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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccattttttgcaatctcagtttgccagatgtcaaatttgaacttgctgaacagttcagaatgttgccatttgacatgaattctctcttttgtgtgaatagGCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCCATCTGCATGGCCAAGACCCAGTACTCATTTTCACACACCGCTTCTGTGA

Basic information

species Vitis vinifera
transcript Vv06s0004g01160.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g01160.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G824944_T02 (Zea mays), 3'ss of exon 4
ccattttttgcaatctcagtttgccagatgtcaaatttgaacttgctgaacagttcagaatgttgccatttgacatgaattctctcttttgtgtgaatagGCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCCATCTGCATGGCCAAGACCCAGTACTCATTTTCACACACCGCTTCTGTGA
   | | |||   | | |   ||||   |||     |||  |||  ||  |     | | | |    | ||  | |||     | ||        || |||||||||| ||||||||||||||||  |  |||||||| || |  || ||||| |||||||| |||||||||||||| || |||||   | | ||  |||
--gtatcttgt--tgtaaccatgccgtgtgtg----ttggtctttttggtcctcatacactctgctgacttctcttgaccgacccctccc-----aacagGCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCATTTGCATGGCGAAGACCCAGTACTCGTTCTCACATGTCCCGTCCATGA

upper sequence: Vv06s0004g01160.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G824944_T01 (Zea mays), 3'ss of exon 4
ccattttttgcaatctcagtttgccagatgtcaaatttgaacttgctgaacagttcagaatgttgccatttgacatgaattctctcttttgtgtgaatagGCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCCATCTGCATGGCCAAGACCCAGTACTCATTTTCACACACCGCTTCTGTGA---
    || ||| || |      ||   | ||     ||||  | |  |  ||  | | || |  |     |||||  ||   ||| |         || |||||||||| ||||||||||||||||  |  |||||||| || |  || ||||| |||||||| |||||||||||||| || |||||   | | ||  |||   
--tcttgttgtaaccatgccgtgtgtgttggtctttttggtcctcatacactctgctgacttct----cttgac-cgacccctccc---------aacaggctGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCATTTGCATGGCGAAGACCCAGTACTCGTTCTCACATGTCCCGTCCATGAAGG

upper sequence: Vv06s0004g01160.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G50480.1 (Arabidopsis thaliana), 3'ss of exon 4
-ccattttttgcaatctcagtttgccagatgtcaaatttgaact--tgctgaacagttcagaatgttgccatttgacatgaattctctcttttgtgtga-atagGCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCCATCTGCATGGCCAAGACCCAGTACTCATTTTCACACACCGCTTCTGTGA
   |||  || | |   |   ||     || ||   |||| | |  ||   ||     |    |  ||  | ||  |    || || |  | |||   | | |||| ||||||||||||||||||||||    |||||| || || ||||| ||||| |||||| | || || ||||||||||| |||||    || ||   ||
gtgattgattcctagaccgacttcttcaatttc---tttgcattgttgtcaaaagaaacctgtttatgtaacttatctattatcctgtgatatgtaaaatacagGCAGAGAAACAGATTGAGATGTACACACAACAAGGCTTCTCGAATCTTCCCATATGCATGTCGAAAACACAGTACTCATTCTCACATGATGCATCAAAGA

upper sequence: Vv06s0004g01160.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EDP08942 (Chlamydomonas reinhardtii), 3'ss of exon 13
--ccattttttgcaatctca-gtttgccagatgtcaaatttgaacttgctgaacagttcagaatgttgccatttgacatgaattctctcttttgtgtgaatagGCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTC-TAATCTGCCCATCTGCATGGCCAAGACCCAGTACTCATTTTCACACACCGCTTCTGTGA
  ||  ||    |   |  | |  |||    |  |    |  | ||  |||  |  |   |  |||||| |     | |   |   | |            ||||||||   |||||||||| |||||     || ||||||    || ||||||||||||||||||||||| ||||||   ||    |||  |||  ||  ||
ttccccttcccacgcccctacgcctgctgtctacctcgctacacctctctgtgccat---ggttgttgcaagcccccttccctcaaccccgcacccgctgcagGCTGAGGCTCAGATTGAGAAGTACA-CGCGCATGGGTTTCGACAAGCTGCCCATCTGCATGGCCAAGACGCAGTACAGCTTCAGCCACGACGCCGCTAAGA

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|352774079|gb|FQ474602.1|FQ474602
EST:     AGGCAATAGCCAAGTCGTACGGTGCCAGCGGTGTTGAATACTCAGAACAG                         GCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCC
genomic: AGGCAATAGCCAAGTCGTACGGTGCCAGCGGTGTTGAATACTCAGAACAGgtagactctt ... gtgtgaatagGCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCC
EST: gi|110395134|gb|EC960711.1|EC960711
EST:     AGGCAATAGCCAAGTCGTATGGTGCCAGCGGTGTTGAATACTCAGAACAG                         GCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCC
genomic: AGGCAATAGCCAAGTCGTACGGTGCCAGCGGTGTTGAATACTCAGAACAGgtagactctt ... gtgtgaatagGCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCC
EST: gi|352776568|gb|FQ474870.1|FQ474870
EST:     AGGCAATAGCCAAGTCGTACGGTGCCAGCGGTGTTGAATACTCAGAACAG                         GCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCC
genomic: AGGCAATAGCCAAGTCGTACGGTGCCAGCGGTGTTGAATACTCAGAACAGgtagactctt ... gtgtgaatagGCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCC
EST: gi|352764252|gb|FQ471232.1|FQ471232
EST:     AGGCAATAGCCAAGTCGTACGGTGCCAGCGGTGTTGAATACTCAGAACAG                         GCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCC
genomic: AGGCAATAGCCAAGTCGTACGGTGCCAGCGGTGTTGAATACTCAGAACAGgtagactctt ... gtgtgaatagGCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCC
EST: gi|110390579|gb|EC955498.1|EC955498
EST:     AGGCAATAGCCAAGTCGTACGGTGCCAGCGGTGTTGAATACTCAGAACAG                         GCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCC
genomic: AGGCAATAGCCAAGTCGTACGGTGCCAGCGGTGTTGAATACTCAGAACAGgtagactctt ... gtgtgaatagGCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCC
EST: gi|30298388|gb|CB975182.1|CB975182
EST:     AGGCAATAGCCAAGTCGGATGGTGCCAGCGGTGTTGAATACTCAGAACAG                         GCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCC
genomic: AGGCAATAGCCAAGTCGTACGGTGCCAGCGGTGTTGAATACTCAGAACAGgtagactctt ... gtgtgaatagGCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCC
EST: gi|110701034|gb|EE078209.1|EE078209
EST:     AGGCAATAGCCAAGTCGTATGGTGCCAGCGGTGTTGAATACTCAGAACAG                         GCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCC
genomic: AGGCAATAGCCAAGTCGTACGGTGCCAGCGGTGTTGAATACTCAGAACAGgtagactctt ... gtgtgaatagGCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCC
EST: gi|110725828|gb|EE102739.1|EE102739
EST:     AGGCAATAGCCAAGTCGTATGGTGCCAGCGGTGTTGAATACTCAGAACAG                         GCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCC
genomic: AGGCAATAGCCAAGTCGTACGGTGCCAGCGGTGTTGAATACTCAGAACAGgtagactctt ... gtgtgaatagGCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCC
EST: gi|352773997|gb|FQ473129.1|FQ473129
EST:     CGGTGCCAGCGGTGTTGAATCCTCTGAACAG                         GCTGAGAAACAGATTGAGATGTACGGTAGACAAGGGTTTTCTAATCTGCCC
genomic: CGGTGCCAGCGGTGTTGAATACTCAGAACAGgtagactctt ... gtgtgaatagGCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCC
EST: gi|352768982|gb|FQ468173.1|FQ468173
EST:     GGTGTTGAATACTCAGAACAG                         GCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCC
genomic: GGTGTTGAATACTCAGAACAGgtagactctt ... gtgtgaatagGCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCC
EST: gi|110687523|gb|EE065027.1|EE065027
EST:     AGGCAATAGCCAAGTCGTACGGTGCCAGCGGTGTTGAATACTCAGAACAG                         GCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCC
genomic: AGGCAATAGCCAAGTCGTACGGTGCCAGCGGTGTTGAATACTCAGAACAGgtagactctt ... gtgtgaatagGCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCC
EST: gi|110425091|gb|EC991468.1|EC991468
EST:     AGGCAATAGCCAAGTCGTATGGTGCCAGCGGTGTTGAATACTCAGAACAG                         GCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCC
genomic: AGGCAATAGCCAAGTCGTACGGTGCCAGCGGTGTTGAATACTCAGAACAGgtagactctt ... gtgtgaatagGCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCC
EST: gi|22012114|gb|BQ797148.1|BQ797148
EST:     AGGCAATAGCCAAGTCGTATGGTGCCAGCGGTGTTGAATACTCAGAACAG                         GCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCC
genomic: AGGCAATAGCCAAGTCGTACGGTGCCAGCGGTGTTGAATACTCAGAACAGgtagactctt ... gtgtgaatagGCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCC
EST: gi|352776754|gb|FQ472641.1|FQ472641
EST:     AGGCAATAGCCAAGTCGTACGGTGCCAGCGGTGTTGAATACTCAGAACAG                         GCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCC
genomic: AGGCAATAGCCAAGTCGTACGGTGCCAGCGGTGTTGAATACTCAGAACAGgtagactctt ... gtgtgaatagGCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCC
EST: gi|110379958|gb|EC945186.1|EC945186
EST:     AGGCAATAGCCAAGTCGTATGGTGCCAGCGGTGTTGAATACTCAGAACAG                         GCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCC
genomic: AGGCAATAGCCAAGTCGTACGGTGCCAGCGGTGTTGAATACTCAGAACAGgtagactctt ... gtgtgaatagGCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgaacagttcagaatgttgccatttgacatgaattctctcttttgtgtgaatagGCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCCATCTGCATGGCCAAGACCCAGTACTCATTTTCACACACCGCTTCTGTGA
                      atttgac  putative branch site (score: 4)
                                  ttctctcttttgtgt  putative PPT
                             atgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccattttttgcaatctcagtttgccagatgtcaaatttgaacttgctgaacagttcagaatgttgccatttgacatgaattctctcttttgtgtgaatagGCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCCATCTGCATGGCCAAGACCCAGTACTCATTTTCACACACCGCTTCTGTGA

ccatttt
- - - - - caatctc
- - - - - - - - - gtttgcc
- - - - - - - - - - - - - - - - - - - - -cttgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -cagaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgccat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gacatga