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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttactaagacactctatttctatctttttccattagacattcttattaaaatattttatatgcagattatcatatatactaactattttttttttcttagGTGAGTATTGTTATGGAGCAGATGATTCGATTGCTTCATCATTGTGGGTTGCCTATGGAGGATCTTGACTTTATAAATTCTGATGGAAAGACAATGAACA

Basic information

species Vitis vinifera
transcript Vv17s0000g05800.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g05800.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA17G10610.1 (Glycine max), 3'ss of exon 8
ttactaagacactctatttctatctttttccattagacattcttattaaaat--attttatatgcagattatcata-tatactaactattttttttttcttagGTGAGTATTGTTATGGAGCAGATGATTCGATTGCTTCATCATTGTGGGTTGCCTATGGAGGATCTTGACTTTATAAATTCTGATGGAAAGACAATGAACA
||  | |   | |  ||||      | |  | ||     ||  ||||||| |  | | | | ||||| | |  ||  |  | ||   | |    || |  |||||||| ||||||||||| || ||| | ||  ||||||||   ||||| || ||| | || ||| | ||||| |||||||||||||| |||||||||||||
ttcttcatctattggattttggaaatgtgacttttat--ttgctattaaattcaaatctttctgcag-tgacaatgctgaattattgactcaaattgttgtagGTGAGCATTGTTATGGAACAAATGTTGCGCCTGCTTCATACCTGTGGCTTACCTCTAGAAGATGTAGACTTCATAAATTCTGATGGGAAGACAATGAACA

upper sequence: Vv17s0000g05800.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA05G01290.1 (Glycine max), 3'ss of exon 7
ttactaagacactctatttctatctttttccattagacattcttattaaaat--attttatatgcagattatcata-tatactaactattttttttttcttagGTGAGTATTGTTATGGAGCAGATGATTCGATTGCTTCATCATTGTGGGTTGCCTATGGAGGATCTTGACTTTATAAATTCTGATGGAAAGACAATGAACA
 |  | |   | |  ||||    | | |   |||  |  || || ||||| |  | | | | | ||| |||  ||  |  || | | | |    || |  |||||||| ||||||||||| || ||| | ||  |||||||| | ||||| || ||| | || ||| | ||||| ||||||||||| || |||||||||||||
ctcttcatctattggattttggacatgtga-attttat-ttgtttttaaattcaaatctttctacag-ttacaatgctgaaccatcgactcaaattgttgtagGTGAGCATTGTTATGGACCAAATGTTGCGCCTGCTTCATAACTGTGGTTTACCTCTAGAAGATGTAGACTTCATAAATTCTGACGGGAAGACAATGAACA

upper sequence: Vv17s0000g05800.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA05G01300.2 (Glycine max), 3'ss of exon 8
---tta-ctaagacactctatttctatctttttccattagacattcttattaaaatattttatatgcagattatcata-tatactaactattttttttttcttagGTGAGTATTGTTATGGAGCAGATGATTCGATTGCTTCATCATTGTGGGTTGCCTATGGAGGATCTTGACTTTATAAATTCTGATGGAAAGACAATGAACA
   | | |||  | | | |      ||   |||  ||| | | ||   ||| |||| ||| |   ||| ||||| ||  |  | ||   | |    ||    |||||||| ||||||||||| || ||| | ||  ||||||||   ||||| || |||   || ||| | ||||| |||||||||||||| |||||||||||||
ttttcatctatcagattttggaaacattaatttt-atttgcctttaaaattcaaatctttca---gca-attataattctgaattattgactcaaattaatgtagGTGAGCATTGTTATGGAACAAATGTTGCGCCTGCTTCATACCTGTGGCTTACCTGCAGAAGATGTAGACTTCATAAATTCTGATGGGAAGACAATGAACA

upper sequence: Vv17s0000g05800.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT5G62530.1 (Arabidopsis thaliana), 3'ss of exon 8
ttactaagacactctatttctatctttttccattagacattcttattaaaatattttatatgcagattatcatatatactaac-tattttttttttcttagGTGAGTATTGTTATGGAGCAGATGATTCGATTGCTTCATCATTGTGGGTTGCCTATGGAGGATCTTGACTTTATAAATTCTGATGGAAAGACAATGAACA
              |||   |  || ||  |||||   ||  || |   |||    | |||       ||| | | |  |||  || | || |||  |||||| || |||||||||||||| ||||| |||||||| ||  ||||||| || ||    || ||| | |||||||||||||||||||| |||||||||||||
-------------gtataaattactcttcacattac-tatagttctcgtaat----tgtattggttccatc-tgtttgataatataatgttatttgattagGTAAGCATTGTTATGGAGCAAATGATGCGATTGCTCCACTATTGTGGTTTACCCGCTGAAGATGTGGACTTTATAAATTCTGATGGGAAGACAATGAACA

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|110718820|gb|EE096093.1|EE096093
EST:     TGGGAGCCCTTTACATGGGCAACAAACCCATTCTTAAGGTTGATAGCAAG                         GTGAGTATTGTTATGGAGCAGATGATTCGATTGCTTCATCATTGTGGGTTG
genomic: TGGGAGCCCTTTACATGGGCAACAAACCCATTCTTAAGGTTGATAGCAAGgtatgctctc ... tttttcttagGTGAGTATTGTTATGGAGCAGATGATTCGATTGCTTCATCATTGTGGGTTG
EST: gi|37184316|gb|CF603670.1|CF603670
EST:     TGGGAGCCCTTTACATGGGCAACAAACCCATTCTTAAGGTTGATAGCAAG                         GTGAGTATTGTTATGGAGCAGATGATTCGATTGCTTCATCATTGTGGGTTG
genomic: TGGGAGCCCTTTACATGGGCAACAAACCCATTCTTAAGGTTGATAGCAAGgtatgctctc ... tttttcttagGTGAGTATTGTTATGGAGCAGATGATTCGATTGCTTCATCATTGTGGGTTG
EST: gi|110731235|gb|EE109223.1|EE109223
EST:     ATGGGCAACAAACCCATTCTTAAGGTTGATAGCAAG                         GTGAGTATTGTTATGGAGCAGATGATTCGATTGCTTCATCATTGTGGGTTG
genomic: ATGGGCAACAAACCCATTCTTAAGGTTGATAGCAAGgtatgctctc ... tttttcttagGTGAGTATTGTTATGGAGCAGATGATTCGATTGCTTCATCATTGTGGGTTG
EST: gi|110698054|gb|EE075624.1|EE075624
EST:     TGGGAGCCCTTTACATGGGCAACAAACCCATTCTTAAGGTTGATAGCAAG                         GTGAATATTGTTATGGAGCACATGATTC
genomic: TGGGAGCCCTTTACATGGGCAACAAACCCATTCTTAAGGTTGATAGCAAGgtatgctctc ... tttttcttagGTGAGTATTGTTATGGAGCAGATGATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaaatattttatatgcagattatcatatatactaactattttttttttcttagGTGAGTATTGTTATGGAGCAGATGATTCGATTGCTTCATCATTGTGGGTTGCCTATGGAGGATCTTGACTTTATAAATTCTGATGGAAAGACAATGAACA
                               tactaac  putative branch site (score: 0)
                                     ctattttttttttctt  CT-rich tract
                  agattatcatatatac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttactaagacactctatttctatctttttccattagacattcttattaaaatattttatatgcagattatcatatatactaactattttttttttcttagGTGAGTATTGTTATGGAGCAGATGATTCGATTGCTTCATCATTGTGGGTTGCCTATGGAGGATCTTGACTTTATAAATTCTGATGGAAAGACAATGAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - -aagacac
- - - - - - - - - - - - - - -ccattag
- - - - - - - - - - - - - - - - - - - - - - attaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgcag