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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctattgctgttgatgtacttattatcgaatacaaactcatgtacattacatgctctttgtggatctgacattattctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGGGAAGTCCCTCTACCCAAA

Basic information

species Vitis vinifera
transcript Vv08s0105g00280.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0105g00280.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G009876_T01 (Zea mays), 3'ss of exon 4
gtctattgctgttgatg--tacttattatcgaatacaaactcatgtacattacatgctctttgtggatctgacattattctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGGGAAGTCCCTCTACCCAAA
||  ||| |||||  ||  | ||    | | |||    |  ||   || ||  |||   ||  |    |||| ||         | |||||||| ||||| || ||||||||||| ||||| || || ||||| |||||||| || ||||| || || 
gtgaattactgttcttggcttctctccagctaattatgatacagtaacgttttatggcattgatca--ctgatatctggtgaagtgtagGTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAG

upper sequence: Vv08s0105g00280.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G35500.1 (Glycine max), 3'ss of exon 4
gtctattgc-tgttgatgtacttattatcgaatacaaactcatgtacattacatgctctttgtgg---atctgacattattctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGGGAAGTCCCTCTACCCAAA
       || |||| ||||  | |     |  |      |  | |      | ||    |||      ||||||||   |||| | | |||||||||||||| || || |||||||| ||||| ||||| || ||||||||||| || |||||||| || 
-------gcatgttcatgtcttgaaagaaggttttgcctttttttttcagtcttgtaagttgaaagcaatctgacaaatttctatttttagGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAG

upper sequence: Vv08s0105g00280.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G00490.1 (Glycine max), 3'ss of exon 4
gtctattgctgttgatgtacttattatcgaatacaaactcatgtacatt-acatgctctttgtggatctgacattattctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGGGAAGTCCCTCTACCCAAA
              |||| | | |  |  || |        |||   ||  ||  ||  |     ||||||   | |||| | | |||||||||||||| || || |||||||| ||||| ||||| || || |||||||| || |||||||| || 
------------gcatgttcatgtcttgaaagatggttgtgtgtgtgtttgcagacttgtaagtaatctgatggttttctatttttagGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAG

upper sequence: Vv08s0105g00280.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G10000.1 (Glycine max), 3'ss of exon 4
gtctattgctgttgatgtacttattatcgaatacaaactcatgtacatt---acatgctctttgtggatctgacattattctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGGGAAGTCCCTCTACCCAAA
              |||| | | |  |  || |        |||   ||    ||  ||  |     ||||||     ||||   | |||||||||||||| || || |||||||| ||||| ||||| || || |||||||| || |||||||| || 
------------gcatgttcatgtcttgaaagatggttgtgtgtgtgtttttgcagacttgtaagtaatctgatggctttctacttttagGTTCTTAGCAACACAATTAAGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAG

upper sequence: Vv08s0105g00280.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G06360.1 (Arabidopsis thaliana), 3'ss of exon 4
gtctatt-gctgttgatgtacttattatcgaatacaaactcatgtacattac---atgctctttgtggatctg-acattattctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGGGAAGTCCCTCTACCCAAA
|| | || | | ||  | | |   ||     ||  | | |  ||||  ||       ||  |   |  |   |    |  || ||  | |||||||||||||| || || || ||||| ||||||||||||||||| |||||||| |||||||| || || 
gtttgtttgttttttcttttcaagttgagatatctataattctgtaacttggtgacggcattacattaacaagtgtgtgtttttgggtgtagGTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAG

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|351034903|gb|FQ458260.1|FQ458260
EST:     GGGCCGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAG                         GTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
genomic: GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAGgtctattgct ... ctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
EST: gi|37189315|gb|CF608664.1|CF608664
EST:     GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAG                         GTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
genomic: GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAGgtctattgct ... ctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
EST: gi|110388463|gb|EC953218.1|EC953218
EST:     GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAG                         GTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
genomic: GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAGgtctattgct ... ctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
EST: gi|351034907|gb|FQ458264.1|FQ458264
EST:     GGGCCGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAG                         GTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
genomic: GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAGgtctattgct ... ctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
EST: gi|110689931|gb|EE066589.1|EE066589
EST:     GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAG                         GTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
genomic: GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAGgtctattgct ... ctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
EST: gi|349827619|gb|FQ422487.1|FQ422487
EST:     GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAG                         GTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
genomic: GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAGgtctattgct ... ctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
EST: gi|351012282|gb|FQ429967.1|FQ429967
EST:     GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAG                         GTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
genomic: GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAGgtctattgct ... ctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
EST: gi|351053282|gb|FQ459150.1|FQ459150
EST:     GGGCTGTTCCTGCCTATCTACCAGATCGTGAAACAACAACGCGTGCAAAG                         GTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
genomic: GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAGgtctattgct ... ctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
EST: gi|110691373|gb|EE069403.1|EE069403
EST:     GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAG                         GTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
genomic: GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAGgtctattgct ... ctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
EST: gi|351025564|gb|FQ426380.1|FQ426380
EST:     GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAG                         GTTCTCAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
genomic: GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAGgtctattgct ... ctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
EST: gi|71875347|gb|DT024402.1|DT024402
EST:     GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAG                         GTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
genomic: GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAGgtctattgct ... ctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
EST: gi|110686904|gb|EE063847.1|EE063847
EST:     GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAG                         GTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
genomic: GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAGgtctattgct ... ctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
EST: gi|351035636|gb|FQ463481.1|FQ463481
EST:     GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAG                         GTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
genomic: GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAGgtctattgct ... ctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
EST: gi|349827505|gb|FQ422373.1|FQ422373
EST:     GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAG                         GTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
genomic: GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAGgtctattgct ... ctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
EST: gi|351056948|gb|FQ443575.1|FQ443575
EST:     GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAG                         GTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
genomic: GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAGgtctattgct ... ctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
EST: gi|351032431|gb|FQ458796.1|FQ458796
EST:     GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAG                         GTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
genomic: GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAGgtctattgct ... ctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
EST: gi|351049548|gb|FQ429170.1|FQ429170
EST:     GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAG                         GTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
genomic: GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAGgtctattgct ... ctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
EST: gi|349830525|gb|FQ416835.1|FQ416835
EST:     GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAG                         GTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
genomic: GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAGgtctattgct ... ctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
EST: gi|77588634|gb|DV223535.1|DV223535
EST:     GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAG                         GTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
genomic: GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAGgtctattgct ... ctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
EST: gi|351049014|gb|FQ431558.1|FQ431558
EST:     GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAG                         GTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
genomic: GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAGgtctattgct ... ctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
EST: gi|351056833|gb|FQ443460.1|FQ443460
EST:     GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAG                         GTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
genomic: GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAGgtctattgct ... ctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
EST: gi|71875464|gb|DT024519.1|DT024519
EST:     GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAG                         GTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
genomic: GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAGgtctattgct ... ctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
EST: gi|110701282|gb|EE078674.1|EE078674
EST:     GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAG                         GTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
genomic: GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAGgtctattgct ... ctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
EST: gi|161720669|gb|FC070613.1|FC070613
EST:     GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAG                         GTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG
genomic: GGGCTGTTCCTGCCTATCTACTAGATCGTGAAACAACAACACGTGCAAAGgtctattgct ... ctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaaactcatgtacattacatgctctttgtggatctgacattattctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGGGAAGTCCCTCTACCCAAA
                                atctgac  putative branch site (score: 3)
                                           ttctgtct  putative PPT
                                     acattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctattgctgttgatgtacttattatcgaatacaaactcatgtacattacatgctctttgtggatctgacattattctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGGGAAGTCCCTCTACCCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG