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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctttttatatatgctgtctccatctcttgcattggctttcccaattgatcttaaatttattttcttcagtacctaatgcttaccttttttaacggacagAAATACGTTGCTCTAAAGATCCAGAAAAGTGCAGTACAATTTGCTCAAGCTGCTCTTCATGAGATTGAAGTCCTTTCAGCTATTGCTAATGGTGACCCCT

Basic information

species Vitis vinifera
transcript Vv07s0031g02130.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g02130.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA01G36260.1 (Glycine max), 3'ss of exon 1
tctttttatatatgctgtctccatctcttgcattggctttcccaattgatcttaaatttattttcttcagtacctaatgcttacctt----ttttaacggacagAAATACGTTGCTCTAAAGATCCAGAAAAGTGCAGTACAATTTGCTCAAGCTGCTCTTCATGAGATTGAAGTCCTTTCAGCTATTGCTAATGGTGACCCCT
| | || || |||  | | |  |  ||    |    || |     |  | | |  || |||||| ||  ||| || || || |  ||    || |      |||  ||| |||||||| |||||||||||||||||||  || |||||||| ||||| ||||||||||||||| | |||||| | |||||| |     | ||  
tttgttcatgtat-ttatgtttaattcaaaaaccttctatgaaggtgaaacatgtatgtattttttt--gtatcttat-ctgattttaagattgtggttttcagTCATATGTTGCTCTCAAGATCCAGAAAAGTGCAGCTCAGTTTGCTCAGGCTGCCCTTCATGAGATTGAACTTCTTTCATCCATTGCTGACCACAATCCAA

upper sequence: Vv07s0031g02130.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA16G21430.1 (Glycine max), 3'ss of exon 1
tctttttatatatgctgtctccatctcttgcattggctttcccaattgatcttaaatttattttcttcagtacctaatgcttaccttttttaacggacagAAATACGTTGCTCTAAAGATCCAGAAAAGTGCAGTACAATTTGCTCAAGCTGCTCTTCATGAGATTGAAGTCCTTTCAGCTATTGCTAATGGTGACCCCT
  |||    | |   ||    | | | ||  |||   ||     |    | ||   ||| | ||  ||| ||  |  |  ||     |||  |    |||  ||| |||||||| ||||||||||||||||| |  || |||| ||| ||||| |||||||| ||||| || |||||| |  ||||| |||||| |    
attttgctcagacagtgataactttttttatattattttagttcagcagtattttttttttgtttgtcaatatattctaattttaaatttggattttcagGCATATGTTGCTCTCAAGATCCAGAAAAGTGCTGCCCAGTTTGTTCAGGCTGCCCTTCATGAAATTGATGTTCTTTCATCCCTTGCTGATGGTGTCGATA

upper sequence: Vv07s0031g02130.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA11G09180.1 (Glycine max), 3'ss of exon 1
tctttttatatatgctgtctccatctcttgc-attggctttcccaattgatcttaaatttattttcttcagtacctaatgcttacctt----ttttaacggacagAAATACGTTGCTCTAAAGATCCAGAAAAGTGCAGTACAATTTGCTCAAGCTGCTCTTCATGAGATTGAAGTCCTTTCAGCTATTGCTAATGGTGACCCCT
 |||||     || |  |    || |||||  |||   |||    |    | |   |||| ||||||||| || || || || |  ||    || |      |||  ||| |||||||| ||||||||||||||| | |  || |||||||| ||||| |||||||||||  |  | |||||| | |||||| |  |||| || |
ccttttgccccatccaatgataatttcttgttattatttttgtgcaccagtgt---attttttttcttca-tatcttat-ctaattttaagattgtcgttttcagTCATATGTTGCTCTCAAGATCCAGAAAAGTTCGGCCCAGTTTGCTCAGGCTGCCCTTCATGAGATCAATCTTCTTTCATCCATTGCTGACCGTGATCCGT

upper sequence: Vv07s0031g02130.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G35500.2 (Arabidopsis thaliana), 3'ss of exon 2
tctttttatatatgctgtctccatctcttgcattggctttcccaattgatcttaaatttattttcttcagtacctaatgcttaccttttttaacggacagAAATACGTTGCTCTAAAGATCCAGAAAAGTGCAGTACAATTTGCTCAAGCTGCTCTTCATGAGATTGAAGTCCTTTCAGCTATTGCTAATGGTGACCCCT-----------------------------
                                                                                                  |||  || |||||| | ||||| ||||| ||||||  |||||||||||||||||| ||||| || || ||| | |||||||||  |||| |||| || | |                              
---------------------------------------------------------------------------------------------gttgtagacttatgttgctttgaagattcagaagagTGCACAACAATTTGCTCAAGCTGCACTTCACGAAATCGAATTTCTTTCAGCTGCTGCTGATGGGGATCTCGACAAGACGAAATGTGTTGTTCGTCTTATT

upper sequence: Vv07s0031g02130.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G35500.1 (Arabidopsis thaliana), 3'ss of exon 1
tctttttatatatgctgtctccatctcttg-----cattggctttcccaattgatcttaaatttattttcttcagtacctaatgcttaccttttttaacggacagAAATACGTTGCTCTAAAGATCCAGAAAAGTGCAGTACAATTTGCTCAAGCTGCTCTTCATGAGATTGAAGTCCTTTCAGCTATTGCTAATGGTGACCCCT
  |  ||||| |  || |   |||     |       |   | |    | |  ||| |||   | ||||  |  |||     |  |||  | | ||   |   |||  || |||||| | ||||| ||||| ||||||  |||||||||||||||||| ||||| || || ||| | |||||||||  |||| |||| || | | 
aatggttatagaatctttaatcataggaaggtaactgtcaccctataaagtatatcctaagaatgttttgctttgtat---gtttttatgtctcttgttg--tagACTTATGTTGCTTTGAAGATTCAGAAGAGTGCACAACAATTTGCTCAAGCTGCACTTCACGAAATCGAATTTCTTTCAGCTGCTGCTGATGGGGATCTCG

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|161716130|gb|FC066486.1|FC066486
EST:     GTTGGGGCGAGTTCTCCACCGTCTGGCTTGCTTACGACACGCGATCCTCT                         AAATACGTTGCTCTAAAGATCCAGAAAAGTGCAGTACAATTTGCTCAAGCT
genomic: GTTGGGGCGAGTTCTCCACCGTCTGGCTTGCTTACGACACGCGATCCTCTgtacgttctt ... taacggacagAAATACGTTGCTCTAAAGATCCAGAAAAGTGCAGTACAATTTGCTCAAGCT
EST: gi|161721479|gb|FC070457.1|FC070457
EST:     GTTGGGGCGAGTTCTCCACCGTCTGGCTTGCTTACGACACGCGATCCTCT                         AAATACGTTGCTCTAAAGATCCAGAAAAGTGCAGTACAATTTGCTCAAGCT
genomic: GTTGGGGCGAGTTCTCCACCGTCTGGCTTGCTTACGACACGCGATCCTCTgtacgttctt ... taacggacagAAATACGTTGCTCTAAAGATCCAGAAAAGTGCAGTACAATTTGCTCAAGCT
EST: gi|110380651|gb|EC945934.1|EC945934
EST:     GTTGGGGCGAGTTCTCCACCGTCTGGCTTGCTTACGACACGCGATCCTCT                         AAATACGTTGCTCTAAAGATCCAGAAAAGTGCAGTACAATTTGCTCAAGCT
genomic: GTTGGGGCGAGTTCTCCACCGTCTGGCTTGCTTACGACACGCGATCCTCTgtacgttctt ... taacggacagAAATACGTTGCTCTAAAGATCCAGAAAAGTGCAGTACAATTTGCTCAAGCT
EST: gi|110718392|gb|EE095169.1|EE095169
EST:     GTTGGGGCGAGTTCTCCACCGTCTGGCTTGCTTACGACACGCGATCCTCT                         AAATACGTTGCTCTAAAGATCCAGAAAAGTGCAGTACAATTTGCTCAAGCT
genomic: GTTGGGGCGAGTTCTCCACCGTCTGGCTTGCTTACGACACGCGATCCTCTgtacgttctt ... taacggacagAAATACGTTGCTCTAAAGATCCAGAAAAGTGCAGTACAATTTGCTCAAGCT
EST: gi|161713794|gb|FC064359.1|FC064359
EST:     GTTGGGGCGAGTTCTCCACCGTCTGGCTTGCTTACGACACGCGATCCTCT                         AAATACGTTGCTCTAAAGATCCAGAAAAGTGCAGTACAATTTGCTCAAGCT
genomic: GTTGGGGCGAGTTCTCCACCGTCTGGCTTGCTTACGACACGCGATCCTCTgtacgttctt ... taacggacagAAATACGTTGCTCTAAAGATCCAGAAAAGTGCAGTACAATTTGCTCAAGCT
EST: gi|294966786|gb|GW837805.1|GW837805
EST:     GTTGGGGCGAGTTCTCCACCGTCTGGCTTGCTTACGACACGCGATCCTCT                         AAATACGTTGCTCTAAAGATCCAGAAAAGTGCAGTACAATTTGCTCAAGCT
genomic: GTTGGGGCGAGTTCTCCACCGTCTGGCTTGCTTACGACACGCGATCCTCTgtacgttctt ... taacggacagAAATACGTTGCTCTAAAGATCCAGAAAAGTGCAGTACAATTTGCTCAAGCT
EST: gi|30134233|gb|CB919571.1|CB919571
EST:     GTTGGGGCGAGTTCTCCACCGTCTGGCTTGCTTACGACACGCGATCCTCT                         AAATACGTTGCTCTAAAGATCCAGAAAAGTGCAGTACAATTTGCTCAAGCT
genomic: GTTGGGGCGAGTTCTCCACCGTCTGGCTTGCTTACGACACGCGATCCTCTgtacgttctt ... taacggacagAAATACGTTGCTCTAAAGATCCAGAAAAGTGCAGTACAATTTGCTCAAGCT
EST: gi|161717661|gb|FC067899.1|FC067899
EST:     GTTGGGGCGAGTTCTCCACCGTCTGGCTTGCTTACGACACGCGATCCTCT                         AAATACGTTGCTCTAAAGATCCAGAAAAGTGCAGTACAATTTGCTCAAGCT
genomic: GTTGGGGCGAGTTCTCCACCGTCTGGCTTGCTTACGACACGCGATCCTCTgtacgttctt ... taacggacagAAATACGTTGCTCTAAAGATCCAGAAAAGTGCAGTACAATTTGCTCAAGCT
EST: gi|110712263|gb|EE089688.1|EE089688
EST:     GTTGGGGCGAGTTCTCCACCGTCTGGCTTGCTTACGACACGCGATCCTCT                         AAATACGTTGCTCTAAAGATCCAGAAAAGTGCAGTACAATTTGCTCAAGCT
genomic: GTTGGGGCGAGTTCTCCACCGTCTGGCTTGCTTACGACACGCGATCCTCTgtacgttctt ... taacggacagAAATACGTTGCTCTAAAGATCCAGAAAAGTGCAGTACAATTTGCTCAAGCT
EST: gi|110720865|gb|EE097171.1|EE097171
EST:     GTTGGGGCGAGTTCTCCACCGTCTGGCTTGCTTACGACACGCGATCCTCT                         AAATACGTTGCTCTAAAGATCCAGAAAAGTGCAGCACAATTTGCTCAAGCT
genomic: GTTGGGGCGAGTTCTCCACCGTCTGGCTTGCTTACGACACGCGATCCTCTgtacgttctt ... taacggacagAAATACGTTGCTCTAAAGATCCAGAAAAGTGCAGTACAATTTGCTCAAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatcttaaatttattttcttcagtacctaatgcttaccttttttaacggacagAAATACGTTGCTCTAAAGATCCAGAAAAGTGCAGTACAATTTGCTCAAGCTGCTCTTCATGAGATTGAAGTCCTTTCAGCTATTGCTAATGGTGACCCCT
                                          ttttaac  putative branch site (score: 2)
                                tgcttacctttttt  CT-rich tract
      ttaaatttattttctt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctttttatatatgctgtctccatctcttgcattggctttcccaattgatcttaaatttattttcttcagtacctaatgcttaccttttttaacggacagAAATACGTTGCTCTAAAGATCCAGAAAAGTGCAGTACAATTTGCTCAAGCTGCTCTTCATGAGATTGAAGTCCTTTCAGCTATTGCTAATGGTGACCCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - tatgctg
- - - - - - - - - - ccatctc
- - - - - - - - - - - - - - tgcattg
- - - - - - - - - - - - - - - - - - ctttccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaatgc