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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGATGACATTGAGGAGATGTACAAGAAGGTTCATGCTGCCATCCGTGCAAACCCAATTCAAAAGAAGGTTGAGAAGCAGCCACCGAAAGAGCACAAGAGgtgaggctgagattaaattgattcttttttctattcggttggcatttattatgctattatctgtaggttgtttaattaccatttgtttttattcttctat...

Basic information

species Vitis vinifera
transcript Vv05s0094g00870.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0094g00870.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: LOC_Os01g67134.1 (Oryza sativa), 5'ss of exon 8
CAGATGACATTGAGGAGATGTACAAGAAGGTTCATGCTGCCATCCGTGCAAACCCAATTCAAAAGAAGGTTGAGAAGCAGCCACCGAAAGAGCACAAGAGgtgaggctgagattaaattgattcttttttctattcggttggcatttattatgctattatctgtaggttgtttaattaccatttgtttttattcttctat
| |||| ||| || |   ||||||||||||| |||||||||||||||||  | || |        ||       ||| ||  ||||      ||||||||||    |    ||     ||||  ||| |   |   | ||   |||| | |||    | | ||   ||   | | || |   ||  | | |         
CTGATGGCATGGAAGCACTGTACAAGAAGGTCCATGCTGCCATCCGTGCTGATCCTACCATGGCCAAATCAACCAAGAAGGAACCGGCGACCCACAAGAGgta---catgaatctggctgatgatttctggaaa--gatt---atttgtgatgtccatgtatgattgtaactaacttgcatctttgtctcag--------

upper sequence: Vv05s0094g00870.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G163081_T04 (Zea mays), 5'ss of exon 8
CAGATGACATTGAGGAGATGTACAAGAAGGTTCATGCTGCCATCCGTGCAAACCCAATTCAAAAGAAGGTTGAG-AAGCAGCCACCGAAAGAGCACAAGAGgtgaggctgagattaaattgattcttttttctattcggttggcatttattatgctattatctgtaggttgtttaattaccatttgtttttattcttctat
| ||||| || || | | ||||||||||||| |||||||||||||||||  | ||  | ||     | ||  |  ||||||||||| || ||||| |||||||   |  |  | |       || | | |    || ||| | |||     || | ||  | ||        | |  | || | ||  | | |        
CTGATGAAATAGAAGCGCTGTACAAGAAGGTCCATGCTGCCATCCGTGCCGATCCT-TCCATTGTTAAGTCAACCAAGCAGCCACCAAAGGAGCATAAGAGgtatagtagctact-------ttttatatatagtttggtcgacata----atccaatcgtttgctctgccctgacctgccttctgcgtgtttcag-----

upper sequence: Vv05s0094g00870.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM5G815894_T03 (Zea mays), 5'ss of exon 8
CAGATGACATTGAGGAGATGTACAAGAAGGTTCATGCTGCCATCCGTGCAAACCCAATTCAAAAGAAGGTTGAGAAGCAGCCACCGAAAGAGCACAAGAGgtgaggctgagattaaattgattcttttttctattcggttggcatttattatgctattatctgtaggttgtttaattaccatttgtttttattcttctat
| |||||||| || |   ||||||||||||| |||||||||||||||||  | ||   |      |||      ||||||||||| || |||||||||||||   |  |    |        |||||||| ||| |  | | ||   || || ||||||| ||        | | || || | || | | ||||      
CTGATGACATGGAAGCTCTGTACAAGAAGGTCCATGCTGCCATCCGTGCTGATCCTTCTGTGGTCAAGTCAACCAAGCAGCCACCAAAGGAGCACAAGAGgtatagtagccgctg-------tcttttttttatactatggtcacc-ataatcctattatttgctctgccctgacttcccttctgctct-attcag----

upper sequence: Vv05s0094g00870.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA16G03170.1 (Glycine max), 5'ss of exon 8
CAGATGACATTGAGGAGATGTACAAGAAGGTTCATGCTGCCATCCGTGCAAACCCAATTCAAAAGAAGGTTGAGAAGCAGCCACCGAAAGAGCACAAGAGgtgaggctgagatt-aaattgattcttttttctattcggttggcatttattatgctat-tat-ctgtaggttgtttaattaccatttgtttttattcttctat
| ||||  |||||||   |||||||||||||||||||||||||||||||  | ||   ||  |||||   |||||||||||| ||||| || |||||||||| | | |||  ||  | ||||       | |||     |||  ||    ||   ||| |||  | |  ||  ||| ||| ||      ||   || | |   
CTGATGGTATTGAGGCACTGTACAAGAAGGTTCATGCTGCCATCCGTGCTGATCCTTCTCTCAAGAAATCTGAGAAGCAGCCCCCGAAGGAACACAAGAGgtaaagttgatttttgacttgaactagaatactagattcttgaaatagggtaatgtatgtatattttttgtcatttgatttccggcaaattgatttgtac---

upper sequence: Vv05s0094g00870.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA13G35590.1 (Glycine max), 5'ss of exon 8
CAGATGACATTGAGGAGATGTACAAGAAGGTTCATGCTGCCATCCGTGCAAACCCAATTCAAAAGAAGGTTGAGAAGCAGCCACCGAAAGAGCACAAGAGgtgaggctgagattaaattgattct---tttttctattcggttggcatttat-tatgctattatctgtaggttgtttaattaccatttgtttttattcttctat
| ||||  |||||||   | |||||||||||||||||||||||||||||  | || | ||  | |||   ||| |||||||| ||||| ||||||||||||| | | |||  ||  | |    ||    |  |  ||||       | | || |||||   ||| |     ||   |   |  ||||  |||||   ||     
CTGATGGTATTGAGGCACTTTACAAGAAGGTTCATGCTGCCATCCGTGCTGATCCTACTCTCAGGAAATCTGATAAGCAGCCCCCGAAGGAGCACAAGAGgtaaagttgattttttacttgaactggaatactagattctagaaatagtaatgtatgcatctattttctcatttgatttctggcattaatttttgacctg----

upper sequence: Vv05s0094g00870.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA13G35580.2 (Glycine max), 5'ss of exon 8
CAGATGACATTGAGGAGATGTACAAGAAGGTTCATGCTGCCATCCGTGCAAACCCAATTCAAAAGAAGGTTGAGAAGCAGCCACCGAAAGAGCACAAGAGgtgaggctga------gattaaattgattcttttttctattcggttggcatttattatgctattatctgtaggttgtttaattaccatttgtttttattcttctat
| ||||  |||||||   | |||||||||||||||||||||||||||||  | || | ||  | |||   ||| ||| |||| ||||| ||||||||||||| | | |||        || || ||      |    | |     | |  |    |||||   ||| |     ||   |   |  ||||  ||||||         
CTGATGGTATTGAGGCACTTTACAAGAAGGTTCATGCTGCCATCCGTGCTGATCCTACTCTCAGGAAATCTGATAAGGAGCCCCCGAAGGAGCACAAGAGgtaaagttgattttttacttgaactggaatactagattctggaaatagtgtaatgtatgcatctattttctcatttgatttctggcattaatttttacct------

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|351028159|gb|FQ426060.1|FQ426060
EST:     AACCCAATTCAAAAGAAGGTTGAGAAGCAGCCACCGAAAGAGCACAAGAG                         GTACAATTTGAAGAAGCTGACCTACGAGGAAAGGAAAGCTAAGTTGATTGA
genomic: AACCCAATTCAAAAGAAGGTTGAGAAGCAGCCACCGAAAGAGCACAAGAGgtgaggctga ... tgcatcacagGTACAATTTGAAGAAGCTGACCTACGAGGAAAGGAAAGCTAAGTTGATTGA
EST: gi|110700226|gb|EE078022.1|EE078022
EST:     A-CCCAATTCAAATGAAGGT-GAGAAGCAGCCACCGAAAGAGCACAAGAA                         GTACAATTTTGA-GAAGCTGACC
genomic: AACCCAATTCAAAAGAAGGTTGAGAAGCAGCCACCGAAAGAGCACAAGAGgtgaggctga ... tgcatcacagGTACAATTT-GAAGAAGCTGACC
EST: gi|110689577|gb|EE065921.1|EE065921
EST:     AACCCAATTCAAAAGAAAGTTGANAAGCAGCCTCCGAAAAAGCACAAGAG                         GTACAATTTGAAGAAGCTGACCTACGAGGAAAGCAAAGCTAAATTGAATGA
genomic: AACCCAATTCAAAAGAAGGTTGAGAAGCAGCCACCGAAAGAGCACAAGAGgtgaggctga ... tgcatcacagGTACAATTTGAAGAAGCTGACCTACGAGGAAAGGAAAGCTAAGTTGATTGA
EST: gi|110686174|gb|EE063536.1|EE063536
EST:     ACC-AATTCAAAAGAAG-TTGAGAAGCAGCCTCCGAAAAGAGCACA-GAG                         GTTACA-TTTGAAGAAGCTGACCTACGNNAG-AAAGGAA-GCTAAGTTG
genomic: ACCCAATTCAAAAGAAGGTTGAGAAGCAGCCACCGAAA-GAGCACAAGAGgtgaggctga ... tgcatcacagGT-ACAATTTGAAGAAGCTGACCTACG--AGGAAAGGAAAGCTAAGTTG
EST: gi|110685135|gb|EE063210.1|EE063210
EST:     CCCA-TTCAAAAGAAG-TTGANGA-GCAGCCACCCGAA-GAGCACA-GAG                         GTACAATTTGAAAGA-GCTGAC
genomic: CCCAATTCAAAAGAAGGTTGA-GAAGCAGCCACC-GAAAGAGCACAAGAGgtgaggctga ... tgcatcacagGTACAATTTGAA-GAAGCTGAC
EST: gi|110701654|gb|EE079474.1|EE079474
EST:     AACCCAATTCAAAAGAAAGTTGAGAAGCAGCCACCGAAAGAGCACAAGAG                         GTACAATTTGAAGAAGCTGACCTACGAAGAAAGGAAAGCTAAGTTGATTGA
genomic: AACCCAATTCAAAAGAAGGTTGAGAAGCAGCCACCGAAAGAGCACAAGAGgtgaggctga ... tgcatcacagGTACAATTTGAAGAAGCTGACCTACGAGGAAAGGAAAGCTAAGTTGATTGA
EST: gi|110708835|gb|EE086828.1|EE086828
EST:     AACCCAATTCAAAAGAAAGTTGAGAAGCAGCCACCGAAAGAGCACAAGAA                         GTACAATTTGAAGAAGCTGACCTACCAGGAAAGGAAAGCTAAATTGATTGA
genomic: AACCCAATTCAAAAGAAGGTTGAGAAGCAGCCACCGAAAGAGCACAAGAGgtgaggctga ... tgcatcacagGTACAATTTGAAGAAGCTGACCTACGAGGAAAGGAAAGCTAAGTTGATTGA
EST: gi|352791507|gb|FQ481086.1|FQ481086
EST:     AACCCAATTCAAAAGAAGGTTGAGAAGCAGCCACCGAAAGAGCACAAGAG                         GTACAATTTGAAGAAGCTGACCTACGAGGAAAGGAAAGCTAAGTTGATCGA
genomic: AACCCAATTCAAAAGAAGGTTGAGAAGCAGCCACCGAAAGAGCACAAGAGgtgaggctga ... tgcatcacagGTACAATTTGAAGAAGCTGACCTACGAGGAAAGGAAAGCTAAGTTGATTGA
EST: gi|34546375|gb|CF514607.1|CF514607
EST:     AACCCAATTCAAAAGAAGGTTGAGAAGCAGCCACCGAAAGAGCACAAGAG                         GTACAATTTGAAGAAGCTGACCTACGAGGAAAGGATCGCTAAGTTG
genomic: AACCCAATTCAAAAGAAGGTTGAGAAGCAGCCACCGAAAGAGCACAAGAGgtgaggctga ... tgcatcacagGTACAATTTGAAGAAGCTGACCTACGAGGAAAGGAAAGCTAAGTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGATGACATTGAGGAGATGTACAAGAAGGTTCATGCTGCCATCCGTGCAAACCCAATTCAAAAGAAGGTTGAGAAGCAGCCACCGAAAGAGCACAAGAGgtgaggctgagattaaattgattcttttttctattcggttggcatttattatgctattatctgtaggttgtttaattaccatttgtttttattcttctat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaattga