||||| ||||| |||||| | |  |||||| | ||||| |  || || | ||||||||| |||||||| ||||| ||||| ||||||| |  |     ||||   | |   || | | ||||   |      |||     |||  |||    |      |  | |   ||| |      |||     
-ATCTGATCCTGTGTGGGTGATCAATGTAGTTCCTGCACTAAAGCCACCCACTCTTGATGTTATCTTTGACAGAGGCCTTATTGGAGTCTATCATGACTGGtgagctttttctgaatgtttcagt---gtatccagaatctttcgagctctgatcttttggcatgttaggaaaataaacctttttttaactgatgacatgattt

upper sequence: Vv15s0048g01990.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT4G00740.1 (Arabidopsis thaliana), 5'ss of exon 5
CGTCTGATCCTGTGTGGGTGATGAATGTTGTTCCTCCCCGCAAGCCATCAACTCTGGGAGTCATTTATGACAGAGGTCTTATTGGGGTCTACCATGATTGgtgagttac-tgtgtcatgtgctactcttgtctacggaataaatatgcacctgggttgaaatgaagtgttttagagtcatag--attagccaccttcat-atcg----------------------------------------------------
| ||||||||||||||||| ||||||||  ||||  | || ||||||| |||||| |  || ||||||||||||||||| || || || ||||||||||||| ||| || | |||  | |  ||   |||   |   |||||| |   |  |  ||| |  |    |||| |  | || |||  ||| ||  |  | |  ||||                                                    
CATCTGATCCTGTGTGGGTTATGAATGTCATTCCAGCTCGGAAGCCATTAACTCTTGACGTGATTTATGACAGAGGTCTCATCGGTGTTTACCATGATTGgttagtcacatttgttgttta-tatatttgatca--aaataaagacttagatatgtt-atctctcttgttctgta-tcttagccattggcagcaatgaggatcgaaatatgtcacaattccttaatagtcaaaaccctattatttgtttgttgcag

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|71868271|gb|DT017326.1|DT017326
EST:     ACTCTGGGAGTCATTTATGACAGAGGTCTTATTGGGGTCTACCATGATTG                         GTGCGAGCCATTCTCAACATACCCTCGGACTTATGATCTCATCCATGTAAC
genomic: ACTCTGGGAGTCATTTATGACAGAGGTCTTATTGGGGTCTACCATGATTGgtgagttact ... gtgctgatagGTGCGAGCCATTCTCAACATACCCTCGGACTTATGATCTCATCCATGTAAC
EST: gi|110701114|gb|EE078359.1|EE078359
EST:     ACTCTGGGAGTCATTTATGACAGAAGTCTTATTGGGGTCTACCATGATTG                         GTGCGAAGC-ATTCTCAACATACCCTCGGAACT-ATGATCTCATCCATGTA
genomic: ACTCTGGGAGTCATTTATGACAGAGGTCTTATTGGGGTCTACCATGATTGgtgagttact ... gtgctgatagGTGCGA-GCCATTCTCAACATACCCTCGGA-CTTATGATCTCATCCATGTA
EST: gi|30300158|gb|CB976952.1|CB976952
EST:     ACTCTGGGAGTCATTTATGACAGAGGTCTTATTGGGGTCTCCCATGATTG                         GTGCGAGCCATTCTCAACATACCCTCGGACTTATGATCTCATCCATGTAAC
genomic: ACTCTGGGAGTCATTTATGACAGAGGTCTTATTGGGGTCTACCATGATTGgtgagttact ... gtgctgatagGTGCGAGCCATTCTCAACATACCCTCGGACTTATGATCTCATCCATGTAAC
EST: gi|29783073|gb|CB348973.2|CB348973
EST:     ACTCTGGGAGTCATTTATGACAGAGGTCTTATTGGGGTCTACCATGATTG                         GTGCGAGCCATTCTCAACATACCCTCGGACTTATGATCTCATCCATGTAAC
genomic: ACTCTGGGAGTCATTTATGACAGAGGTCTTATTGGGGTCTACCATGATTGgtgagttact ... gtgctgatagGTGCGAGCCATTCTCAACATACCCTCGGACTTATGATCTCATCCATGTAAC
EST: gi|110425458|gb|EC991843.1|EC991843
EST:     ACTCTGGGAGTCATTTATGACAGAGGTCTTATTGGGGTCTACCATGATTG                         GTGCGAGCCATTCTCAACATACCCTCGGACTTATGATCTCATCCATGTAAC
genomic: ACTCTGGGAGTCATTTATGACAGAGGTCTTATTGGGGTCTACCATGATTGgtgagttact ... gtgctgatagGTGCGAGCCATTCTCAACATACCCTCGGACTTATGATCTCATCCATGTAAC
EST: gi|34544982|gb|CF513214.1|CF513214
EST:     ACTCTGGGAGTCATTTATGACAGAGGTCTTATTGGGGTCTACCATGATTG                         GTGCGAGCCATTCTCAACATACCCTCGGACTTATGATCTCATCCATGTAAC
genomic: ACTCTGGGAGTCATTTATGACAGAGGTCTTATTGGGGTCTACCATGATTGgtgagttact ... gtgctgatagGTGCGAGCCATTCTCAACATACCCTCGGACTTATGATCTCATCCATGTAAC
EST: gi|30300088|gb|CB976882.1|CB976882
EST:     ACTCTGGGAGTCATTTATGACAGAGGTCTTATTGGGGTCTACCATGATTG                         GTGCGAGCCATTCTCAACATACCCTCGGACTTATGATCTCATCCATGTAAC
genomic: ACTCTGGGAGTCATTTATGACAGAGGTCTTATTGGGGTCTACCATGATTGgtgagttact ... gtgctgatagGTGCGAGCCATTCTCAACATACCCTCGGACTTATGATCTCATCCATGTAAC
EST: gi|34545974|gb|CF514206.1|CF514206
EST:     ACTCTGGGAGTCATTTATGACAGAGGTCTTATTGGGGTCTACCATGATTG                         GTGCGAGCCATTCTCAACATACCCTCGGACTTATGATCTCATCCATGTAAC
genomic: ACTCTGGGAGTCATTTATGACAGAGGTCTTATTGGGGTCTACCATGATTGgtgagttact ... gtgctgatagGTGCGAGCCATTCTCAACATACCCTCGGACTTATGATCTCATCCATGTAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTCTGATCCTGTGTGGGTGATGAATGTTGTTCCTCCCCGCAAGCCATCAACTCTGGGAGTCATTTATGACAGAGGTCTTATTGGGGTCTACCATGATTGgtgagttactgtgtcatgtgctactcttgtctacggaataaatatgcacctgggttgaaatgaagtgttttagagtcatagattagccaccttcatatcg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaatgaa