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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcataattgtgctccatgtgtttatatatgtggtttacaatgttagcaagtgtttataattagcctaaaacttttaagtcactttcgtattctttgcagACCAAAATACCACTGCTTTTAAAGAGGTAGCTATCATCCGTCATCCACGTGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTTCAG

Basic information

species Vitis vinifera
transcript Vv07s0031g02010.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g02010.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g64780.4 (Oryza sativa), 3'ss of exon 3
agcataattgtgctcc---atgtgtttat-atatgtggtttacaatgttagcaagtgtttataattagcctaaaacttttaagtcactttcgtattctttgcagACCAAAATACCACTGCTTTTAAAGAGGTAGCTATCATCCGTCATCCACGTGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTTCAG
 | ||| ||     |    || | || || | |  | |     |   | ||| |   |  | || |   || |     | || |||  ||       || ||||| ||||| || || ||||||||||| || || || || |||||||||||| ||||||||||||||||||| ||||| |||||||| ||  | ||||||
-gtatacttccatacacaaatatattcatgacacattgacactatcatcagccacattggacaaatgaacttacctcataaaatcatcttg-----tttggcagATCAAAACACAACAGCTTTTAAAGAAGTTGCGATAATTCGTCATCCACGTATTGGTGAATATGCATTTGGATTTATAACATCAACTGTTGTTCTTCAG

upper sequence: Vv07s0031g02010.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g36110.2 (Oryza sativa), 3'ss of exon 4
----agcataat-tgtgctccatgtgtttatatatgtggtttacaatgttagca-agtgtttataattagcctaaaacttttaagtcactttcgtattctttgcagACCAAAATACCACTGCTTTTAAAGAGGTAGCTATCATCCGTCATCCACGTGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTTCAG
    ||  |||| | |  |     |  ||||||     |||| |||  ||     | |   | |  | | ||  ||  ||||      |||   | || ||  |||| |||||||| || || |||||||| || || || ||  ||||||| ||| ||||||||||||||||||| || || ||||| ||  | |||||||||
tgataggttaatgtatcattttaatcattatattacaagtttccaactttgttgtaattcattttctcaaccagaatttttt------cttatttcttattgacagATCAAAATACAACGGCATTTAAAGAAGTTGCAATAATTAGTCATCCCCGTATTGGTGAATATGCATTTGGATTCATAACATCGACGATGATCCTTCAG

upper sequence: Vv07s0031g02010.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g36110.4 (Oryza sativa), 3'ss of exon 4
----agcataat-tgtgctccatgtgtttatatatgtggtttacaatgttagca-agtgtttataattagcctaaaacttttaagtcactttcgtattctttgcagACCAAAATACCACTGCTTTTAAAGAGGTAGCTATCATCCGTCATCCACGTGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTTCAG--
    ||  |||| | |  |     |  ||||||     |||| |||  ||     | |   | |  | | ||  ||  ||||      |||   | || ||  |||| |||||||| || || |||||||| || || || ||  ||||||| ||| ||||||||||||||||||| || || ||||| ||  | |||||||||  
tgataggttaatgtatcattttaatcattatattacaagtttccaactttgttgtaattcattttctcaaccagaatttttt------cttatttcttattgacagATCAAAATACAACGGCATTTAAAGAAGTTGCAATAATTAGTCATCCCCGTATTGGTGAATATGCATTTGGATTCATAACATCGACGATGATCCTTCAGGT

upper sequence: Vv07s0031g02010.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G149662_T01 (Zea mays), 3'ss of exon 4
agcataattgtgctccatgtgtttatatatgtggttt-acaatgttagc--aagtgtttataattagcctaaaacttttaagtcactttcgtattctttgcagACCAAAATACCACTGCTTTTAAAGAGGTAGCTATCATCCGTCATCCACGTGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTTCAG
    | |    ||| | | ||  |  || | |  ||| | ||  |||    || | | | |         | |  | ||| || | | |  | || |   |||| |||||||| |||||||| ||||| || || || || |||||||||||  ||||||||||||||||||| || || |||||||| ||  ||||||||
---gtcaggcagcttcttttgcatgcatttctttttttataagtttaatttaaatatattttgcagaagaatatttcttatgtaattattctgttgt---cagATCAAAATACGACTGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAATTGGTGAATATGCATTTGGATTCATAACATCAACTGTGGTCCTTCAG

upper sequence: Vv07s0031g02010.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G052855_T01 (Zea mays), 3'ss of exon 4
agcataattgtgctccatgtgtttatatatgtggtttacaatgttagcaagtgtttataattagcctaaa-acttttaagtcactttcgtattctttgcagACCAAAATACCACTGCTTTTAAAGAGGTAGCTATCATCCGTCATCCACGTGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTTCAG
 |  ||  |      ||   |||| ||| |||     ||  | || | |  |  || |     ||  |||   | ||| | |  |||  |  |||   |||| |||||||| || || || ||||| ||||| |||||  ||||||| ||||||||||||||||||||||| || || ||||||||  |  | ||||||
tgtttacatagatatcagcagtttgtatttgtttccaactttctt-gtagttccttttgtcaggcagaaatgttcttaggactttttttttctctggacagATCAAAATACAACAGCATTCAAAGAAGTAGCAATCATTAGTCATCCCCGTGTTGGTGAATATGCATTTGGATTCATAACATCAACCATGGTTCTTCAG

upper sequence: Vv07s0031g02010.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G046098_T02 (Zea mays), 3'ss of exon 4
---agcataattgtgctccatgtgtttatatatgtggtttacaatgttagcaagtgtttataattagcctaaaacttttaagtcactttcgtattctttgcagACCAAAATACCACTGCTTTTAAAGAGGTAGCTATCATCCGTCATCCACGTGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTTCAG
   || |    |    | ||||||||| | | | |   ||  || | |||    | |  | ||  ||  |     | ||| || | | |  | || ||   ||| |||||||| || ||||| ||||| || || || || |||||||||||  ||||||||||||||||||| || || |||||||| ||  ||||||||
gtcaggaagcatccattgcatgtgtttctttttttatattttaaagatag----tttgcacaagaagttt-----tcttatgtaattattttgttgtt---agATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAATTGGTGAATATGCATTTGGATTCATAACATCAACGGTGGTCCTTCAG

upper sequence: Vv07s0031g02010.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G048150_T03 (Zea mays), 3'ss of exon 4
---agcataattgtgctccatgtgtttatatatgtggtttacaatgttagcaagtgtttataattagcctaaaacttttaagtcactttcgtattctttgcagACCAAAATACCACTGCTTTTAAAGAGGTAGCTATCATCCGTCATCCACGTGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTTCAG--
    |  | || |     ||   |||| ||| |||     ||  | ||     ||   | |  | || |  |||  ||      |  ||  |  | |   |||| |||||||| || || || ||||| ||||| || ||  ||||||| ||||||||||||||||| ||||| || || ||||||||  |  | ||||||  
ttgtgtttcatag-atatcacaagtttgtatttgtttccaactttcttgtt--gttccttttgtcagacagaaatgttcttaggatattttttctttggacagATCAAAATACAACAGCATTCAAAGAAGTAGCAATTATTAGTCATCCCCGTGTTGGTGAATATGCGTTTGGATTCATAACATCAACCATGGTTCTTCAGGT

upper sequence: Vv07s0031g02010.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G073415_T03 (Zea mays), 3'ss of exon 5
---agcataattgtgctccatgtgtttatatatgtggtttacaatgttagcaagtgtttataattagcctaaaacttttaagtcactttcgtattctttgcagACCAAAATACCACTGCTTTTAAAGAGGTAGCTATCATCCGTCATCCACGTGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTTCAG
    |  | || |     ||   |||| ||| |||     ||  | ||     ||   | |  | || |  |||  ||      |  ||  |  | |   |||| |||||||| || || || ||||| ||||| || ||  ||||||| ||||||||||||||||| ||||| || || ||||||||  |  | ||||||
ttgtgtttcatag-atatcacaagtttgtatttgtttccaactttcttgtt--gttccttttgtcagacagaaatgttcttaggatattttttctttggacagATCAAAATACAACAGCATTCAAAGAAGTAGCAATTATTAGTCATCCCCGTGTTGGTGAATATGCGTTTGGATTCATAACATCAACCATGGTTCTTCAG

upper sequence: Vv07s0031g02010.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G39490.1 (Glycine max), 3'ss of exon 4
agcataattgtgctccatgtgtttatatatgtggtttacaatgttagcaagtgtttataattagcctaaaac--ttttaagtcactttcgta-----ttctttgcagACCAAAATACCACTGCTTTTAAAGAGGTAGCTATCATCCGTCATCCACGTGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTTCAG
    | | || | |   |||   ||  |    | || || || ||  ||| | ||  ||   ||  |  |||  |||    | | |||  ||     | |||| |||| |||||||||||||| |||||||||||||| || |||||||| || ||||||||||||||||||||||| |||||||||||||| || || || |||
----tcagtgagttat-tgttgatacttgatagattgacgatttt--caaatattggtaccaaggatgtaaccatttgtcatgatttttttacaatctccttttcagATCAAAATACCACTGCCTTTAAAGAGGTAGCAATTATCCGTCACCCGCGTGTTGGTGAATATGCATTTGGCTTTATTACATCAACTGTTATTCTACAG

upper sequence: Vv07s0031g02010.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G15360.2 (Glycine max), 3'ss of exon 4
agcataattgtgctccatgtgtt-tatatatgtggtttacaa-tgttagcaa-gtgtttataattagcc-taaaacttttaagtcactttcgtattctttgcagACCAAAATACCACTGCTTTTAAAGAGGTAGCTATCATCCGTCATCCACGTGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTTCAG
||   | || |  |  || | |  || ||      ||| ||| | || |  |   |  | |||  |    | |   ||||   |   ||   | |||||| |||| |||||||||||||| |||||||||||||| || |||||||| || ||||||||||||||||| ||||| |||||||||||||| || |  || |||
agtg-agttattgttgatatttgatagattgacaattttcaaatattggtgacaaggatgtaaccatttgtcatgatttt---ttttttaaattttcttttcagATCAAAATACCACTGCCTTTAAAGAGGTAGCAATTATCCGTCACCCGCGTGTTGGTGAATATGCGTTTGGATTTATTACATCAACTGTTACTCTACAG

upper sequence: Vv07s0031g02010.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G43130.1 (Arabidopsis thaliana), 3'ss of exon 4
--agcataattgtgctccatgtgtttatatatgtggtttacaatgttagcaagtgtttataattagcctaaaacttttaagtcactttcgtattctttgcagACCAAAATACCACTGCTTTTAAAGAGGTAGCTATCATCCGTCATCCACGTGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTTCAG
  |  || |||    | ||   ||  |  | | |   || | ||||| |   |  ||| |  |   | |   | |   |   |  ||   | || ||  |||||||||| || ||||| |||||||||||||| ||||||||||| || ||| |||||||||| |||||||| |||||||||||| | || |  ||||||
acacaatgatttgaattcacaagta-acctttttatgttgctatgtt-gtttgcctttttcgtgtcctttgtaatggaagaacctttgatttttgttctcagACCAAAACACTACTGCCTTTAAAGAGGTAGCAATCATCCGTCACCCTCGTATTGGTGAATACGCATTTGGATTTATTACATCATCGGTGACACTTCAG

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|22014341|gb|BQ799375.1|BQ799375
EST:     TAAGCATATATACTCGGCCTCCAAGCAAATTAGTGCCGCAATTTCTCCAG                         ACCAAAATACCACTGCTTTCAAAGAGGTAGCTATCATCCGTCATCCACGTG
genomic: TAAGCATATATACTCGGCCTCCAAGCAAATTAGTGCCGCAATTTCTCCAGgtaactcctg ... ttctttgcagACCAAAATACCACTGCTTTTAAAGAGGTAGCTATCATCCGTCATCCACGTG
EST: gi|110712883|gb|EE088318.1|EE088318
EST:     TAAGCATATATACTCGGCCTCCAAGCAAATTAGTGCCGCAATTTCTCCAG                         ACCAAAATACCACTGCTTTTAAAGAGGTAGCTATCATCCGTCATCCACGTG
genomic: TAAGCATATATACTCGGCCTCCAAGCAAATTAGTGCCGCAATTTCTCCAGgtaactcctg ... ttctttgcagACCAAAATACCACTGCTTTTAAAGAGGTAGCTATCATCCGTCATCCACGTG
EST: gi|110700237|gb|EE078049.1|EE078049
EST:     TAAGCATATATACTCGGCCTCCAAGCAAATTACTGCCGCAATTTCTCCAG                         ACCAAAATACCACTGCTTTTAAAGAGGTAGCTATCATCCGTCATCCACGTG
genomic: TAAGCATATATACTCGGCCTCCAAGCAAATTAGTGCCGCAATTTCTCCAGgtaactcctg ... ttctttgcagACCAAAATACCACTGCTTTTAAAGAGGTAGCTATCATCCGTCATCCACGTG
EST: gi|110365975|gb|EC929565.1|EC929565
EST:     TAAGCATATATACTCGGCCTCCAAGCAAATTAGTGCCGCAATTTCTCCAG                         ACCAAAATACCACTGCTTTTAAAGAGGTAGCTATCATCCGTCATCCACGTG
genomic: TAAGCATATATACTCGGCCTCCAAGCAAATTAGTGCCGCAATTTCTCCAGgtaactcctg ... ttctttgcagACCAAAATACCACTGCTTTTAAAGAGGTAGCTATCATCCGTCATCCACGTG
EST: gi|161713089|gb|FC062465.1|FC062465
EST:     TAAGCATATATACTCGGCCTCCAAGCAAATTAGTGCCGCAATTTCTCCAG                         ACCAAAATACCACTGCTTTTAAAGAGGTAGCTATCATCCGTCATCCACGTG
genomic: TAAGCATATATACTCGGCCTCCAAGCAAATTAGTGCCGCAATTTCTCCAGgtaactcctg ... ttctttgcagACCAAAATACCACTGCTTTTAAAGAGGTAGCTATCATCCGTCATCCACGTG
EST: gi|110425265|gb|EC991647.1|EC991647
EST:     TAAGCATATATACTCGGCCTCCAAGCAAATTAGTGCCGCAATTTCTCCAG                         ACCAAAATACCACTGCTTTTAAAGAGGTAGCTATCATCCGTCATCCACGTG
genomic: TAAGCATATATACTCGGCCTCCAAGCAAATTAGTGCCGCAATTTCTCCAGgtaactcctg ... ttctttgcagACCAAAATACCACTGCTTTTAAAGAGGTAGCTATCATCCGTCATCCACGTG
EST: gi|110398629|gb|EC965098.1|EC965098
EST:     TAAGCATATATACTCGGCCTCCAAGCAAATTAGTGCCGCAATTTCTCCAG                         ACCAAAATACCACTGCTTTTAAAGAGGTAGCTATCATCCGTCATCCACGTG
genomic: TAAGCATATATACTCGGCCTCCAAGCAAATTAGTGCCGCAATTTCTCCAGgtaactcctg ... ttctttgcagACCAAAATACCACTGCTTTTAAAGAGGTAGCTATCATCCGTCATCCACGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcaagtgtttataattagcctaaaacttttaagtcactttcgtattctttgcagACCAAAATACCACTGCTTTTAAAGAGGTAGCTATCATCCGTCATCCACGTGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTTCAG
                  gcctaaa  putative branch site (score: 3)
                                     ctttcgtattcttt  putative PPT
                     taaaacttttaagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcataattgtgctccatgtgtttatatatgtggtttacaatgttagcaagtgtttataattagcctaaaacttttaagtcactttcgtattctttgcagACCAAAATACCACTGCTTTTAAAGAGGTAGCTATCATCCGTCATCCACGTGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTTCAG

- - - - - - ctccatg
- - - - - - - - - - - - - - - - - - - caatgtt
- - - - - - - - - - - - - - - - - - - - - - - -caagtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaaaac