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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaaaagaggggtgcttggacagtgggaatattatgggctagaaatgttgggctttggcatagatattaatgtatgcttcattttgtttctctaatctagGTTTCTTAGAGAGCTTGACTTGCAAGAAAATGAAGTTGAGGATCGCAAAGGCCAATGGCTTAGCTGCTTCCCTGACAGCTGCACATCACTAGTCTCCTTG

Basic information

species Vitis vinifera
transcript Vv14s0068g01330.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0068g01330.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G27280.2 (Glycine max), 3'ss of exon 1
tgaaaagaggggtgcttggacagtgggaatattatgggctagaaatgttgggctttggcatagatattaatgtatgcttcattttgtttctct--aatctagGTTTCTTAGAGAGCTTGACTTGCAAGAAAATGAAGTTGAGGATCGCAAAGGCCAATGGCTTAGCTGCTTCCCTGACAGCTGCACATCACTAGTCTCCTTG
 |   |      |  |  |    | |  | ||   | |   ||  |   |    |   | |   | |  ||||    |   |||  ||  | |  ||| |||||| ||||| ||||| ||  |||||||||||||||||||||||| ||||||||||||||| || ||||| ||||| | |||||||||||| || ||  | 
-gttgatgattctattctgctgattgaga-atggcgtgtaggatgttcggtatgtgttcttgactctcgatgttgattgtgtttaattgttttgaaatgtagGTTCCTTAGGGAGCTGGATCTGCAAGAAAATGAAGTTGAGGATCACAAAGGCCAATGGCTAAGTTGCTTTCCTGATAACTGCACATCACTTGTTTCTCTT

upper sequence: Vv14s0068g01330.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G05500.1 (Glycine max), 3'ss of exon 1
tgaaaagaggggtgcttggacagtg---ggaatattatgggctagaaatgttgggctttggcatagatattaatgtatgcttcattttgtttctctaatctagGTTTCTTAGAGAGCTTGACTTGCAAGAAAATGAAGTTGAGGATCGCAAAGGCCAATGGCTTAGCTGCTTCCCTGACAGCTGCACATCACTAGTCTCCTTG
  |  |      |  |  ||  | |   ||  | |     | | |  ||||     |    |  | || || || | ||  | ||  |  || |  |||  ||||||||||| ||||| ||  ||||||||||||| ||||| |||| ||||||||| ||||| || ||||| ||||||| |||||||||||| || ||  | 
--atgattctattcttctgattgagaatggtgtgtaggatgttcggtatgtgttcttgactcccaaatgttgat-tgtgtgttataattgttttgaaatgcagGTTTCTTAGGGAGCTGGATCTGCAAGAAAATGAGGTTGAAGATCACAAAGGCCAGTGGCTAAGTTGCTTTCCTGACAACTGCACATCACTTGTTTCACTT

upper sequence: Vv14s0068g01330.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G07240.1 (Glycine max), 3'ss of exon 1
tgaaaagaggggtgcttggacagtgggaatattatgggctagaaatgttgggctttggcatagatattaatgtatgcttcattttgtttctctaa--tctagGTTTCTTAGAGAGCTTGACTTGCAAGAAAATGAAGTTGAGGATCGCAAAGGCCAATGGCTTAGCTGCTTCCCTGACAGCTGCACATCACTAGTCTCCTTG
 || ||          ||  |||    |   |  | || | ||  |   ||   || |  | | | |   |  |    ||| ||   |  | |||  | |||||| ||||  ||||| || ||||| |||||||||||||| || | || |||||| ||||| |||||||| |||||  |||| |||||||| || ||  | 
agataaatttcagaaatgttcagaaatatattctttggattgacctacaggttgttagacttgttgtc--ttgacttctcagttcactgttataaaatgtagGTTCCTTAAGGAGCTGGATTTGCAGGAAAATGAAGTTGATGACCACAGAGGCCAGTGGCTAAGCTGCTTTCCTGATTGCTGTACATCACTTGTTTCTCTT

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|71880936|gb|DT029991.1|DT029991
EST:     TGTGAAGGGTTTACCACCGATGGACTTGCAGCCGTTGCTGCAAATTGCAG                         GTTTCTTAGAGAGCTTGACTTGCAAGAAAATGAAGTTGAGGATCGCAAAGG
genomic: TGTGAAGGGTTTACCACCGATGGACTTGCAGCCGTTGCTGCAAATTGCAGgtaggagctg ... tctaatctagGTTTCTTAGAGAGCTTGACTTGCAAGAAAATGAAGTTGAGGATCGCAAAGG
EST: gi|110724289|gb|EE099987.1|EE099987
EST:     TGTGAAGGGTTTACCACCGATGGACTTGCAGCCGTTGCTGCAAATTGCAG                         GTTTCTTAGAGAGCTTGACTTGCAAGAAAATGAAGTTGAGGATCGCAAAGG
genomic: TGTGAAGGGTTTACCACCGATGGACTTGCAGCCGTTGCTGCAAATTGCAGgtaggagctg ... tctaatctagGTTTCTTAGAGAGCTTGACTTGCAAGAAAATGAAGTTGAGGATCGCAAAGG
EST: gi|71861796|gb|DT010851.1|DT010851
EST:     TGTGAAGGGTTTACCACCGATGGACTTGCAGCCGTTGCTGCAAATTGCAG                         GTTTCTTAGAGAGCTTGACTTGCAAGAAAATGAAGTTGAGGATCGCAAAGG
genomic: TGTGAAGGGTTTACCACCGATGGACTTGCAGCCGTTGCTGCAAATTGCAGgtaggagctg ... tctaatctagGTTTCTTAGAGAGCTTGACTTGCAAGAAAATGAAGTTGAGGATCGCAAAGG
EST: gi|71879828|gb|DT028883.1|DT028883
EST:     TGTGAAGGGTTTACCACCGATGGACTTGCAGCCGTTGCTGCAAATTGCAG                         GTTTCTTAGAGAGCTTGACTTGCAAGAAAATGAAGTTGAGGATCGCAAAGG
genomic: TGTGAAGGGTTTACCACCGATGGACTTGCAGCCGTTGCTGCAAATTGCAGgtaggagctg ... tctaatctagGTTTCTTAGAGAGCTTGACTTGCAAGAAAATGAAGTTGAGGATCGCAAAGG
EST: gi|71880512|gb|DT029567.1|DT029567
EST:     TGTGAAGGGTTTACCACCGATGGACTTGCAGCCGTTGCTGCAAATTGCAG                         GTTTCTTAGAGAGCTTGACTTGCAAGAAAATGAAGTTGAGGATCGCAAAGG
genomic: TGTGAAGGGTTTACCACCGATGGACTTGCAGCCGTTGCTGCAAATTGCAGgtaggagctg ... tctaatctagGTTTCTTAGAGAGCTTGACTTGCAAGAAAATGAAGTTGAGGATCGCAAAGG
EST: gi|71865080|gb|DT014135.1|DT014135
EST:     TGTGAAGGGTTTACCACCGATGGACTTGCAGCCGTTGCTGCAAATTGCAG                         GTTTCTTAGAGAGCTTGACTTGCAAGAAAATGAAGTTGAGGATCGCAAAGG
genomic: TGTGAAGGGTTTACCACCGATGGACTTGCAGCCGTTGCTGCAAATTGCAGgtaggagctg ... tctaatctagGTTTCTTAGAGAGCTTGACTTGCAAGAAAATGAAGTTGAGGATCGCAAAGG
EST: gi|46917985|gb|CN547314.1|CN547314
EST:     TGTGAAGGGTTTACCACCGATGGACTTGCAGCCGTTGCTGCAAATTGCAG                         GTTTCTTAGAGAGCTTGACTTGCAAGAAAATGAAGTTGAGGATCGCAAAGG
genomic: TGTGAAGGGTTTACCACCGATGGACTTGCAGCCGTTGCTGCAAATTGCAGgtaggagctg ... tctaatctagGTTTCTTAGAGAGCTTGACTTGCAAGAAAATGAAGTTGAGGATCGCAAAGG
EST: gi|71880441|gb|DT029496.1|DT029496
EST:     TGTGAAGGGTTTACCACCGATGGACTTGCAGCCGTTGCTGCAAATTGCAG                         GTTTCTTAGAGAGCTTGACTTGCAAGAAAATGAAGTTGAGGATCGCAAAGG
genomic: TGTGAAGGGTTTACCACCGATGGACTTGCAGCCGTTGCTGCAAATTGCAGgtaggagctg ... tctaatctagGTTTCTTAGAGAGCTTGACTTGCAAGAAAATGAAGTTGAGGATCGCAAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgggctttggcatagatattaatgtatgcttcattttgtttctctaatctagGTTTCTTAGAGAGCTTGACTTGCAAGAAAATGAAGTTGAGGATCGCAAAGGCCAATGGCTTAGCTGCTTCCCTGACAGCTGCACATCACTAGTCTCCTTG
                               cttcattttgtttctc  CT-rich tract
              atagatattaatgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaaaagaggggtgcttggacagtgggaatattatgggctagaaatgttgggctttggcatagatattaatgtatgcttcattttgtttctctaatctagGTTTCTTAGAGAGCTTGACTTGCAAGAAAATGAAGTTGAGGATCGCAAAGGCCAATGGCTTAGCTGCTTCCCTGACAGCTGCACATCACTAGTCTCCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
-gaaaaga
- - - - - -gtgcttg
- - - - - - - - - - - - - - - - - -gggctag
- - - - - - - - - - - - - - - - - - - - - - -tgttggg