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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGGGTTTGATAGGTGCGGGTACCAACAATGCTCGAATTGCTGGCATGCTCCGTAATCTTTCAAGCTATTACTACAAAGAAGCTAGCCTTCTGTTCTGTgtaaagattcttttattacctttaaattctctagattttctttcattcatccaatgggttctatatattttcacaccaatattgttttggccacttgtgcag

Basic information

species Vitis vinifera
transcript Vv12s0028g03130.t01
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: LOC_Os02g05340.1 (Oryza sativa), 5'ss of exon 21
CTTGGGTTTGATAGGTGCGGGTACCAACAATGCTCGAATTGCTGGCATGCTCCGTAATCTTTCAAGCTATTACTACAAAGAAGCTAGCCTTCTGTTCTGTgtaaagattcttttattacctttaaattctctagattt-tctttcattca--tccaatgggttctatatattttcacaccaatattgtt----ttggccacttgtgcag
 |||||||| || ||||| ||||| ||||||||| |||| ||||| ||||| || ||||||||||| || || ||||||||||||   | |||||| |||||||   ||  |  ||   |  | |    | || |  | |  | |||||   |  |   |||| |||||| |  |  ||  ||||||      ||   ||  | | |||
ATTGGGTTTCATTGGTGCTGGTACAAACAATGCTAGAATAGCTGGTATGCTTCGCAATCTTTCAAGTTACTATTACAAAGAAGCTGCGCATCTGTTTTGTgtaag--ttaataaatccacaatgatccttttaaacctgtgctccattctgttgtacctggttgtatataatg-cgtacatatattgacaaaattttgcatgtattcag

upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: LOC_Os09g15750.1 (Oryza sativa), 5'ss of exon 21
CTTGGGTTTGATAGGTGCGGGTACCAACAATGCTCGAATTGCTGGCATGCTCCGTAATCTTTCAAGCTATTACTACAAAGAAGCTAGCCTTCTGTTCTGTgtaaa---gattcttttattacctttaaat-tctctagattttctttcattc--atccaatgg-gttctatatat-tttcacaccaatattgttttggccacttgtgcag
| |||| |||||||| || ||||| |||||||| ||||| ||||| ||||| || || || ||||| ||||| |||||||||||  | | |||||| |||||||     | |||   || | | ||   | ||| |   ||  |  | ||||  |||  |||  ||| |||  |  ||||| | || | || ||      ||||      
CCTGGGCTTGATAGGGGCTGGTACAAACAATGCCCGAATAGCTGGGATGCTTCGGAACCTCTCAAGTTATTATTACAAAGAAGCAGGACATCTGTTTTGTgtaagttcaaatctaaaataaacattttttatctttgttttgccaattattctgatctcatgctgttgtattcaagtttcatatcagtttttttcatttgactttcag--

upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: LOC_Os06g48640.2 (Oryza sativa), 5'ss of exon 21
CTTGGGTTTGATAGGTGCGGGTACCAACAATGCTCGAATTGCTGGCATGCTCCGTAATCTTTCAAGCTATTACTACAAAGAAGCTAGCCTTCTGTTCTGTgtaaa---gattcttttattacctttaaattctctagattttctttcatt--catccaatgg-gttctatatat-tttcacaccaatattgttttggccacttgtgcag
| |||| |||||||| || ||||| |||||||| || || ||||| ||||| || || || ||||| ||||| |||||||||||  | | |||||| |||||||     | |||   || | | ||    ||| |   ||  |  | |||   |||  |||  |||  ||  |  ||||| | || |    ||      ||||  |   
CCTGGGCTTGATAGGGGCTGGTACAAACAATGCCCGTATAGCTGGGATGCTTCGGAACCTCTCAAGTTATTATTACAAAGAAGCAGGACATCTGTTTTGTgtaagttcaaatctaaaataaacatttttatctttgttttgccagttattgtgatctcatgctgttgcattcaagtttcatatcagttcatttcatttgacttcag---

upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: GRMZM2G155384_T02 (Zea mays), 5'ss of exon 21
CTTGGGTTTGATAGGTGCGGGTACCAACAATGCTCGAATTGCTGGCATGCTCCGTAATCTTTCAAGCTATTACTACAAAGAAGCTAGCCTTCTGTTCTGTgtaaagat---tcttttattacctttaaattctctagattttctttcattcatccaatgggttctatatattttcacaccaat-attgttttggccacttgtgcag----
 ||||||||||| ||||| || || ||||||||  |||| ||||||||||| || ||||||||||| ||||||||||||||||||   | |||||| |||||||  ||   ||    |  |  |||       ||  || | ||   | |  | |  ||| |||  ||||  |||   ||| | ||   |||   |   |  |  |    
ATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGAATAGCTGGCATGCTTCGCAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTgtaagtatatatcaacgacgatattttggcatccttcatgtactaataatggttccttggtttcgttataagttccatccattgatccgttttatcgtgttcgtcgtcag

upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: GRMZM2G155384_T01 (Zea mays), 5'ss of exon 21
CTTGGGTTTGATAGGTGCGGGTACCAACAATGCTCGAATTGCTGGCATGCTCCGTAATCTTTCAAGCTATTACTACAAAGAAGCTAGCCTTCTGTTCTGTgtaaagattcttttattac---ctttaaattctctagattttctttcattcatccaatgggttctatatattttcacaccaat-attgttttggccacttgtgcag---------
    |||||||| ||||| || || ||||||||  |||| ||||||||||| || ||||||||||| ||||||||||||||||||   | |||||| |||||||  ||   |  |  ||    |||       ||  || | ||   | |  | |  ||| |||  ||||  |||   ||| | ||   |||   |   |  |  |         
----GGTTTGATTGGTGCTGGCACAAACAATGCCAGAATAGCTGGCATGCTTCGCAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTAAgtatatatcaacgacgatattttggcatccttcatgtactaataatggttccttggtttcgttataagttccatccattgatccgttttatcgtgttcgtcgtcaggttag

upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: GRMZM5G816609_T01 (Zea mays), 5'ss of exon 7
CTTGGGTTTGATAGGTGCGGGTACCAACAATGCTCGAATTGCTGGCATGCTCCGTAATCTTTCAAGCTATTACTACAAAGAAGCTAGCCTTCTGTTCTGTgtaaagat---tcttttattacctttaaattctctagattttctttcattcatccaatgggttctatatattttcacaccaatattgttttggccacttgtgcag----
 ||||||||||| ||||| || || ||||||||  |||| |||| |||||| || ||||||||||| |||||||||||||||||    | |||||| |||||||  ||   ||  | || | | ||       ||  ||   ||||   |      || | || |   || |||||  |    |||  |||       |          
ATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGAATAGCTGCCATGCTTCGCAATCTTTCAAGTTATTACTACAAAGAAGCAGCTCATCTGTTTTGTgtaagtatagatcgataatgatcatttggcatccttcatggacttttggttccttgattgttttt---tagtttcatgctttgattaattttattgtgtacatcatcag

upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: GLYMA12G13410.1 (Glycine max), 5'ss of exon 21
CTTGGGTTTGATAGGTGCGGGTACCAACAATGCTCGAATTGCTGGCATGCTCCGTAATCTTTCAAGCTATTACTACAAAGAAGCTAGCCTTCTGTTCTGTgtaaagattcttttattacctttaaattctctagattttctttcattcatccaatgggttctatatattttcacaccaatattgttttggccacttgtgcag
||||||| |||||||||| || || |||||||||||||||||||||||||| || |||||||| || ||||||||||| ||  | |||||||| ||||||||||     ||||      || |||  ||||    |  || ||  ||  || |||     || | | | |   |||| || || ||||  ||   | |  ||
CTTGGGTCTGATAGGTGCTGGAACGAACAATGCTCGAATTGCTGGCATGCTTCGCAATCTTTCTAGTTATTACTACAAGGATACCAGCCTTCTATTCTGTgtaag----cttt------ctctaagctctcc---tcctccttattt--tctaatttccactgtttttatggtcacccattttctttta-ccttatctatag

upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: GLYMA06G44340.1 (Glycine max), 5'ss of exon 21
CTTGGGTTTGATAGGTGCGGGTACCAACAATGCTCGAATTGCTGGCATGCTCCGTAATCTTTCAAGCTATTACTACAAAGAAGCTAGCCTTCTGTTCTGTgtaaagattctttta--ttacctttaaattctctagattttctttcattcat--ccaatgggttctatatattttcacaccaatattgttttggccacttgtgcag
||||||| | |||||||| || || |||||||||||||||||||||||||| || ||||||||||| ||||||||||| ||  | |||||||| ||||| ||||   |||| | |  || |||    ||| ||||  ||    |   || ||   ||     ||   | ||  ||  |   |                        
CTTGGGTCTAATAGGTGCTGGAACGAACAATGCTCGAATTGCTGGCATGCTTCGCAATCTTTCAAGTTATTACTACAAGGATACCAGCCTTCTATTCTGCgtaagctttctctaagctttcctccttattttctaatttccactgtttttatggtcaccaattttcttttaccttatctatag-----------------------

upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: AT4G28470.1 (Arabidopsis thaliana), 5'ss of exon 19
CTTGGGTTTGATAGGTGCGGGTACCAACAATGCTCGAATTGCTGGCATGCTCCGTAATCTTTCAAGCTATTACTACAAAGAAGCTAGCCTTCTGTTCTGTgtaaagattcttttattacctttaaattctctagattttctttcattcatccaatgggttctatatatttt---cacaccaatattgttttggccacttgtgcag
| | || |||||||| || || |||||||||||  | || |||||||||||  | ||||| || |||||||| ||||| || || |||||||| |||||||||| |    |||||| |  | |      | ||  ||||| |  | | | |  | || |||||  |||  |   |        ||||| ||         |||||
CCTTGGATTGATAGGCGCTGGAACCAACAATGCAAGGATAGCTGGCATGCTTAGAAATCTCTCCAGCTATTATTACAAGGATGCCAGCCTTCTTTTCTGTgtaacg----ttttatgatttct-----ttttaagttttcatggaataaac--acggtttctacttatgataggcttgttctcattgtcttaagtcacaatgcag

upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: PP1S414_22V6.1 (Physcomitrella patens), 5'ss of exon 21
CTTGGGTTTGATAGGTGCGGGTACCAACAATGCTCGAATTGCTGGCATGCTCCGTAATCTTTCAAGCTATTACTACAAAGAAGCTAGCCTTCTGTTCTGTgtaaagattcttttattacctttaaattct-ctagattttctttcattcatccaatgggttctatatattttcacaccaatattgttttggccacttgtgcag------
 |||||  | || || || || || || ||||| ||||||||||||||||| || || ||||| ||||| || ||||| ||  | |||||||| |||||||||      | | ||     | |  ||||| ||     || |||||||| | ||  |  |    |   |||| | || | ||||   ||    | |  ||  |      
TTTGGGACTTATTGGAGCTGGGACTAATAATGCCCGAATTGCTGGCATGCTTCGCAACCTTTCTAGCTACTATTACAAGGACCCAAGCCTTCTATTCTGTgta----cgcctctaccctttctgcattctgctcttaattttttcattcctgca--gaataactttctttttgagactactatt-ccttacatattaatgtcgttgcag

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|110370776|gb|EC932910.1|EC932910
EST:     TCCGTAATCTTTCAAGCTATTACTACAAAGAAGCTAGCCTTCTGTTCTGT                         GTGCGGATTGCTCAAGGTCTTGTCCATTTGGGAAAAGGATTATTGACTCTT
genomic: TCCGTAATCTTTCAAGCTATTACTACAAAGAAGCTAGCCTTCTGTTCTGTgtaaagattc ... acttgtgcagGTGCGGATTGCTCAAGGTCTTGTCCATTTGGGAAAAGGATTATTGACTCTT
EST: gi|37183929|gb|CF603283.1|CF603283
EST:     TCCGTAATCTTTCAAGCTATTACTACAAAGAAGCTAGCCTTCTGTTCTGT                         GTGCGGATTGCTCAAGGTCTTGTCCATTTGGG
genomic: TCCGTAATCTTTCAAGCTATTACTACAAAGAAGCTAGCCTTCTGTTCTGTgtaaagattc ... acttgtgcagGTGCGGATTGCTCAAGGTCTTGTCCATTTGGG
EST: gi|110699529|gb|EE076605.1|EE076605
EST:     TCCGTAATCTTTCAAGCTATTACTACAAAGAAGCTAGCCTTCTGTTCTGT                         GTGCGGATTGCTCAAGGTCTTGTCCATTTGGGAAAAGGATTATTGACTCTT
genomic: TCCGTAATCTTTCAAGCTATTACTACAAAGAAGCTAGCCTTCTGTTCTGTgtaaagattc ... acttgtgcagGTGCGGATTGCTCAAGGTCTTGTCCATTTGGGAAAAGGATTATTGACTCTT
EST: gi|110416060|gb|EC982014.1|EC982014
EST:     TCCGTAATCTTTCAAGCTATTACTACAAAGAAGCTAGCCTTCTGTTCTGT                         GTGCGGATTGCTCAAGGTCTTGTCCATTTGGGAAAAGGATTATTGACTCTT
genomic: TCCGTAATCTTTCAAGCTATTACTACAAAGAAGCTAGCCTTCTGTTCTGTgtaaagattc ... acttgtgcagGTGCGGATTGCTCAAGGTCTTGTCCATTTGGGAAAAGGATTATTGACTCTT
EST: gi|27584813|gb|CB007508.1|CB007508
EST:     CTTTCAAGCTATTACTACAAAGAAGCTAGCCTTCTGTTCTGT                         GTGCGGATTGCTCAAGGTCTTGTCCATTTGGGAAAAGGATTATTGACTCTT
genomic: CTTTCAAGCTATTACTACAAAGAAGCTAGCCTTCTGTTCTGTgtaaagattc ... acttgtgcagGTGCGGATTGCTCAAGGTCTTGTCCATTTGGGAAAAGGATTATTGACTCTT
EST: gi|110365725|gb|EC929133.1|EC929133
EST:     TCCGTAATCTTTCAAGCTATTACTACAAAGAAGCTAGCCTTCTGTTCTGT                         GTGCGGATTGCTCAAGGTCTTGTCCATTTGGGAAAAGGATTATTGACTCTT
genomic: TCCGTAATCTTTCAAGCTATTACTACAAAGAAGCTAGCCTTCTGTTCTGTgtaaagattc ... acttgtgcagGTGCGGATTGCTCAAGGTCTTGTCCATTTGGGAAAAGGATTATTGACTCTT
EST: gi|110708175|gb|EE085416.1|EE085416
EST:     TCCGTAATCTTTCAAGCTATTACTACAAAGAAGCTAGCCTTCTGTTCTGT                         GTGCGGATTGCTCAAGGTCTTGTCCATTTGGGAAAAGGATTATTGACTCTT
genomic: TCCGTAATCTTTCAAGCTATTACTACAAAGAAGCTAGCCTTCTGTTCTGTgtaaagattc ... acttgtgcagGTGCGGATTGCTCAAGGTCTTGTCCATTTGGGAAAAGGATTATTGACTCTT
EST: gi|161716967|gb|FC068834.1|FC068834
EST:     TCCGTAATCTTTCAAGCTATTACTACAAAGAAGCTAGCCTTCTGTTCTGT                         GTGCGGATTGCTCAAGGTCTTGTCCATTTGGGAAAAGGATTATTGACTCTT
genomic: TCCGTAATCTTTCAAGCTATTACTACAAAGAAGCTAGCCTTCTGTTCTGTgtaaagattc ... acttgtgcagGTGCGGATTGCTCAAGGTCTTGTCCATTTGGGAAAAGGATTATTGACTCTT
EST: gi|161713613|gb|FC062533.1|FC062533
EST:     TCCGTAATCTTTCAAGCTATTACTACAAAGAAGCTAGCCTTCTGTTCTGT                         GTGCGGATTGCTCAAGGTCTTGTCCATTTGGGAAAAGGATTATTGACTCTT
genomic: TCCGTAATCTTTCAAGCTATTACTACAAAGAAGCTAGCCTTCTGTTCTGTgtaaagattc ... acttgtgcagGTGCGGATTGCTCAAGGTCTTGTCCATTTGGGAAAAGGATTATTGACTCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGGGTTTGATAGGTGCGGGTACCAACAATGCTCGAATTGCTGGCATGCTCCGTAATCTTTCAAGCTATTACTACAAAGAAGCTAGCCTTCTGTTCTGTgtaaagattcttttattacctttaaattctctagattttctttcattcatccaatgggttctatatattttcacaccaatattgttttggccacttgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC