Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTAGGGTTTGCAAAAGCATAGAGAAACCCGAGCTCAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAGgtctgatcatatgttcttttattttcctttgttttctgagctaccaatcggaaagttatgtttgttaaagtttcggtaacttattttgttttctcttacag

Basic information

species Vitis vinifera
transcript Vv11s0016g01380.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g01380.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA09G28440.1 (Glycine max), 5'ss of exon 1
-ATTAGGGTTTGCAAA--------AGCATAGA--GAAACCCGA----GCTCAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAGgtc----------tgatcatatgttcttttattttcctttgttttctgagctaccaatcggaaagttatgtttgttaaagtttcggtaacttattttgttttctcttacag
 |||||||||||||           |  ||||    |||| ||    | ||   |||   |   ||||||||||| |||||||||||||||||||||||||||          |||   ||||   |||||||||  ||| | |  || | |   ||  | ||   ||  ||   ||  |||    |||  |                   
AATTAGGGTTTGCAGTCACTGCTTTGTTTAGATCAGAACCAGATCGTGTTCTCTTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAGgtcagtggtacaatgaatctatgaatttttattttattttttctattgtgtttgaaagtgaaactgtaaattgaatagtgttat--taatgtgcag---------------

upper sequence: Vv11s0016g01380.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA16G33230.1 (Glycine max), 5'ss of exon 1
--------------ATTAGGGTTTGCAAAAGCATAGAGAAACCCGAGCTCAGA-TCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAGgtctg-----------atcatatgttcttttattttcc-tttgttttctgagctaccaatcggaaagttatgtttgttaaagtttcggtaacttattttgttttctcttacag
                  | |||||       | |    ||||  | |      |||   |   ||||||||||| ||||||||||||||||||||||||||| |           |||  |         ||||||  |||||  | |   || |   ||      || ||| || |||    | |   | ||   | |  ||    |  ||
TCACTGCTCTGTTTCACCGAGTTTGGGCGTTTAGATCAGAACCAAATCGTGTTCTCTTCCATTGGCAAACATGGCAACTCAAATGAGCAAGAAGAGAAAGgtcagtggttcaatgaatcgcaaacagcaacattttctatttgtggttttttcttct--tcattcctttgtgtatgctaa----ttgaacatttgaatggcgttaatgtgtag

upper sequence: Vv11s0016g01380.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA16G33240.1 (Glycine max), 5'ss of exon 1
---------------ATTAGGGTTTGCAAAAGCATAGAG-AAACCCGAGCTCAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAGgtctg-----------atcatatgttcttttattttcctttgttttctgagctaccaatcggaaagttatgtttgttaaagtttcggtaacttattttgttttctcttacag
               |  ||  |  |     |  |   | |    ||  |    || || |   | ||||||||||| |||| ||||||||||||||||||||  |           |||  |         ||||||  ||  | | |    |  |         ||| ||| ||| ||   || |   | ||   | |  ||    |  ||
TCACACTGTGTTTGGAGCAGAATCAGATCGTGTGTTCCGTACGTTCGTTCGTTCATTTCCAGTGT-CAAACATGGCGTCTCAGATGAGCAAGAAGAGAAAGgtaagtgctagagagaatcgaaaacagcagcattttctatttgtgtttattttttcttcattcttgttgtgtatgtgaa---tttgaacatttgaatggcgttaatgtgtag

upper sequence: Vv11s0016g01380.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA10G26790.1 (Glycine max), 5'ss of exon 1
----------------ATTAGGGTTTGCAAAAGCATAGAGAAACCCGAGCTCAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAGgt---ctgatcatatgttcttttattttcctttgttttctgagctaccaatcggaaagttatgtttgttaaagtttcggtaacttattttgttttctcttacag----
                   |    | ||    |||    |       ||| | | ||||  | || | |  |||||||| |||||||||||||||||||||||       ||||   | |    ||  |||||       |||  |   |       | |||   |   || | ||||  |   ||||  ||| ||    |        
GGGTTTAGCGCCACACCCCAATCGTAGCCGTCGCACTCTGTGTTTTCAGCGCCG-TCTCCGATCTCCGACAATGGCGACCCAAATGAGCAAGAAGAGAAAGgtgactcactcattcataccacaatcatccttcaccaattgaaattaaacctcatcaattaa--taactataatttcaatt-tttatcgtgtgtttctgtgtgcgcag

upper sequence: Vv11s0016g01380.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA10G26890.1 (Glycine max), 5'ss of exon 1
----------------ATTAGGGTTTGCAAAAGCATAGAGAAACCCGAGCTCAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAGgt---ctgatcatatgttcttttattttcctttgttttctgagctaccaatcggaaagttatgtttgttaaagtttcggtaacttattttgttttctcttacag----
                   |    | ||    |||    |        || | | ||||  | || | |  |||||||| |||||||||||||||||||||||       ||||   | |    ||   ||||       |||  |   |       | |||   |   ||   ||||  |   ||||  ||| ||    |        
GGGTTTAGCGCCACACTCCAATCGTAGCCGTCGCACTCTGTGTTTTCTGCGCCG-TCTCCGATCTCCGACAATGGCGACCCAAATGAGCAAGAAGAGAAAGgtgactcactcattcataccacaatcagccttcaccaattgaaattaaacctcatcaattaa--taactatgatttcaattttttatcgtgtgtttctgtgtgcgcag

upper sequence: Vv11s0016g01380.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AT2G31610.1 (Arabidopsis thaliana), 5'ss of exon 1
----------ATTAGGGTTTGCAAAAGCATAGAGAAACCC-GAGCTCAGAT----CTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAGgtc--tgatcatatgttcttttattttcctttgttttctg-agct--accaatcggaaagttatgtttgttaaagtttcggtaacttattttgttttctcttacag
            |    || |    | |||  ||     | ||| || | |     ||| | |  |||  |||||||||||||| |||||||||||||||||   |  | || |  | |||| |||||  | |  ||||  ||||  | |     | || | ||  | ||||  || |  |||                       
CGAGCTTACCGATTCTCTTCGTCTCAACATTTAGGGTTTCAGAGATCGGCTGATTTTCACATCCACAAGTATGGCGACTCAAATCAGCAAGAAGAGAAAGgtgaattgtgatttcattttttgttttcagtggacttctctagctgtatcgtattggaactgat-ctggttactgtgtttgtag----------------------

upper sequence: Vv11s0016g01380.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AT3G53870.1 (Arabidopsis thaliana), 5'ss of exon 1
---ATTAGGGTTTGCAAAAGCATAGAGAAACCCGAGCTCAGAT-CTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAGgtctgatcatatg-ttcttttattttcctttgttttctgagctaccaatcggaaagttatgtttgttaaagtttcggtaactt-attttgttttctcttacag
   |||| |     ||     |  |    |        ||||| |||| |  |||||||||| ||||||| || |||||||||||||||||   ||  | || |||| ||  |||  ||  ||   ||   |     |     |  | | || || |  || | |  |  || |||||||            
GAGATTACGCCGCTCATTTTTAGGGTTTCAGATATAGGCAGATTCTCACATTTGCAAACATGACGACTCAGATCAGCAAGAAGAGAAAGgtg-aattgtgtgattctgttcattttgttctttcaatggatttatcgtattggaactgttttggtaactgtgttgagattttgattttgtag----------

upper sequence: Vv11s0016g01380.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: EFJ34676 (Selaginella moellendorffii), 5'ss of exon 1
ATTAGGGTTTGCAAAAGCATAGAGAAACCCGAGCTCAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAGgtctgatcatatgttcttttattttcctttgttttctgagctaccaatcggaaagttatgtttgttaaagtttcggtaacttattttgttttctcttacag
                                                ||    |||||||||||| || ||||||||||||||||| ||   |    | |   |   | |  |  || |||   || |||                                                       
--------------------------------------GCTAGGGCTTTGGCGGCATGGCGACTCAGATCAGCAAGAAGAGAAAGgtttgtcaagcaatgccgctccctcctctgattctct---cttccag------------------------------------------------------

upper sequence: Vv11s0016g01380.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: EFJ31038 (Selaginella moellendorffii), 5'ss of exon 1
----------ATTAGGGTTTG-CAAAAGCA-TAGAGAAACCCGAGCTCAGATCTCAAA---CCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAGgtctgatcatatgttcttttattttcctttgttttctgagctaccaatcggaaagttatgtttgttaaagtttcggtaacttattttgttttctcttacag
          || |   |||| |||||||  ||||  | ||| |  |  ||   | |      ||    |||||||||||| || ||||||||||||||||| || |||    | |   | |   | | || |  ||||  |     |   |                                                 
GGCATACTGCATAATAATTTGTCAAAAGCCCTAGAAGAGCCCTAATTAGGACGGCTAGGGCTTTGGCGGCATGGCGACTCAGATCAGCAAGAAGAGAAAGgtttgttcagcaatgccgctctccccttctgct--ctgatttgattcttccag------------------------------------------------

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|33402276|gb|CF207903.1|CF207903
EST:     CAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAG                         TTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
genomic: CAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAGgtctgatcat ... tctcttacagTTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
EST: gi|351015000|gb|FQ444289.1|FQ444289
EST:     CAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAG                         TTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
genomic: CAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAGgtctgatcat ... tctcttacagTTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
EST: gi|26262026|gb|CA813089.1|CA813089
EST:     CAGATCTCAAATCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAG                         TTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
genomic: CAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAGgtctgatcat ... tctcttacagTTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
EST: gi|26261974|gb|CA813037.1|CA813037
EST:     CAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAG                         TTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
genomic: CAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAGgtctgatcat ... tctcttacagTTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
EST: gi|349832316|gb|FQ420877.1|FQ420877
EST:     CAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAG                         TTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
genomic: CAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAGgtctgatcat ... tctcttacagTTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
EST: gi|71869842|gb|DT018897.1|DT018897
EST:     CAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAG                         TTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
genomic: CAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAGgtctgatcat ... tctcttacagTTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
EST: gi|351043060|gb|FQ443902.1|FQ443902
EST:     CAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAG                         TTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
genomic: CAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAGgtctgatcat ... tctcttacagTTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
EST: gi|110712407|gb|EE089992.1|EE089992
EST:     CAGATCCCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAG                         TTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
genomic: CAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAGgtctgatcat ... tctcttacagTTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
EST: gi|37184104|gb|CF603458.1|CF603458
EST:     CAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAG                         TTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
genomic: CAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAGgtctgatcat ... tctcttacagTTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
EST: gi|26267581|gb|CA818644.1|CA818644
EST:     ACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAG                         TTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
genomic: ACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAGgtctgatcat ... tctcttacagTTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
EST: gi|351025652|gb|FQ426666.1|FQ426666
EST:     CAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAG                         TTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
genomic: CAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAGgtctgatcat ... tctcttacagTTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
EST: gi|34546837|gb|CF515069.1|CF515069
EST:     CAGATCTCAAACCTGGATACATGGCGACTCAAATGAGCAAGAAGAGAAAG                         TTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
genomic: CAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAGgtctgatcat ... tctcttacagTTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
EST: gi|33402921|gb|CF208548.1|CF208548
EST:     CAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAG                         TTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
genomic: CAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAGgtctgatcat ... tctcttacagTTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
EST: gi|110684969|gb|EE062852.1|EE062852
EST:     CAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGATGAGAACG                         TTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
genomic: CAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAGgtctgatcat ... tctcttacagTTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
EST: gi|110687640|gb|EE065280.1|EE065280
EST:     CAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAG                         TTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
genomic: CAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAGgtctgatcat ... tctcttacagTTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
EST: gi|110360898|gb|EC924341.1|EC924341
EST:     CAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAG                         TTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
genomic: CAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAGgtctgatcat ... tctcttacagTTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
EST: gi|110425974|gb|EC992370.1|EC992370
EST:     CAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAG                         TTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
genomic: CAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAGgtctgatcat ... tctcttacagTTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
EST: gi|37184006|gb|CF603360.1|CF603360
EST:     CAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAG                         TTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA
genomic: CAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAGgtctgatcat ... tctcttacagTTCGTAGCTGATGGAGTTTTCTTTGCTGAGCTGAACGAGGTTCTCACCAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTAGGGTTTGCAAAAGCATAGAGAAACCCGAGCTCAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAGgtctgatcatatgttcttttattttcctttgttttctgagctaccaatcggaaagttatgtttgttaaagtttcggtaacttattttgttttctcttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA