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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catatcaacaaacagcatacatactccatttgtttaattttagggcatgtgtttattacttaaagctgattgattcttgtttcttgctatcttatggtagGAGGGTTATTCATACTGTGGGTCCCAAGTATGCAGTAAAATATCATACTGCTGCAGAGAATGCTTTGAGTCACTGCTATCGGTCTTGCCTTGAACTTCTT

Basic information

species Vitis vinifera
transcript Vv01s0011g00870.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g00870.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os03g05660.1 (Oryza sativa), 3'ss of exon 3
catatcaacaaacagcatacatactccatttgtttaattttagggcatgtgtttat-tacttaaagctgattgattcttgtttcttgcta-tcttatggtagGAGGGTTATTCATACTGTGGGTCCCAAGTATGCAGTAAAATATCATACTGCTGCAGAGAATGCTTTGAGTCACTGCTATCGGTCTTGCCTTGAACTTCTT
  || |     |    |    || | |||    |   ||| ||   ||    | || ||| |     | | |||    |  | |||   | |  | ||| |||| ||| |||||||||||||| || || ||||| || || ||||| || ||||||||||||||  | || ||||||||  |||||||  | |||||||| 
-ctacctgaggatgtta-gtttatttcatgatatggttttgagatgatacactgatatacatgctcttcactgacctataatgcttatgaatggtctggcagGAAGGTAATTCATACTGTGGGCCCTAAATATGCTGTCAAGTATCACACAGCTGCAGAGAATGCACTTAGCCACTGCTACAGGTCTTGTTTGGAACTTCTC

upper sequence: Vv01s0011g00870.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os10g30750.1 (Oryza sativa), 3'ss of exon 3
-------catatcaacaaacagcatacatactccatttgtttaattttagggcatgtgtttattacttaaagctgattgattcttgtttcttgctatcttatggtagGAGGGTTATTCATACTGTGGGTCCCAAGTATGCAGTAAAATATCATACTGCTGCAGAGAATGCTTTGAGTCACTGCTATCGGTCTTGCCTTGAACTTCTT
       |||||    |||     |  ||     ||||  |   ||| |  |   ||||   ||  ||    |  | | | | || | |||   | | ||||   |||| ||| |||||||| || || ||||| ||||| || || ||||| || ||||||||||||||  | ||||||||||| || |||||  | ||||| || 
aatctgacatatatgaaaaagttgttgattactgatttact--gtttcacagtg-gtgtgatttctttgttac--actaaattttttatctcaatttattat--cagGAAGGTCATTCATACAGTCGGCCCCAAATATGCTGTCAAGTATCACACAGCTGCAGAGAATGCACTTAGTCACTGCTACCGTTCTTGTTTGGAACTCCTC

upper sequence: Vv01s0011g00870.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM5G836588_T01 (Zea mays), 3'ss of exon 3
------catatcaacaaacagcatacatactccatttgtttaattttagggcatgtgtttattacttaaagctgattgattcttgtttcttgctatcttatggtagGAGGGTTATTCATACTGTGGGTCCCAAGTATGCAGTAAAATATCATACTGCTGCAGAGAATGCTTTGAGTCACTGCTATCGGTCTTGCCTTGAACTTCTT
         | ||   ||     |||  |  | |  ||||   | |  ||   | ||| |  |   | | ||| |  ||| | ||| ||     ||  |   | |||| ||| || ||||| ||||| ||||| ||||| || || ||||| || ||||||||||||||  | ||||||||||||||||| ||| | ||||| || 
tagcggttgaacactcaaagatttactcatccaacatgtt-gttctgtggttgtctgtattcttagttatgctaa--gatgcatgtatcaattgattat---gcagGAAGGTCATCCATACCGTGGGCCCCAAATATGCTGTCAAGTATCACACAGCTGCAGAGAATGCACTTAGTCACTGCTATCGGTCCTGCTTGGAACTGCTC

upper sequence: Vv01s0011g00870.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G100707_T01 (Zea mays), 3'ss of exon 3
catatcaacaaacagcatacatactccatttgtttaa----ttttagggcatgtgtttattacttaaagctgattgattcttgtttcttgctatcttatggtagGAGGGTTATTCATACTGTGGGTCCCAAGTATGCAGTAAAATATCATACTGCTGCAGAGAATGCTTTGAGTCACTGCTATCGGTCTTGCCTTGAACTTCTT
  | | |||       ||        |||||| || |    | | |   ||    |||| | || || | | |         |||  ||      ||||| ||||| ||| || ||||||||||| || || ||||| ||||| ||||| || ||||||||||||||  | || ||||||||  ||||||| || ||||| || 
-gtttgaacct-tgatatttgagaatcatttgcttgaaacatatcacatcagaactttaatgctcaacgttaagct-caaaagttaattatctggttatg-tagGAAGGTCATCCATACTGTGGGCCCAAAATATGCTGTAAAGTATCACACAGCTGCAGAGAATGCGCTTAGCCACTGCTACAGGTCTTGTCTAGAACTGCTC

upper sequence: Vv01s0011g00870.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G12670.1 (Glycine max), 3'ss of exon 4
-----catatcaacaaacagcatacatactccatttgtttaattttagggcatgtgtttattacttaaagctgattgattcttgtttcttgctatcttatggtagGAGGGTTATTCATACTGTGGGTCCCAAGTATGCAGTAAAATATCATACTGCTGCAGAGAATGCTTTGAGTCACTGCTATCGGTCTTGCCTTGAACTTCTT
     | |||           |     |    |||   ||   |  | |  |  |   ||   ||   | ||||   |||  ||  | |   ||  || | | ||||  ||||| |||||||| || || ||||||||    || || || |||||||||||||||||||| || || |||||||| |||||||| |||||| | 
gctgccctatatttcttttttagttgcatgtaattctcttggctaaaagttagattcctac--ctagcatctga--aatttatgcct-tcaataatttcttgcagGAAAGTTATCCATACTGTTGGCCCAAAGTATGCTTCGAAGTACCAAACTGCTGCAGAGAATGCTTTAAGCCATTGCTATCGTTCTTGCCTAGAACTTTTA

upper sequence: Vv01s0011g00870.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA20G03330.1 (Glycine max), 3'ss of exon 4
-catatcaacaaacagcatacatactccatttgtttaattttagggcatgtgtttattacttaaagctgattgattcttgtttcttgctatcttatg-gtagGAGGGTTATTCATACTGTGGGTCCCAAGTATGCAGTAAAATATCATACTGCTGCAGAGAATGCTTTGAGTCACTGCTATCGGTCTTGCCTTGAACTTCTT
    ||           |  | |     | |||   |  | | |   || | ||   | ||||      |     | || ||  ||| ||  |||   | ||||   |||| || ||||| || || ||||||||  |||| || |||| |||||||||||||||||| ||||| |||||||| |||||| | || ||||| 
ttgcattgtacttttatactcctttgttacttgccaatctcttgtctatattttggattcttagtat--accatgttttattctttgataaattacccgcagGAAAATTATCCACACTGTTGGCCCAAAGTATGCTATAAAGTACCATAATGCTGCAGAGAATGCTTTAAGTCATTGCTATCGTTCTTGCTTGGAGCTTCTG

upper sequence: Vv01s0011g00870.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA01G06730.1 (Glycine max), 3'ss of exon 4
catatcaacaaacagcatacatactccatttg--tttaattttagggcatgtgtttattacttaaagctgattgattcttgtttcttgctatcttatggtagGAGGGTTATTCATACTGTGGGTCCCAAGTATGCAGTAAAATATCATACTGCTGCAGAGAATGCTTTGAGTCACTGCTATCGGTCTTGCCTTGAACTTCTT
  | |       |   ||     |   | |||  | ||||| |   |  |     |   | |   |||  ||  | | |      |   ||  ||   | ||||  ||||| |||||||| || || ||||||||    || || || ||||||||||||||||| || || || |||||||| |||||||| |||||| | 
--tgttgctgccctatatttcctccttagttgcatataattctcttggctaaaagttagattcctagcatatgaaatttatgccttcaataatttcgtgcagGAAAGTTATCCATACTGTTGGCCCAAAGTATGCTTCGAAGTACCAAACTGCTGCAGAGAATGCCTTAAGCCATTGCTATCGTTCTTGCCTAGAACTTTTA

upper sequence: Vv01s0011g00870.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G69340.1 (Arabidopsis thaliana), 3'ss of exon 4
catatcaacaaacagcatacatactccatttgtttaatttta-gggcatgtgtttattacttaaagctgattgattcttgtttcttgctatcttatggt-agGAGGGTTATTCATACTGTGGGTCCCAAGTATGCAGTAAAATATCATACTGCTGCAGAGAATGCTTTGAGTCACTGCTATCGGTCTTGCCTTGAACTTCTT
 ||| |||   |     | |    |  || ||     |   |  |   ||||  |    |   ||    |   | | |  ||| |   | |||| || | ||||||||||| ||||| || || ||||||||||||||||| |||||||| ||||| ||||||||| | |||||||||||| | ||||| || |||||||| 
-ataccaa-gcattctgtgcgactttaatatggactgtgaaatagatttgtgccttagtccccaactcaaaaaaatgtgttttttgtttgtcttttgttcagGAGGGTTATCCATACAGTAGGACCCAAGTATGCAGTAAAGTATCATACAGCTGCTGAGAATGCTCTAAGTCACTGCTATAGATCTTGTCTGGAACTTCTC

upper sequence: Vv01s0011g00870.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S37_110V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------------------------------catatcaacaaacagcatacat----actccatttgtttaattttagggcatgtgtttattacttaaagctgattgattcttgtttcttgctatctta--tggtagGAGGGTTATTCATACTGTGGGTCCCAAGTATGCAGTAAAATATCATACTGCTGCAGAGAATGCTTTGAGTCACTGCTATCGGTCTTGCCTTGAACTTCTT
                                                                   ||||  |   || || |||    | ||| | ||| || || |   | || | |  || |  |       ||| |   | |    | |||   ||   | | ||| | || |||||||| ||||| || |  ||||||| |   || || || || || |||||||| ||||||||||||||||| || ||||| |||||||||
gtatgttattggttaaggatttctgccgattttttcagcagcattgtttgcctactctagtaagtccatcactaggtagtatccatcggcaatccttctgtatacttgttcagaat-tctaaatcagatggttacaatttacagtaggggttggcttggttgatttgcagGCGTGTGATTCATACAGTGGGACCTAGATATGCAGCACGGTACCACACAGCAGCTGAGAATGCATTGAGTCACTGCTATCGTTCATGCCTGGAACTTCTT

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|110698158|gb|EE075402.1|EE075402
EST:     TGCCGTACAGGGATGGCTAAAGTAACTAATGCGTACGACCTTCCTGCTAG                         GAGGGTTATTCATACTGTGGGTCCCAAGTATGCAGTAAAATATCATACTGC
genomic: TGCCGTACAGGGATGGCTAAAGTAACTAATGCGTACGACCTTCCTGCTAGgtaggtatat ... cttatggtagGAGGGTTATTCATACTGTGGGTCCCAAGTATGCAGTAAAATATCATACTGC
EST: gi|110698826|gb|EE076764.1|EE076764
EST:     TAATGCGTACGACCTTCCTGCTAG                         GAGGGTTATTCATACTGTGGGTCCCAAGTATGCAGCAAAATATCATACTGC
genomic: TAATGCGTACGACCTTCCTGCTAGgtaggtatat ... cttatggtagGAGGGTTATTCATACTGTGGGTCCCAAGTATGCAGTAAAATATCATACTGC
EST: gi|161715719|gb|FC067810.1|FC067810
EST:     TGCCGTACAGGGATGGCTAAAGTAACTAATGCGTACGACCTTCCTGCTAG                         GAGGGTTATTCATACTGTGGGTCCCAAGTATGCAGTAAAATATCATACTGC
genomic: TGCCGTACAGGGATGGCTAAAGTAACTAATGCGTACGACCTTCCTGCTAGgtaggtatat ... cttatggtagGAGGGTTATTCATACTGTGGGTCCCAAGTATGCAGTAAAATATCATACTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtgtttattacttaaagctgattgattcttgtttcttgctatcttatggtagGAGGGTTATTCATACTGTGGGTCCCAAGTATGCAGTAAAATATCATACTGCTGCAGAGAATGCTTTGAGTCACTGCTATCGGTCTTGCCTTGAACTTCTT
                      gattgat  putative branch site (score: 4)
                                  tttcttgctatctt  putative PPT
      tttattacttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catatcaacaaacagcatacatactccatttgtttaattttagggcatgtgtttattacttaaagctgattgattcttgtttcttgctatcttatggtagGAGGGTTATTCATACTGTGGGTCCCAAGTATGCAGTAAAATATCATACTGCTGCAGAGAATGCTTTGAGTCACTGCTATCGGTCTTGCCTTGAACTTCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - -acaaaca
- - - - - - - gcataca
- - - - - - - - - - - actccat
- - - - - - - - - - - - - - - - - - - - - - -catgtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgattg