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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatgtatagctgtatgtagaacttgcatttttttaccctgtgtttttgataggcatagaagttgttgcaaattattgctcatagattgcatattttgcagGCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGGAAGGCAGTTGGTCGCTTGCAATCTCACAGCTTAACAGTGACACAGATTG

Basic information

species Vitis vinifera
transcript Vv01s0011g04130.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g04130.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G042371_T01 (Zea mays), 3'ss of exon 5
--------gatgtatagctgtatgtagaacttgc--atttttttaccctgtgtttttg--ataggcatagaagttgttgcaaattattgctcatagattgcatattttgcagGCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGGAAGGCAGTTGGTCGCTTGCAATCTCACAGCTTAACAGTGACACAGATTG
          |  ||   |  |||  | |  |||  | || || |   | || ||||    || |||| | |  | |     | | |  |||  |            | ||||||||||||||   ||||||||| || ||||| ||| | || ||  ||||||| || ||||  |||||||||||||||||  ||||||||||||| || |
ttgacataattacatcagttgatgctggatatgcttaattattaatggtttgattttactgtatgcatgggaaatatgatggaatttcactccca------------ttcagGCTCAATCAGCAGCAGTTGCAGAGATCTGGCTCTGGGAGGTTGGAACATGGAAAGCTGTTGCCCGCTTGCAATCTCACAGTCTAACAGTGACACAAATGG

upper sequence: Vv01s0011g04130.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA20G25600.1 (Glycine max), 3'ss of exon 8
---gatgtatagctgtatgtagaacttgcatttttttaccctgtgtttttgataggcatagaagttgttgcaaattattgctcatagattgcatattttgcagGCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGGAAGGCAGTTGGTCGCTTGCAATCTCACAGCTTAACAGTGACACAGATTG
     |  || | |||  ||    ||   | || | |||| |||    ||    |   ||  | |  |       |||||| ||||  ||  ||   |||||||||||||| ||   |||||||||  ||||||| ||||| |||||||||||||| ||||| || ||| ||||||| ||||||||||||||||||||||| |
tgctttagattgttgttagttagtctc-tagttctctaccttgttcacttttctgctttatcactgatattg--ctattgcacatacgttttatgcattgcagGCTCAATCTGCAGCAGTTGCAGAGGTATGGCTTTGGCAGGTGGGTTCATGGAAAGCAGTCGGCCGCCTGCAATCCCACAGCTTAACAGTGACACAGATGG

upper sequence: Vv01s0011g04130.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA10G41620.1 (Glycine max), 3'ss of exon 8
gatgtatagctgtatgtagaacttgcatttttttaccctgtgtttttgataggcatagaagttgttgcaaat-----tattgctcatagattgcatattttgcagGCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGGAAGGCAGTTGGTCGCTTGCAATCTCACAGCTTAACAGTGACACAGATTG
     | |||||  | ||||  |||   ||  | |  || |   ||    |    |     || |  |  ||     |||||| ||||  |||  |   |||||||| ||||| ||   |||||| ||  ||||||| ||||| |||||||||||||| |||||||| | | ||||||| ||||||||||||||||||||||| |
--accaaagctg-gtttaga--ttgttgttagtcagtctctaccttgctcacttttctgctttatctctgatattgctattgcacatatgttgtgtgcattgcagGCCCAATCTGCAGCAGTTGCTGAGGTATGGCTTTGGCAGGTGGGTTCATGGAAAGCAGTTGGCCACCTGCAATCCCACAGCTTAACAGTGACACAGATGG

upper sequence: Vv01s0011g04130.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT1G49540.1 (Arabidopsis thaliana), 3'ss of exon 8
--gatgtatagctgtatgtagaac----ttgcatttttttaccctgt--gtttttga---taggcata---------gaagttgttgc-aaattattgct------catagattgcata-ttttgcagGCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGGAAGGCAGTTGGTCGCTTGCAATCTCACAGCTTAACAGTGACACAGATTG
   |  ||  || || |  ||||     || || || || |  ||    | ||| ||   |||   ||         ||     || | ||||||||  |       ||  |   || | || | ||||||||||| ||     | ||||| |||||||||||| | || ||  ||||||| || |||||||| ||||||||||||||||| || ||||| ||  | |
gtaagttaatgcagttttcagaatttttttacacttcttcaatctcctagatttagattttagatctaactgagcaggattccattactaaattattatttttatatatgaaccacaaacttcttcagGCTCAATCTGCATCCATGGCAGAGATATGGCTATGGGAGGTTGGGACATGGAAAGCTGTTGGTCGTTTGCAATCTCACAGCTTGACGGTGACGCACTTGG

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|351031220|gb|FQ445047.1|FQ445047
EST:     TTTCTTTGTGCTGTGACCAGGGAGGGAAGCTTGTTGCTTCATCATGTAAG                         GCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGG
genomic: TTTCTTTGTGCTGTGACCAGGGAGGGAAGCTTGTTGCTTCATCATGTAAGgtatatcttt ... tattttgcagGCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGG
EST: gi|349832389|gb|FQ420950.1|FQ420950
EST:     TTTCTTTGTGCTGTGACCAGGGAGGGAAGCTTGTTGCTTCATCATGTAAG                         GCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTTGGTTCA
genomic: TTTCTTTGTGCTGTGACCAGGGAGGGAAGCTTGTTGCTTCATCATGTAAGgtatatcttt ... tattttgcagGCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCA
EST: gi|34547373|gb|CF515605.1|CF515605
EST:     TTTCTTTGTGCTGTGACCAGGGAGGGAAGCTTGTTGCTTCATCATGTAAG                         GCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGG
genomic: TTTCTTTGTGCTGTGACCAGGGAGGGAAGCTTGTTGCTTCATCATGTAAGgtatatcttt ... tattttgcagGCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGG
EST: gi|351054132|gb|FQ450214.1|FQ450214
EST:     TTTCTTTGTGCTGTGACCAGGGAGGGAAGCTTGTTGCTTCATCATGTAAG                         GCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGG
genomic: TTTCTTTGTGCTGTGACCAGGGAGGGAAGCTTGTTGCTTCATCATGTAAGgtatatcttt ... tattttgcagGCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGG
EST: gi|351038018|gb|FQ460760.1|FQ460760
EST:     TTTCTTTGTGCTGTGACCAGGGAGGGAAGCTTGTTGCTTCATCATGTAAG                         GCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGG
genomic: TTTCTTTGTGCTGTGACCAGGGAGGGAAGCTTGTTGCTTCATCATGTAAGgtatatcttt ... tattttgcagGCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGG
EST: gi|351016289|gb|FQ446149.1|FQ446149
EST:     TTTCTTTGTGCTGTGACCAGGGAGGGAAGCTTGTTGCTTCATCATGTAAG                         GCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGG
genomic: TTTCTTTGTGCTGTGACCAGGGAGGGAAGCTTGTTGCTTCATCATGTAAGgtatatcttt ... tattttgcagGCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGG
EST: gi|351036140|gb|FQ463985.1|FQ463985
EST:     TTTCTTTGTGCTGTGACCAGGGAGGGAAGCTTGTTGCTTCATCATGTAAG                         GCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGG
genomic: TTTCTTTGTGCTGTGACCAGGGAGGGAAGCTTGTTGCTTCATCATGTAAGgtatatcttt ... tattttgcagGCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGG
EST: gi|352793961|gb|FQ479203.1|FQ479203
EST:     TTTCTTTGTGCTGTGACCAGGGAGGGAAGCTTGTTGCTTCATCATGTAAG                         GCTCAATCAGCGAAAGTTGCAAAAATATGGCTATGGCA
genomic: TTTCTTTGTGCTGTGACCAGGGAGGGAAGCTTGTTGCTTCATCATGTAAGgtatatcttt ... tattttgcagGCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCA
EST: gi|34546608|gb|CF514840.1|CF514840
EST:     TTGTGCTGTGACCAGGGAGGGAAGCTTGTTGCTTCATCATGTAAG                         GCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGG
genomic: TTGTGCTGTGACCAGGGAGGGAAGCTTGTTGCTTCATCATGTAAGgtatatcttt ... tattttgcagGCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGG
EST: gi|34546788|gb|CF515020.1|CF515020
EST:     TTTCTTTGTGCTGTGACCAGGGAGGGAAGCTTGTTGCTTCATCATGTAAG                         GCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGG
genomic: TTTCTTTGTGCTGTGACCAGGGAGGGAAGCTTGTTGCTTCATCATGTAAGgtatatcttt ... tattttgcagGCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGG
EST: gi|351054298|gb|FQ450381.1|FQ450381
EST:     TTTCTTTGTGCTGTGACCAGGGAGGGAAGCTTGTTGCTTCATCATGTAAG                         GCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGG
genomic: TTTCTTTGTGCTGTGACCAGGGAGGGAAGCTTGTTGCTTCATCATGTAAGgtatatcttt ... tattttgcagGCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGG
EST: gi|37187736|gb|CF607089.1|CF607089
EST:     TTTCTTTGTGCTGTGACCAGGGAGGGAAGCTTGTTGCTTCATCATGTAAG                         GCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGG
genomic: TTTCTTTGTGCTGTGACCAGGGAGGGAAGCTTGTTGCTTCATCATGTAAGgtatatcttt ... tattttgcagGCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGG
EST: gi|351043253|gb|FQ443974.1|FQ443974
EST:     TTTCTTTGTGCTGTGACCAGGGAGGGAAGCTTGTTGCTTCATCATGTAAG                         GCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGG
genomic: TTTCTTTGTGCTGTGACCAGGGAGGGAAGCTTGTTGCTTCATCATGTAAGgtatatcttt ... tattttgcagGCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGG
EST: gi|349817591|gb|FQ407381.1|FQ407381
EST:     TTTCTTTGTGCTGTGACCGGGGAGGGAAGCTTGTTGCTTCATCATGTAAG                         GCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGG
genomic: TTTCTTTGTGCTGTGACCAGGGAGGGAAGCTTGTTGCTTCATCATGTAAGgtatatcttt ... tattttgcagGCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgataggcatagaagttgttgcaaattattgctcatagattgcatattttgcagGCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGGAAGGCAGTTGGTCGCTTGCAATCTCACAGCTTAACAGTGACACAGATTG
 ttttgat  putative branch site (score: 4)
                       aaattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatgtatagctgtatgtagaacttgcatttttttaccctgtgtttttgataggcatagaagttgttgcaaattattgctcatagattgcatattttgcagGCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGGAAGGCAGTTGGTCGCTTGCAATCTCACAGCTTAACAGTGACACAGATTG

- - - - -ctgtatg
- - - - - - - - - - -cttgcat
- - - - - - - - - - - - - - - - -taccctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaatta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctcata