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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttcactggtttgagtcttatgaaacattagaatactgtaccagtctcatgccatttattgcatgatttgcagGCATGGATGATCCGGGTAATGTCACCCTTTCTCAGGGATTGCATGACACAAAAAGGGTCAACTTCTACACAAACTATTTGACTGAGCTAAAGAAGGCAAT

Basic information

species Vitis vinifera
transcript Vv17s0000g02680.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g02680.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA09G30910.1 (Glycine max), 3'ss of exon 10
-------------------gtatgcttcactggtttgagtcttatgaaacattagaatactg---taccagtctcatgccatttattgcatgatttgcagGCATGGATGATCCGGGTAATGTCACCCTTTCTCAGGGATTGCATGACACAAAAAGGGTCAACTTCTACACAAACTATTTGACTGAGCTAAAGAAGGCAAT
                      |||||   |  |||      |  |  |||||||  | |||   |  || | |||||  |  ||||  |||   || |||||||||||||||||||||||| || ||| |  |||| ||||||||||| | |||| | ||||  |||| |  |||||||||| | |||||||| ||| |
gtaacgttatatatcaatttcttgctttgttctttttttggcttggtgacattagtgttctgttgtttcaatgtcatgtgacatattttatggcatgtagGCATGGATGATCCGGGTAATGTGACTCTTCCCAAGGGTTTGCATGACACCACAAGGATAAACTATTACAAAGGCTATTTGACTCAACTAAAGAAAGCAGT

upper sequence: Vv17s0000g02680.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA07G11310.1 (Glycine max), 3'ss of exon 10
----------gtatgcttcactggtttgagtcttatgaaacattagaa----tactgtaccagtctcatgccatttattgcatgatttgcagGCATGGATGATCCGGGTAATGTCACCCTTTCTCAGGGATTGCATGACACAAAAAGGGTCAACTTCTACACAAACTATTTGACTGAGCTAAAGAAGGCAAT
           |||   |  || | ||    ||| |      || |      |  |||  || | |||||  |  ||||  ||||  || ||||||||||||||||||||| || || ||| |  |||| ||||||||||| | |||| | ||||  |||| |  |||||||||| | |||||||||||| |
gtaacattatatatcaatttcttgctttttcctttttttggcttggtgattctgttgtttcaatgtcatgtgacatattttatgacatgtagGCATGGATGATCCGGGTAACGTGACTCTTCCCAAGGGTTTGCATGACACCACAAGGATAAACTATTACAAAGGCTATTTGACTCAACTAAAGAAGGCAGT
















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|110685535|gb|EE062350.1|EE062350
EST:     CTACATAAAAGAGCGATATGGAAACCCCACTGTGATTTTGTCAGAAAATG                         GCATGGATGATCCGGGTAATGTCACCCTTTCTCAGGGATTGCATGACACAA
genomic: CTACATAAAAGAGCGATATGGAAACCCCACTGTGATTTTGTCAGAAAATGgtatgcttca ... tgatttgcagGCATGGATGATCCGGGTAATGTCACCCTTTCTCAGGGATTGCATGACACAA
EST: gi|349807989|gb|FQ402380.1|FQ402380
EST:     CTACATAAAAGAGCGATATGGAAACCCCACTGTGATTTTGTCAGAAAATG                         GCATGGATGATCCGGGTAATGTCACCCTTTCTCAGGGATTGCATGACACAA
genomic: CTACATAAAAGAGCGATATGGAAACCCCACTGTGATTTTGTCAGAAAATGgtatgcttca ... tgatttgcagGCATGGATGATCCGGGTAATGTCACCCTTTCTCAGGGATTGCATGACACAA
EST: gi|349819506|gb|FQ413390.1|FQ413390
EST:     CTACATAAAAGAGCGATATGGAAACCCCACTGTGATTTTGTCAGAAAATG                         GCCTGGATGATCCGGGTAATGTCACCCTTTCTCAGGGATTGCATGACACAA
genomic: CTACATAAAAGAGCGATATGGAAACCCCACTGTGATTTTGTCAGAAAATGgtatgcttca ... tgatttgcagGCATGGATGATCCGGGTAATGTCACCCTTTCTCAGGGATTGCATGACACAA
EST: gi|32246242|gb|CD712061.1|CD712061
EST:     TGTGATTTTGTCAGAAAATG                         GTCATGGATGATCCGGGTAATGTCACCCTTTCTCAGGGATTGCATGACACA
genomic: TGTGATTTTGTCAGAAAATGgtatgcttca ... tgatttgcagG-CATGGATGATCCGGGTAATGTCACCCTTTCTCAGGGATTGCATGACACA
EST: gi|30256158|gb|CB972001.1|CB972001
EST:     CTACATAAAAGAGCGATATGGAAACCCCACTGTGATTTTGTCAGAAAATG                         GCATGGATGATCCGGGTAATGTCACCCTTTCTCAGGGGTTGCATGACACAA
genomic: CTACATAAAAGAGCGATATGGAAACCCCACTGTGATTTTGTCAGAAAATGgtatgcttca ... tgatttgcagGCATGGATGATCCGGGTAATGTCACCCTTTCTCAGGGATTGCATGACACAA
EST: gi|349829069|gb|FQ419601.1|FQ419601
EST:     CTACATAAAAGAGCGATATGGAAACCCCACTGTGATTTTGTCAGAAAATG                         GCATGGATGATCCGGGTAATGTCACCCTTTCTCAGGGATTGCATGACACAA
genomic: CTACATAAAAGAGCGATATGGAAACCCCACTGTGATTTTGTCAGAAAATGgtatgcttca ... tgatttgcagGCATGGATGATCCGGGTAATGTCACCCTTTCTCAGGGATTGCATGACACAA
EST: gi|27584907|gb|CB007602.1|CB007602
EST:     CTACATAAAAGAGCGATATGGAAACCCCACTGTGATTTTGTCAGAAAATG                         GCATGGATGATCCGGGTAATGTCACCCTTTCTCAGGGATTGCATGACACAA
genomic: CTACATAAAAGAGCGATATGGAAACCCCACTGTGATTTTGTCAGAAAATGgtatgcttca ... tgatttgcagGCATGGATGATCCGGGTAATGTCACCCTTTCTCAGGGATTGCATGACACAA
EST: gi|351055976|gb|FQ453437.1|FQ453437
EST:     CTACATAAAAGAGCGATATGGAAACCCCACTGTGATTTTGTCAGAAAATG                         GCATGGATGATCCGGGTAATGTCACCCTTTCTCAGGGATTGCATGACACAA
genomic: CTACATAAAAGAGCGATATGGAAACCCCACTGTGATTTTGTCAGAAAATGgtatgcttca ... tgatttgcagGCATGGATGATCCGGGTAATGTCACCCTTTCTCAGGGATTGCATGACACAA
EST: gi|30256233|gb|CB972076.1|CB972076
EST:     CTACATAAAAGAGCGATATGGAAACCCCACTGTGATTTTGTCAGAAAATG                         GCATGGATGATCCGGGTAATGTCACCCTTTCTCAGGGGTTGCATGACACAA
genomic: CTACATAAAAGAGCGATATGGAAACCCCACTGTGATTTTGTCAGAAAATGgtatgcttca ... tgatttgcagGCATGGATGATCCGGGTAATGTCACCCTTTCTCAGGGATTGCATGACACAA
EST: gi|110685849|gb|EE062930.1|EE062930
EST:     CTACATAAAAGAGCGATATGGGAACCCCACTGTGATTTTGTCAGAAAATG                         GCATGGATGATCCGGGTAATGTCACCCTTT-TCTAGGGATTGCATGACACA
genomic: CTACATAAAAGAGCGATATGGAAACCCCACTGTGATTTTGTCAGAAAATGgtatgcttca ... tgatttgcagGCATGGATGATCCGGGTAATGTCACCCTTTCTC-AGGGATTGCATGACACA
EST: gi|34544676|gb|CF512908.1|CF512908
EST:     CTACATAAAAGAGCGATATGGAAACCCCACTGTGATTTTGTCAGAAAATG                         GCATGGATGATCCGGGTAATGTCACCCTTTCTCAGGGATTGCGTGACACAA
genomic: CTACATAAAAGAGCGATATGGAAACCCCACTGTGATTTTGTCAGAAAATGgtatgcttca ... tgatttgcagGCATGGATGATCCGGGTAATGTCACCCTTTCTCAGGGATTGCATGACACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgaaacattagaatactgtaccagtctcatgccatttattgcatgatttgcagGCATGGATGATCCGGGTAATGTCACCCTTTCTCAGGGATTGCATGACACAAAAAGGGTCAACTTCTACACAAACTATTTGACTGAGCTAAAGAAGGCAAT
        attagaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcttcactggtttgagtcttatgaaacattagaatactgtaccagtctcatgccatttattgcatgatttgcagGCATGGATGATCCGGGTAATGTCACCCTTTCTCAGGGATTGCATGACACAAAAAGGGTCAACTTCTACACAAACTATTTGACTGAGCTAAAGAAGGCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG