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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaatttttcccaaaatcattcataatttcacattgtttgattagataagtccactttctgaaatcgcacttcattactttatttgctgcctgtcttcagATCTTCCACCAGACAAGGAGCCTCTGGACTGGAACACAAGGATGAAGATTGCTGCTGGTGCAGCTAAAGGTTTGGAGTATTTGCATGATAAAGCAAGCCC

Basic information

species Vitis vinifera
transcript Vv05s0020g01770.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os07g47270.1 (Oryza sativa), 3'ss of exon 3
acaatttttcccaaaatcattcataatttcacattgtttgattagataagtccactttctgaaatcgcacttcattactttatt-----tgctgc-ctgtctt--cagATCTTCCACCAGACAAGGAGCCTCTGGACTGGAACACAAGGATGAAGATTGCTGCTGGTGCAGCTAAAGGTTTGGAGTATTTGCATGATAAAGCAAGCCC
   |   ||| |    | | |  || |||   | ||    |  | ||         ||  || || ||  |  || | |||||      ||  || || ||||   |||||  ||||||| |||| | ||||| ||||||||  |||||||||||||||||| ||||||||| || |||||||||||  |||||||||| ||||  ||
---acccttcactgtcttact-gtagtttgctactg----acaacatttaattttctttagacattgctatctatcattttataactcatggggcactttcttaatagATCGCCCACCAGGCAAGAAACCTCTTGACTGGAATGCAAGGATGAAGATTGCTGTTGGTGCAGCGAAGGGTTTGGAGTACCTGCATGATAAGGCAAATCC

upper sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g30870.1 (Oryza sativa), 3'ss of exon 3
acaatttttcccaaaatcattcataatttcacattgtttgattagataagtccactttctgaaatcgcacttcattactttatttgctgcctgtcttcagATCTTCCACCAGACAAGGAGCCTCTGGACTGGAACACAAGGATGAAGATTGCTGCTGGTGCAGCTAAAGGTTTGGAGTATTTGCATGATAAAGCAAGCCC
| | | ||   |  | |  ||  | ||   || |  || | ||   ||| |  | || |   | ||  |  |    || || | | ||        | |||| ||||||| |||||||| ||||| |||||||| ||| ||||||||||||||||||||||||| || || ||||| |  |||||||| || ||||  ||
agactcttaagcgcattgtttgttcataagacgtatttagtttgtttaaattaatttgcatgattcataaatggcaacgttttgtacttttgtgtgttagATATTCCACCTGACAAGGAACCTCTCGACTGGAATACACGGATGAAGATTGCTGCTGGTGCAGCCAAGGGCTTGGAATTCTTGCATGACAAGGCAAATCC

upper sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g71000.1 (Oryza sativa), 3'ss of exon 3
-acaatttttcccaaaatcattcataatttcacattgtt-tgattagataagtccactttctgaaatcgcacttcattactttatttgctgcctgtcttcagATCTTCCACCAGACAAGGAGCCTCTGGACTGGAACACAAGGATGAAGATTGCTGCTGGTGCAGCTAAAGGTTTGGAGTATTTGCATGATAAAGCAAGCCC
     |  ||   | |    ||  ||||  ||   |||| || ||| |            ||  ||  | |  | |    |||      | |   | |  |||| | ||||| || ||||| ||||| |||||||||||| |||||||||| ||||| |||||||| || || || || ||  | ||||| || || |||||
cttggtagttagtacagctgtt--taatggcatcctgttatgtttaaagttcaatggcagcttcaaatgaagataaaaggttttccaatttctgttttgtagATTTGCCACCTGATAAGGAACCTCTTGACTGGAACACACGGATGAAGATAGCTGCAGGTGCAGCCAAGGGCTTAGAATACCTACATGACAAGGCGAGCCC

upper sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g15470.1 (Oryza sativa), 3'ss of exon 3
------acaatttttcccaaaatcattcataatttcacattgtttgattagataagtccactttctgaaatcgcacttcattactttatttgctgcctgtcttcagATCTTCCACCAGACAAGGAGCCTCTGGACTGGAACACAAGGATGAAGATTGCTGCTGGTGCAGCTAAAGGTTTGGAGTATTTGCATGATAAAGCAAGCCC
        |||| |||   | ||  | ||  |    || |  |||  |||  ||     | |    || | |    |  |    |      | ||| | | | |||||||   ||| | | | || || || || ||||  ||| |||||||||||||||||| |||||||   |||||||||||| |||||||| | || |  ||
aagaattaaattgttctttacat--tccagtaagctacttaatttccttaagta---ttattactggataccctgttaaaaatttgctgccgatgctt-tttacagATCTCAGACCCGGCCAAGAACCACTAGATTGGACAACACGGATGAAGATTGCTGCTGATGCAGCTGCTGGTTTGGAGTATCTGCATGATGAGGCCATTCC

upper sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G048210_T02 (Zea mays), 3'ss of exon 3
acaatttttcccaaaatcattcataatttc--acattgtttg----attagataagt-ccactttctgaaatcgcacttcattactttatttgctgcctgtcttcagATCTTCCACCAGACAAGGAGCCTCTGGACTGGAACACAAGGATGAAGATTGCTGCTGGTGCAGCTAAAGGTTTGGAGTATTTGCATGATAAAGCAAGCCC---
         ||   |||  ||  | | | |  ||   ||  |    | ||| ||       |  ||   | |    |||   ||  | ||    |  || ||||   |  | ||| ||| |||||| ||||| |||||||| ||||||||||||||||||||||||||||| || ||| |||||||  | ||||| || ||||  ||   
---------ccgtcaatgctttgtgactgctgacgccgtccgcagtaatagctagacattgccatccatatttcttcttttgtaactcatgacgtcactttcttggtagGT-CCAGCAGGCAAGGAACCTCTTGACTGGAATACAAGGATGAAGATTGCTGCTGGTGCAGCGAAGGGTCTGGAGTACCTTCATGACAAGGCAAATCCACC

upper sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G048210_T01 (Zea mays), 3'ss of exon 3
acaatttttcccaaaatcattcataatttcacattgtttgattagataagtccactttctgaaatcgcacttcattactttatttgctgcctgtcttcagATCTTCCACCAGACAAGGAGCCTCTGGACTGGAACACAAGGATGAAGATTGCTGCTGGTGCAGCTAAAGGTTTGGAGTATTTGCATGATAAAGCAAGCCC---------
   ||  ||    |   |   |    |  | || |  | |  |||| |   |||   ||   | |    |||   ||  | ||    |  || ||||   |  | ||| ||| |||||| ||||| |||||||| ||||||||||||||||||||||||||||| || ||| |||||||  | ||||| || ||||  ||         
---atgctttgtgactgctgacgccgtc-cgcagtaatag-ctagacattgcca---tccatatttcttcttttgtaactcatgacgtcactttcttggtaggt-ccagCAGGCAAGGAACCTCTTGACTGGAATACAAGGATGAAGATTGCTGCTGGTGCAGCGAAGGGTCTGGAGTACCTTCATGACAAGGCAAATCCACCAGTCAT

upper sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G140590_T06 (Zea mays), 3'ss of exon 2
------acaatttttcccaaaatcattcataatttcacattgtttgattagataagtccactttctgaaatcgcacttcattactttatttgctgcctgtcttcagATCTTCCACCAGACAAGGAGCCTCTGGACTGGAACACAAGGATGAAGATTGCTGCTGGTGCAGCTAAAGGTTTGGAGTATTTGCATGATAAAGCAAGCCC
      | |   |  |     |   |  ||| | | ||| | | | ||  |  ||    | || |   |||   | || || |  | |||  ||   | | || |||| ||||||| || ||||| |||||||||||||| ||| | |||||||||||||||||||| || || || || ||||| ||||||||||| ||||| ||
taaattatagactaacagcccaatctatatagtctaacaat-tctcatatgccaaa---atttccctgaataaaatttaatcatataattaact-tttatgtt-agATATTCCACCTGATAAGGAACCTCTGGACTGGAATACACGTATGAAGATTGCTGCTGGTGCCGCCAAGGGCTTAGAGTACTTGCATGATAAGGCAAGTCC

upper sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G177061_T02 (Zea mays), 3'ss of exon 2
acaatttttcccaaaatcattcataatttc--acattgtttg----attagataagt-ccactttctgaaatcgcacttcattactttatttgctgcctgtcttcagATCTTCCACCAGACAAGGAGCCTCTGGACTGGAACACAAGGATGAAGATTGCTGCTGGTGCAGCTAAAGGTTTGGAGTATTTGCATGATAAAGCAAGCCC---
         ||   |||  ||  | | | |  ||  |||  |    | ||| ||       |  ||   | |    |||   ||  | ||    |  || ||||   |  | ||| ||| |||||| ||||| |||||||| ||||||||||||||||||||||||||||| || ||| | |||||| | ||||| || ||||  ||   
---------ccgtcaatgctttgtgactgctgacgctgtccgcagtaatagctagacattgccatccatatttcttcttttgtaactcatgacgtcactttcttggtagGT-CCAGCAGGCAAGGAACCTCTTGACTGGAATACAAGGATGAAGATTGCTGCTGGTGCAGCGAAGGGTCTCGAGTATCTTCATGACAAGGCAAATCCACC

upper sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G037585_T02 (Zea mays), 3'ss of exon 2
-----acaatttttcccaaaatcattcataatttcacattgtttgattagataagtccactttctgaaatcgcacttcattactttatttgctgcctgtcttcagATCTTCCACCAGACAAGGAGCCTCTGGACTGGAACACAAGGATGAAGATTGCTGCTGGTGCAGCTAAAGGTTTGGAGTATTTGCATGATAAAGCAAGCCC
     | |   |      ||    || ||  |||| |  | ||  |||       |   | ||| |    ||    |  | |||  |     |   | | |  |||||| |||||||| || || ||||| |||||||||||| |||||||||| ||||| ||||||||||| || || |||||  | || || ||  | || ||
ttttcataggctaaaatgaatatgttgatgttttctctctcttccatttc-----tttgcattcagttcacgggtcttgtaactgaaaagtatttatttgtgtagATCTGCCACCAGATAAAGAACCTCTAGACTGGAACACACGGATGAAGATAGCTGCAGGTGCAGCTAAGGGCTTAGAGTACCTTCACGACAAGACGAGTCC

upper sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G145709_T01 (Zea mays), 3'ss of exon 3
acaatttttcccaaaatcattcataatttcacattgtttgattagataagtccactttctgaaatcgc--acttcattactttatttgctgcctgtcttcagATCTTCCACCAGACAAGGAGCCTCTGGACTGGAACACAAGGATGAAGATTGCTGCTGGTGCAGCTAAAGGTTTGGAGTATTTGCATGATAAAGCAAGCCC
  ||||| | |  |    | |    ||      || |||| |     || ||       | |  ||       |  | |||  |     |   | | |  |||||| |||||||| || |||||||| || ||||||||| |||||||||| ||||| ||||||||||| || || ||  |  | ||||| || || || ||
--aatttcttctgactagagttggtatcctttgttttttgctcttccaattctttgcagtcagttcatgggtcttgtaactgaacagtgtttatttgtatagATCTGCCACCAGATAAAGAGCCTCTTGATTGGAACACACGGATGAAGATAGCTGCAGGTGCAGCTAAGGGCTTAGAACACCTTCATGACAAGGCGAGTCC

upper sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G28730.1 (Glycine max), 3'ss of exon 3
--acaatttttcccaaaatca-ttcataatttcacattgtttgattagataagtccactttctgaaatcgcacttcattactt-tatttgctgcctgtcttcagATCTTCCACCAGACAAGGAGCCTCTGGACTGGAACACAAGGATGAAGATTGCTGCTGGTGCAGCTAAAGGTTTGGAGTATTTGCATGATAAAGCAAGCCC
  || |||   |      | | ||  | |||  | |||     ||   |||||    |   ||  |       |  ||| ||   | ||  |  || | |||||||||||| ||||||||||||||||||||||||||||| |||||||| || || ||||| || || || || ||||| ||||||||||| || ||||  ||
tcaccattagacattgctttagtttgttattagaaattaacccat---ataaggtttcagcctatacataggataaatttctgacacttaatctct-ttttcagATCTTCCTCCAGACAAGGAGCCTCTGGACTGGAACACTAGGATGAAAATAGCAGCTGGAGCTGCAAAGGGATTGGAATATTTGCATGACAAGGCAAATCC

upper sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA15G10360.1 (Glycine max), 3'ss of exon 3
acaatttttcccaaaatcattcataatttcacattg----tttgattagataagtccactttctgaaatcgcacttcattactttatttgctgcctgtcttcagATCTTCCACCAGACAAGGAGCCTCTGGACTGGAACACAAGGATGAAGATTGCTGCTGGTGCAGCTAAAGGTTTGGAGTATTTGCATGATAAAGCAAGCCC
             | ||   |   | |||   |||     ||     | |||||    |   ||  |  |       ||| ||     ||   |   | | |||||||||| || |||||||||||||||||||||||||| |||||||| || || ||||| || || || || ||||| ||||||||||| || ||||  ||
----caccaatagacattgctttcagtttgttattagaaattaacccatataaggtttcagcctatacactggagaaatttctgacactgaatctcttttccagATCTTCCTCCTGACAAGGAGCCTCTGGACTGGAACACTAGGATGAAAATAGCAGCTGGAGCTGCAAAGGGATTGGAATATTTGCATGACAAGGCAAATCC

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|30302616|gb|CB979410.1|CB979410
EST:     GCTTGTCTATGAGTTTATGCCATTGGGATCATTGGAGGATCATTTACATG                         ATCTTCCACCAGACAAGGAGCCTCTGGACTGGAACACAAGGATGAAGATTG
genomic: GCTTGTCTATGAGTTTATGCCATTGGGATCATTGGAGGATCATTTACATGgttagattgc ... ctgtcttcagATCTTCCACCAGACAAGGAGCCTCTGGACTGGAACACAAGGATGAAGATTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataagtccactttctgaaatcgcacttcattactttatttgctgcctgtcttcagATCTTCCACCAGACAAGGAGCCTCTGGACTGGAACACAAGGATGAAGATTGCTGCTGGTGCAGCTAAAGGTTTGGAGTATTTGCATGATAAAGCAAGCCC
                                            cctgtcttc  CT-rich tract
                         ttcattactttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaatttttcccaaaatcattcataatttcacattgtttgattagataagtccactttctgaaatcgcacttcattactttatttgctgcctgtcttcagATCTTCCACCAGACAAGGAGCCTCTGGACTGGAACACAAGGATGAAGATTGCTGCTGGTGCAGCTAAAGGTTTGGAGTATTTGCATGATAAAGCAAGCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - -cccaaaa
- - - - - - - - -cattcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgctgc