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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatttttttgtctattgttgttattatggagtagtggcaactttattaccttaaaaacttatgttgtctttcagTTTGAAACCATGGCTTTTGGGAGCACTGCTATGTGTGGAAGAACTTCTTTCTGGTTCTGGGTAATTTCAGCTGTTCCATTTTATTGTGCAACATGGGAAC

Basic information

species Vitis vinifera
transcript Vv01s0010g00950.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0010g00950.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G466281_T02 (Zea mays), 3'ss of exon 6
gtatgtatttttttgtctattgttgttattatggagtagtggcaactttattaccttaaaaacttatgttgtcttt----cagTTTGAAACCATGGCTTTTGGGAGCACTGCTATGTGTGGAAGAACTTCTTTCTGGTTCTGGGTAATTTCAGCTGTTCCATTTTATTGTGCAACATGGGAAC
   |         |||| ||  || ||||| |  |||      |  || |   | ||   | || || || | | |     |||||||| || |||||||||| ||||| || ||||||||||   || | |||||||| ||| | ||||||||||| |||||||| |  ||||| |||||||
--gtaagaccacctgtcaatattttttatt-tcaagtgcaatgattttcaagtcgttgtgagctcattttttttatatactagTTTGAATCCTTGGCTTTTGGAAGCACGGCGATGTGTGGAAAGGCTACCTTCTGGTTTTGGTTCATTTCAGCTGTCCCATTTTACTTCGCAACCTGGGAAC

upper sequence: Vv01s0010g00950.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA12G08720.1 (Glycine max), 3'ss of exon 7
gtatgtatttttttgtctattgttgttattatggagtagtggcaactttattaccttaaaaacttatgttgtctt----tcagTTTGAAACCATGGCTTTTGGGAGCACTGCTATGTGTGGAAGAACTTCTTTCTGGTTCTGGGTAATTTCAGCTGTTCCATTTTATTGTGCAACATGGGAAC
|||||| | || |||  | | | | ||||| |  | |  | | ||    ||      |   |  |||| |  |||    |||||||||| |  |||||||||||||||| || ||||||||||||||| |||||||||  ||| |||| || ||  || |||||||| ||||||| ||||| |
gtatgtctcttgttgctt-tggctattatttttaaatcattgaaagagaatagagacagtcatctatgataacttcttttcagTTTGAAGCATTGGCTTTTGGGAGCACAGCCATGTGTGGAAGAACTACTTTCTGGTGGTGGTTAATATCTGCAATTACATTTTATGGTGCAACCTGGGAGC

upper sequence: Vv01s0010g00950.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA02G14210.1 (Glycine max), 3'ss of exon 7
gtatgtatttttttgtctattgttgttattatggagtagtggcaactttattaccttaaaaacttatgttgtctttcagTTTGAAACCATGGCTTTTGGGAGCACTGCTATGTGTGGAAGAACTTCTTTCTGGTTCTGGGTAATTTCAGCTGTTCCATTTTATTGTGCAACATGGGAAC
|||||| | || | |  | | | | ||||| |  | |  | | ||    || |   ||      | || | | |||||||||||| |  |||||||||||||||| || ||||||||||||| | |||||||||  ||| |||| || ||  || |||||||| ||||||| ||||| |
gtatgtctcttatagctt-tggctattatttttaaatcattgaaagacaataaagatactcttctgtgatat-tttcagTTTGAAGCATTGGCTTTTGGGAGCACAGCCATGTGTGGAAGAAATACTTTCTGGTGGTGGTTAATATCTGCAATTACATTTTATGGTGCAACCTGGGAGC

upper sequence: Vv01s0010g00950.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT1G13560.1 (Arabidopsis thaliana), 3'ss of exon 7
--------gtatgtatttttttgtctattgttgttattatggagtagtggcaactttattaccttaaaaacttatgttgtcttt-cagTTTGAAACCATGGCTTTTGGGAGCACTGCTATGTGTGGAAGAACTTCTTTCTGGTTCTGGGTAATTTCAGCTGTTCCATTTTATTGTGCAACATGGGAAC
         |||  ||  |||  ||| |  || |||  ||  |||| | |        |    |   ||  || |    |     ||||||||| ||||||| ||||| |||||||| ||||||||||||  | |||||||||||||||| ||||||||| ||||||||||| | || ||||||||||
gtatgctattatcaatcctttaatctttctttttta--attcagtactcgtcttggagtcgattatgaaggttttaccctaaaaacagTTTGAAGCCATGGCATTTGGAAGCACTGCAATGTGTGGAAGAGATACTTTCTGGTTCTGGGTTATTTCAGCTATTCCATTTTATGGAGCTACATGGGAAC

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|351028084|gb|FQ425985.1|FQ425985
EST:     TGGATGTGATGCCCTTGCATGTGCG                         TTTGAAACCATGGCTTTTGGGAGCACTGCTATGTGTGGAAGAACTTCTTTC
genomic: TGGATGTGATGCCCTTGCATGTGCGgtatgtattt ... tgtctttcagTTTGAAACCATGGCTTTTGGGAGCACTGCTATGTGTGGAAGAACTTCTTTC
EST: gi|351043445|gb|FQ444045.1|FQ444045
EST:     TGGATGTGATGCCCTTGCATGTGCG                         TTTGAAACCATGACTTTTGGGAGCACTGCTATGTGTGGAAGAACTTCTTTC
genomic: TGGATGTGATGCCCTTGCATGTGCGgtatgtattt ... tgtctttcagTTTGAAACCATGGCTTTTGGGAGCACTGCTATGTGTGGAAGAACTTCTTTC
EST: gi|349829684|gb|FQ421202.1|FQ421202
EST:     TGGATGTGATGCCCTTGCATGTGCG                         TTTGAAACCATGGCTTTTGGGGAGCACTGCTATGTGTGGAAGAACTTCTTT
genomic: TGGATGTGATGCCCTTGCATGTGCGgtatgtattt ... tgtctttcagTTTGAAACCATGGCTTTTGGG-AGCACTGCTATGTGTGGAAGAACTTCTTT
EST: gi|349824351|gb|FQ417738.1|FQ417738
EST:     TGGATGTGATGCCCTTGCATGTGCG                         TTTGAAACCATGGCTTTTGGGAGCACTGCTATGTGTGGAAGAACTTCTTTC
genomic: TGGATGTGATGCCCTTGCATGTGCGgtatgtattt ... tgtctttcagTTTGAAACCATGGCTTTTGGGAGCACTGCTATGTGTGGAAGAACTTCTTTC
EST: gi|110708043|gb|EE085132.1|EE085132
EST:     TGGATGTGATGCCCTTGCATGTGCG                         TTTGAAACCATGGCTTTTGGGAGCACTGCTATGTGTGGAAGAACTTCTTTC
genomic: TGGATGTGATGCCCTTGCATGTGCGgtatgtattt ... tgtctttcagTTTGAAACCATGGCTTTTGGGAGCACTGCTATGTGTGGAAGAACTTCTTTC
EST: gi|110694296|gb|EE071276.1|EE071276
EST:     TGGATGTGATGCCCTTGCATGTGCG                         TTTGAAACCATGGCTTTTGGGAGCACTGCTATGTGTGGAAGAACTTCTTTC
genomic: TGGATGTGATGCCCTTGCATGTGCGgtatgtattt ... tgtctttcagTTTGAAACCATGGCTTTTGGGAGCACTGCTATGTGTGGAAGAACTTCTTTC
EST: gi|351040557|gb|FQ434690.1|FQ434690
EST:     TGGATGTGATGCCCTTGCATGTGCG                         TTTGAAACCATGGCTTTTGGGAGCACTGCTATGTGTGGAAGAACTTCTTTC
genomic: TGGATGTGATGCCCTTGCATGTGCGgtatgtattt ... tgtctttcagTTTGAAACCATGGCTTTTGGGAGCACTGCTATGTGTGGAAGAACTTCTTTC
EST: gi|351014955|gb|FQ444244.1|FQ444244
EST:     TGGATGTGATGCCCTTGCATGTGCG                         TTTGAAACCATGGCTTTTGGGAGCACTGCTATGTGTGGAAGAACTTCTTTC
genomic: TGGATGTGATGCCCTTGCATGTGCGgtatgtattt ... tgtctttcagTTTGAAACCATGGCTTTTGGGAGCACTGCTATGTGTGGAAGAACTTCTTTC
EST: gi|351029069|gb|FQ435269.1|FQ435269
EST:     TGGATGTGATGCCCTTGCATGTGCG                         TTTGAAACCATGGCTTTTGGGAGCACTGCTATGTGTGGAAGAACTTCTTTC
genomic: TGGATGTGATGCCCTTGCATGTGCGgtatgtattt ... tgtctttcagTTTGAAACCATGGCTTTTGGGAGCACTGCTATGTGTGGAAGAACTTCTTTC
EST: gi|110687900|gb|EE065836.1|EE065836
EST:     TGGATGTGATGCCCTTGCATGTGCG                         TTTGAAACCATGGCTTTTGGGAGCACTGCTATGTGTGGAAGAACTTCTTTC
genomic: TGGATGTGATGCCCTTGCATGTGCGgtatgtattt ... tgtctttcagTTTGAAACCATGGCTTTTGGGAGCACTGCTATGTGTGGAAGAACTTCTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttattatggagtagtggcaactttattaccttaaaaacttatgttgtctttcagTTTGAAACCATGGCTTTTGGGAGCACTGCTATGTGTGGAAGAACTTCTTTCTGGTTCTGGGTAATTTCAGCTGTTCCATTTTATTGTGCAACATGGGAAC
                                            ttgtctttc  CT-rich tract
                      tttattaccttaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtatttttttgtctattgttgttattatggagtagtggcaactttattaccttaaaaacttatgttgtctttcagTTTGAAACCATGGCTTTTGGGAGCACTGCTATGTGTGGAAGAACTTCTTTCTGGTTCTGGGTAATTTCAGCTGTTCCATTTTATTGTGCAACATGGGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT