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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAAGCTCTTGTTGGAATGGCAGAGGTAGAAGCAGCCATACAGGAAATGTTCCAGGCACCTCAAATTCAAgtgagttgaaagcccactttatgttctcaattagaaatcctggttcttgatacaactccatttcattctaagagaaaatggaatcttggaaaaggaggta...

Basic information

species Vitis vinifera
transcript Vv06s0004g02050.t01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g02050.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GRMZM2G168249_T03 (Zea mays), 5'ss of exon 10
GAAAAGCTCTTGTTGGAATGGCAGAGGTAGAAGCAGCCATACAGGAAATGTTCCAGGCACCTCAAATTCAAgtgagttgaaa--gcccactttatgt---tctcaattagaaatcctggttcttgatacaactccatttcattctaagagaaaatggaatcttggaaaaggaggta-----------
|  | ||| |||||   ||||  ||  ||||||| || || |||||| | |||||||||||||| |||||||||||| ||||  |  || ||||||      |  | |   || | |     ||  || || ||  ||     |  |     | | | ||||  | ||      |            
GTGATGCTGTTGTTTCCATGGGTGACATAGAAGCTGCTATTCAGGAAGTCTTCCAGGCACCTCATATTCAAgtgagtggaaaatgtgcattttatgcaagcttgtactcataaccatatcaattatta-aagtcacttgagcacccaccattatttggatctcagcaacatttttgtctctttacag

upper sequence: Vv06s0004g02050.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA15G03900.1 (Glycine max), 5'ss of exon 14
GAAAAGCTCTTGTTGGAATGGCAGAGGTAGAAGCAGCCATACAGGAAATGTTCCAGGCACCTCAAATTCAAgtgagttgaaagcccactttatgttc-tcaattagaaatcctggttcttgatacaactccatttcattctaagagaaaatggaatcttggaaaaggaggta--
|||| |  ||||||||||||| ||| || ||||||||||| || ||||||||||| |||||||| |||||||||||||||||     |  | || |  | | ||    || |   || || |   ||    |  | || | |   |    |   |   || |  | |   |   
GAAAGGGACTTGTTGGAATGGTAGATGTTGAAGCAGCCATTCAAGAAATGTTCCAAGCACCTCATATTCAAgtgagttgaaa-tttgcaatgtgctgattatttcttgataccatttttttactgaatggtagatgatgccatagggc--ttagacagtgaacgaagtcttgag

upper sequence: Vv06s0004g02050.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA13G41490.1 (Glycine max), 5'ss of exon 12
GAAAAGCTCTTGTTGGAATGGCAGAGGTAGAAGCAGCCATACAGGAAATGTTCCAGGCACCTCAAATTCAAgtgagttgaaagcccactttatgttctcaattagaaatcctggttcttga-tacaactccatttcattctaagagaaaatggaat----cttggaaaaggaggta
|||| |  ||||||||||||| ||| || || |||||||| || ||||||||||| |||||||| |||||||||||||||||         |||| || | |||    || || | ||| | | | | |   || |    |   |||  |||  ||    |||  | |  ||   |
GAAAGGGACTTGTTGGAATGGTAGATGTTGAGGCAGCCATTCAAGAAATGTTCCAAGCACCTCATATTCAAgtgagttgaaatttg---caatgtgctgatttatt--tcttgatgcttaagtgccatttttttactgaatggtagatgatgccatagggcttacacagtgaacga

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|30129730|gb|CB915069.1|CB915069
EST:     CAGAGGTAGAAGCAGCCATACAGGAAATGTTCCAGGCACCTCAAATTCAA                         GTGATGAAGAGTAGCTCAAAGCTGAGTAAAATCTTCTTGGTAGCAATGGTG
genomic: CAGAGGTAGAAGCAGCCATACAGGAAATGTTCCAGGCACCTCAAATTCAAgtgagttgaa ... ttgttcccagGTGATGAAGAGTAGCTCAAAGCTGAGTAAAATCTTCTTGGTAGCAATGGTG
EST: gi|110702580|gb|EE081092.1|EE081092
EST:     CAGAGGTAGAAGCAGCCATACAGGAAATGTTCCAGGCACCTCAAATTCAA                         GTGATGAAGAGTAGCTCANAGCTGAGTAAAATCTTCTTGGTAGCAATGGTG
genomic: CAGAGGTAGAAGCAGCCATACAGGAAATGTTCCAGGCACCTCAAATTCAAgtgagttgaa ... ttgttcccagGTGATGAAGAGTAGCTCAAAGCTGAGTAAAATCTTCTTGGTAGCAATGGTG
EST: gi|30136412|gb|CB921750.1|CB921750
EST:     CAGAGGTAGAAGCAGCCATACAGGAAATGTTCCAGGCACCTCAAATTCAA                         GTGATGAAGAGTAGCTCAAAGCTGAGTAAAATCTTCTTGGTAGCAATGGTG
genomic: CAGAGGTAGAAGCAGCCATACAGGAAATGTTCCAGGCACCTCAAATTCAAgtgagttgaa ... ttgttcccagGTGATGAAGAGTAGCTCAAAGCTGAGTAAAATCTTCTTGGTAGCAATGGTG
EST: gi|30126105|gb|CB911444.1|CB911444
EST:     CAGAGGTAGAAGCAGCCATACAGGAAATGTTCCAGGCACCTCAAATTCAA                         GTGATGAAGAGTAGCTCAAAGCTGAGTAAAATCTTCTTGGTAGCAATGGTG
genomic: CAGAGGTAGAAGCAGCCATACAGGAAATGTTCCAGGCACCTCAAATTCAAgtgagttgaa ... ttgttcccagGTGATGAAGAGTAGCTCAAAGCTGAGTAAAATCTTCTTGGTAGCAATGGTG
EST: gi|30130177|gb|CB915516.1|CB915516
EST:     CAGAGGTAGAAGCAGCCATACAGGAAATGTTCCAGGCACCTCAAATTCAA                         GTGATGAAGAGTAGCTCAAAGCTGAGTAAAATCTTCTTGGTAGCAATGGTG
genomic: CAGAGGTAGAAGCAGCCATACAGGAAATGTTCCAGGCACCTCAAATTCAAgtgagttgaa ... ttgttcccagGTGATGAAGAGTAGCTCAAAGCTGAGTAAAATCTTCTTGGTAGCAATGGTG
EST: gi|110361075|gb|EC924528.1|EC924528
EST:     CAGAGGTAGAAGCAGCCATACAGGAAATGTTCCAGGCACCTCAAATTCAA                         GTGATGAAGAGTAGCTCAAAGCTGAGTAAAATCTTCTTGGTAGCAATGGTG
genomic: CAGAGGTAGAAGCAGCCATACAGGAAATGTTCCAGGCACCTCAAATTCAAgtgagttgaa ... ttgttcccagGTGATGAAGAGTAGCTCAAAGCTGAGTAAAATCTTCTTGGTAGCAATGGTG
EST: gi|33405995|gb|CF211622.1|CF211622
EST:     CAGAGGTAGAAGCAGCCATACAGGAAATGTTCCAGGCACCTCAAATTCAA                         GTGATGAAGAGTAGCTCAAAGCTGAGTAAAATCTTCTTGGTAGCAATGGTG
genomic: CAGAGGTAGAAGCAGCCATACAGGAAATGTTCCAGGCACCTCAAATTCAAgtgagttgaa ... ttgttcccagGTGATGAAGAGTAGCTCAAAGCTGAGTAAAATCTTCTTGGTAGCAATGGTG
EST: gi|110362552|gb|EC926095.1|EC926095
EST:     CAGAGGTAGAAGCAGCCATACAGGAAATGTTCCAGGCACCTCAAATTCAA                         GTGATGAAGAGTAGCTCAAAGCTGAGTAAAATCTTCTTGGTAGCAATGGTG
genomic: CAGAGGTAGAAGCAGCCATACAGGAAATGTTCCAGGCACCTCAAATTCAAgtgagttgaa ... ttgttcccagGTGATGAAGAGTAGCTCAAAGCTGAGTAAAATCTTCTTGGTAGCAATGGTG
EST: gi|110363917|gb|EC927549.1|EC927549
EST:     CAGAGGTAGAAGCAGCCATACAGGAAATGTTCCAGGCACCTCAAATTCAA                         GTGATGAAGAGTAGCTCAAAGCTGAGTAAAATCTTCTTGGTAGCAATGGTG
genomic: CAGAGGTAGAAGCAGCCATACAGGAAATGTTCCAGGCACCTCAAATTCAAgtgagttgaa ... ttgttcccagGTGATGAAGAGTAGCTCAAAGCTGAGTAAAATCTTCTTGGTAGCAATGGTG
EST: gi|33406095|gb|CF211722.1|CF211722
EST:     CAGAGGTAGAAGCAGCCATACAGGAAATGTTCCAGGCACCTCAAATTCAA                         GTGATGAAGAGTAGCTCAAAGCTGAGTAAAATCTTCTTGGTAGCAATGGTG
genomic: CAGAGGTAGAAGCAGCCATACAGGAAATGTTCCAGGCACCTCAAATTCAAgtgagttgaa ... ttgttcccagGTGATGAAGAGTAGCTCAAAGCTGAGTAAAATCTTCTTGGTAGCAATGGTG
EST: gi|110363719|gb|EC927329.1|EC927329
EST:     CAGAGGTAGAAGCAGCCATACAGGAAATGTTCCAGGCACCTCAAATTCAA                         GTGATGAAGAGTAGCTCAAAGCTGAGTAAAATCTTCTTGGTAGCAATGGTG
genomic: CAGAGGTAGAAGCAGCCATACAGGAAATGTTCCAGGCACCTCAAATTCAAgtgagttgaa ... ttgttcccagGTGATGAAGAGTAGCTCAAAGCTGAGTAAAATCTTCTTGGTAGCAATGGTG
EST: gi|30329378|gb|CD012640.1|CD012640
EST:     CAGAGGTAGAAGCAGCCATACAGGAAATGTTCCAGGCACCTCAAATTCAA                         GTGATGAAGAGTAGCTCAAAGCTGAGTAAAATCTTCTTGGTAGCAATGGTG
genomic: CAGAGGTAGAAGCAGCCATACAGGAAATGTTCCAGGCACCTCAAATTCAAgtgagttgaa ... ttgttcccagGTGATGAAGAGTAGCTCAAAGCTGAGTAAAATCTTCTTGGTAGCAATGGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAAGCTCTTGTTGGAATGGCAGAGGTAGAAGCAGCCATACAGGAAATGTTCCAGGCACCTCAAATTCAAgtgagttgaaagcccactttatgttctcaattagaaatcctggttcttgatacaactccatttcattctaagagaaaatggaatcttggaaaaggaggta

- - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggaaaa