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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcatggtatggaggtctttaacttctggcacagaatgttccttttgatgcagatttcttttttattgttgttgaaaatattattatttcaacttgtagGCAGAGGGTAAAGTACTCAGAGGGCCACAGGAGGACCTAGAAAGTTACTTGGAATCTATTGATCAGCTAAGAAGCAATATTCGTTTTTTTAGCAGCAACA

Basic information

species Vitis vinifera
transcript Vv13s0073g00170.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0073g00170.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G03540.1 (Arabidopsis thaliana), 3'ss of exon 2
---------------------tttcatggtatggaggtctttaacttctggcacagaatgttccttttgatgcagatttcttttttattgttgttgaaaatattattatttcaacttgtagGCAGAGGGTAAAGTACTCAGAGGGCCACAGGAGGACCTAGAAAGTTACTTGGAATCTATTGATCAGCTAAGAAGCAATATTCGTTTTTTTAGCAGCAACA
                     | | ||  ||   |  |   |   |      | | |   ||  |  ||||  | |||     |  || ||  ||||  ||  | | | ||||| |  |||||||||  |||||||||||  |||||||| |||||||| ||||||||  ||||  | |||| ||| || ||||  | |||||||| |||||  |||||||
gtttgttttacaaatcttgcttctgattttactaacatggatcggtataaatagatagaattgataatgatctacattgagaatagatagtctttgattatgctctcaattcaattc-tagGCAGAGACTAAAGTACTCAAGGGGCCACATGAGGACCTGGAAAGTTATCTGGATGCAATTGCTCAACTCAGAAAGATTATTCGTTATTTTATGAGCAACA
















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|352773552|gb|FQ472334.1|FQ472334
EST:     CTTTGAAGGCTGCCGAGGTTATATTGGCTCAATTCGACCTTTATCGTCAG                         GCAGAGGGTAAAGTACTCAGAGGGCCACAGGAGGACCTAGAAAGTTACTTG
genomic: CTTTGAAGGCTGCCGAGGTTATATTGGCTCAATTCGACCTTTATCGTCAGgttggatttt ... caacttgtagGCAGAGGGTAAAGTACTCAGAGGGCCACAGGAGGACCTAGAAAGTTACTTG
EST: gi|352778158|gb|FQ468820.1|FQ468820
EST:     CTTTGAAGGCTGCCGAGGTTATATTGGCTCAATTCGACCTTTATCGTCAG                         GCAGAGGGTAAAGTACTCAGAGGGCCACAGGAGGACCTAGAAAGTTACTTG
genomic: CTTTGAAGGCTGCCGAGGTTATATTGGCTCAATTCGACCTTTATCGTCAGgttggatttt ... caacttgtagGCAGAGGGTAAAGTACTCAGAGGGCCACAGGAGGACCTAGAAAGTTACTTG
EST: gi|110713084|gb|EE088694.1|EE088694
EST:     CTTTGAAGGCTGCCGAGGTTATATTGGCTCAATTCGACCTTTATCGTCAG                         GCAGAGGGTAAAGTACTCAGAGGGCCACAGGAGGACCTAGAAAGTTACTTG
genomic: CTTTGAAGGCTGCCGAGGTTATATTGGCTCAATTCGACCTTTATCGTCAGgttggatttt ... caacttgtagGCAGAGGGTAAAGTACTCAGAGGGCCACAGGAGGACCTAGAAAGTTACTTG
EST: gi|110724162|gb|EE099748.1|EE099748
EST:     CTTTGAAGGCTGCCGAGGTTATATTGGCTCAATTCGACCTTTATCGTCAG                         GCAGAGGGTAAAGTACTCAGAGGGCCACAGGAGGACCTAGAAAGTTACTTG
genomic: CTTTGAAGGCTGCCGAGGTTATATTGGCTCAATTCGACCTTTATCGTCAGgttggatttt ... caacttgtagGCAGAGGGTAAAGTACTCAGAGGGCCACAGGAGGACCTAGAAAGTTACTTG
EST: gi|352773871|gb|FQ473003.1|FQ473003
EST:     CTTTGAAGGCTGCCGAGGTTATATTGGCTCAATTCGACCTTTATCGTCAG                         GCAGAGGGTAAAGTACTCAGAGGGCCACAGGAGGACCTAGAAAGTTACTTG
genomic: CTTTGAAGGCTGCCGAGGTTATATTGGCTCAATTCGACCTTTATCGTCAGgttggatttt ... caacttgtagGCAGAGGGTAAAGTACTCAGAGGGCCACAGGAGGACCTAGAAAGTTACTTG
EST: gi|30297888|gb|CB974682.1|CB974682
EST:     CTTTGAAGGCTGCCGAGGTTATATTGGCTCAATTCGACCTTTATCGTCAG                         GCAGAGGGTAAAGTACTCAGAGGGCCACAGGAGGACCTAGAAAGTTACTTG
genomic: CTTTGAAGGCTGCCGAGGTTATATTGGCTCAATTCGACCTTTATCGTCAGgttggatttt ... caacttgtagGCAGAGGGTAAAGTACTCAGAGGGCCACAGGAGGACCTAGAAAGTTACTTG
EST: gi|352769773|gb|FQ468701.1|FQ468701
EST:     CTTTGAAGGCTGCCGAGGTTATATTGGCTCAATTCGACCTTTATCGTCAG                         GCAGAGGGTAAAGTACTCAGAGGGCCACAGGAGGACCTAGAAAGTTACTTG
genomic: CTTTGAAGGCTGCCGAGGTTATATTGGCTCAATTCGACCTTTATCGTCAGgttggatttt ... caacttgtagGCAGAGGGTAAAGTACTCAGAGGGCCACAGGAGGACCTAGAAAGTTACTTG
EST: gi|37183965|gb|CF603319.1|CF603319
EST:     CTTTGAAGGCTGCCGAGGTTATATTGGCTCAATTCGACCTTTATCGTCAG                         GCAGAGGGTAAAGTACTCAGAGGGCCACAGGAGGACCTAGAAAGTTACTTG
genomic: CTTTGAAGGCTGCCGAGGTTATATTGGCTCAATTCGACCTTTATCGTCAGgttggatttt ... caacttgtagGCAGAGGGTAAAGTACTCAGAGGGCCACAGGAGGACCTAGAAAGTTACTTG
EST: gi|352781498|gb|FQ468342.1|FQ468342
EST:     CTTTGAAGGCTGCCGAGGTTATATTGGCTCAATTCGACCTTTATCGTCAG                         GCAGAGGGTAAAGTACTCAGAGGGCCACAGGAGGACCTAGAAAGTTACTTG
genomic: CTTTGAAGGCTGCCGAGGTTATATTGGCTCAATTCGACCTTTATCGTCAGgttggatttt ... caacttgtagGCAGAGGGTAAAGTACTCAGAGGGCCACAGGAGGACCTAGAAAGTTACTTG
EST: gi|30297709|gb|CB974503.1|CB974503
EST:     CTTTGAAGGCTGCCGAGGTTATATTGGCTCAATTCGACCTTTATCGTCAG                         GCAGAGGGTAAAGTACTCAGAGGGCCACAGGAGGACCTAGAAAGTTACTTG
genomic: CTTTGAAGGCTGCCGAGGTTATATTGGCTCAATTCGACCTTTATCGTCAGgttggatttt ... caacttgtagGCAGAGGGTAAAGTACTCAGAGGGCCACAGGAGGACCTAGAAAGTTACTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatgcagatttcttttttattgttgttgaaaatattattatttcaacttgtagGCAGAGGGTAAAGTACTCAGAGGGCCACAGGAGGACCTAGAAAGTTACTTGGAATCTATTGATCAGCTAAGAAGCAATATTCGTTTTTTTAGCAGCAACA
 ttttgat  putative branch site (score: 4)
                                       ttatttc  putative PPT
         atttcttttttattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcatggtatggaggtctttaacttctggcacagaatgttccttttgatgcagatttcttttttattgttgttgaaaatattattatttcaacttgtagGCAGAGGGTAAAGTACTCAGAGGGCCACAGGAGGACCTAGAAAGTTACTTGGAATCTATTGATCAGCTAAGAAGCAATATTCGTTTTTTTAGCAGCAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
-ttcatgg
- - - - - - - - - - - - - ctggcac
- - - - - - - - - - - - - - - - - - - - - - - -gatgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaata