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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatgctttgaatgatcagaaaaggtttgatgtttgattgatcgttaatatcttattcagacttgttaaccttggagatttggctattttgattatccagGCCAATTCTGCACAAATATGCCAACGAAGATGTGTCACTTGGTGCCTGGTTTATTGGTCTCGAAGTTGAGCACATAGATGATCGCAACTTATGTTGTGGG

Basic information

species Vitis vinifera
transcript Vv07s0031g03090.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g03090.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os02g35870.1 (Oryza sativa), 3'ss of exon 9
aaatgctttgaatgatcagaaaaggtttgatgtttgattgatcgttaatatcttattcagacttgttaaccttggagatttggctattttgattatccagGCCAATTCTGCACAAATATGCCAACGAAGATGTGTCACTTGGTGCCTGGTTTATTGGTCTCGAAGTTGAGCACATAGATGATCGCAACTTATGTTGTGGG
                      | ||||  | |   ||     |  ||   |||||   |||     ||      |  |||  | ||  || ||   |||||| ||  | ||||||| ||| ||||||||||| ||||||||| | |||||||||||| | |||||  | || || |||||  | ||| | || || |||
--------------------gtatgtttcctatgccatgccatgcaaaatccttat---gaccgaaaaaatactaatgtttc-caatgatgttttgtcagGCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTTTATTGGTTTAGAAGTGAATCATATCGATGAAAGAAACATGTGCTGCGGG

upper sequence: Vv07s0031g03090.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os09g27950.1 (Oryza sativa), 3'ss of exon 9
--aaatgctttgaatgatcagaaaaggtttgatgtttgattgatcgttaatatcttattcagacttgttaaccttggagatttggctattttgattatccagGCCAATTCTGCACAAATATGCCAACGAAGATGTGTCACTTGGTGCCTGGTTTATTGGTCTCGAAGTTGAGCACATAGATGATCGCAACTTATGTTGTGGG
  ||       |||||     | | | ||     |  ||   |   ||   || ||| |  || ||||||    |     | || |       || | ||||||| ||  ||||||||||||| |||||||| || |||||||| || |||||||| ||| | || || |||||||| || ||  |  || | || ||||| 
gtaagcctagagaatggctgcacatgattct---tcagacaaaatatt--cattttact--gaattgttactgatactcttgtgtcccaccatataacccagGCCTATATTGCACAAATATGCAAACGAAGACGTTTCACTTGGCGCATGGTTTATCGGTTTAGACGTGGAGCACATTGACGACAGAGACATGTGCTGTGGA

upper sequence: Vv07s0031g03090.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G77810.2 (Arabidopsis thaliana), 3'ss of exon 9
aaatgctttgaatgatcagaaaaggtttgatgtttgattgatcgttaatatcttattcagacttgttaaccttggagatttggctattttgattatccagGCCAATTCTGCACAAATATGCCAACGAAGATGTGTCACTTGGTGCCTGGTTTATTGGTCTCGAAGTTGAGCACATAGATGATCGCAACTTATGTTGTGGG
                   |     ||     |    || ||    |   |   ||  |    ||||   | |  |   ||  | | ||||  ||| |||||||||| |||| || |||||||| |||||||||||  | ||  | |||||||| ||||| || ||||| || || ||||| |||||||| |||||||||
-----------------gtacgtacttctgcatccttttcataaagagccttccatcaaa---tgtttgtcctaaaaggtttacaactttg--tatgcagGCCAATTTTGCATAAGTATGCCAATGAAGATGTGTCTTTAGGGTCATGGTTTATCGGTCTTGAGGTTGAACATATTGATGACCGCAACTTCTGTTGTGGG

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|352764403|gb|FQ472760.1|FQ472760
EST:     TCAAAGGATCTGGCCACATATATCTTTGTCAACCA                         GCCAATTTTGCACAAATATGCCAACGAAGATGTGTCACTTGGTGCCTGGTT
genomic: TCAAAGGATCTGGCCACATATATCTCTGTCAACCAgtaagaacag ... gattatccagGCCAATTCTGCACAAATATGCCAACGAAGATGTGTCACTTGGTGCCTGGTT
EST: gi|110720016|gb|EE095627.1|EE095627
EST:     AGAATTATGCCATCTCAAAGGATCTGGCCACATATATCTCTGTTCA-CCA                         -CCAATTCTGCACAA-TATGC-AACCAAGAAGTGGTC-CTTGGTGCCTGG
genomic: AGATTTATGCCATCTCAAAGGATCTGGCCACATATATCTCTGT-CAACCAgtaagaacag ... gattatccagGCCAATTCTGCACAAATATGCCAACGAAGATGTG-TCACTTGGTGCCTGG
EST: gi|30128224|gb|CB913563.1|CB913563
EST:     CAGAGTTATGCCATCTCAAAGGATCTGGCCACATATATCTCTGTCAACCA                         GCCAATTCTGCACAAATATGCCAACGAAGATGTGTCACTTGGTGCCTGGTT
genomic: CAGATTTATGCCATCTCAAAGGATCTGGCCACATATATCTCTGTCAACCAgtaagaacag ... gattatccagGCCAATTCTGCACAAATATGCCAACGAAGATGTGTCACTTGGTGCCTGGTT
EST: gi|32267576|gb|CD716539.1|CD716539
EST:     CAGATTTATGCCATCTCAAAGGATCTGGCCACATATATCTCTGTCAACCA                         GCCAATTCTGCACAAATATGCCAACGAAGATGTGTCACTTGGTGCCTGGTT
genomic: CAGATTTATGCCATCTCAAAGGATCTGGCCACATATATCTCTGTCAACCAgtaagaacag ... gattatccagGCCAATTCTGCACAAATATGCCAACGAAGATGTGTCACTTGGTGCCTGGTT
EST: gi|18459326|gb|BM437604.1|BM437604
EST:     CAGATTTATGCCATCTCAAAGGATCTGGCCACATATATCTCTGTCAACCA                         GCCAATTCTGCACAAATATGCCAACGAAGATGTGTCACTTGGTGCCTGGTT
genomic: CAGATTTATGCCATCTCAAAGGATCTGGCCACATATATCTCTGTCAACCAgtaagaacag ... gattatccagGCCAATTCTGCACAAATATGCCAACGAAGATGTGTCACTTGGTGCCTGGTT
EST: gi|37187390|gb|CF606743.1|CF606743
EST:     CAGATTTATGCCATCTCAAAGGATCTGGCCACATATATCTCTGTCAACCA                         GCCAATTCTGCACAAATATGCCAACGAAGATGTGTCACTTGGTGCCTGGTT
genomic: CAGATTTATGCCATCTCAAAGGATCTGGCCACATATATCTCTGTCAACCAgtaagaacag ... gattatccagGCCAATTCTGCACAAATATGCCAACGAAGATGTGTCACTTGGTGCCTGGTT
EST: gi|71887195|gb|DT036250.1|DT036250
EST:     CAGATTTATGCCATCTCAAAGGATCTGGCCACATATATCTCTGTCAACCA                         GCCAATTCTGCACAAATATGCCAACGAAGATGTGTCACTTGGTGCCTGGTT
genomic: CAGATTTATGCCATCTCAAAGGATCTGGCCACATATATCTCTGTCAACCAgtaagaacag ... gattatccagGCCAATTCTGCACAAATATGCCAACGAAGATGTGTCACTTGGTGCCTGGTT
EST: gi|110719628|gb|EE094920.1|EE094920
EST:     CAGATT-ATGCCATCTCAAAG-ATCTGGCCACATATATCTCTGTCAACC-                         GCCAATTCTGCACAA-TATGCCAACGAAGA
genomic: CAGATTTATGCCATCTCAAAGGATCTGGCCACATATATCTCTGTCAACCAgtaagaacag ... gattatccagGCCAATTCTGCACAAATATGCCAACGAAGA
EST: gi|30326867|gb|CD010129.1|CD010129
EST:     CAGATTTATGCCATCTCAAAGGATCTGGCCACATATATCTCTGTCAACCA                         GCCAATTCTGCACAAATATGCCAACGAAGATGTGTCACTTGGTGCCTGGTT
genomic: CAGATTTATGCCATCTCAAAGGATCTGGCCACATATATCTCTGTCAACCAgtaagaacag ... gattatccagGCCAATTCTGCACAAATATGCCAACGAAGATGTGTCACTTGGTGCCTGGTT
EST: gi|30135395|gb|CB920733.1|CB920733
EST:     CAGATTTATGCCATCTCANAGGATCTGGCCACATATATCTCTGTCAACCA                         GCCAATTCTGCACAAATATGCCAACGAAGATGTGTCACTTGGTGCCTGGTT
genomic: CAGATTTATGCCATCTCAAAGGATCTGGCCACATATATCTCTGTCAACCAgtaagaacag ... gattatccagGCCAATTCTGCACAAATATGCCAACGAAGATGTGTCACTTGGTGCCTGGTT
EST: gi|22015488|gb|BQ800522.1|BQ800522
EST:     CAGATTTATGCCATCTCAAAGGATCTGGCCACATATATCTCTGTCAACCA                         GCCAATTCTGCACAAATATGCCAACGAAGATGTGTCACTTGGTGCCTGGTT
genomic: CAGATTTATGCCATCTCAAAGGATCTGGCCACATATATCTCTGTCAACCAgtaagaacag ... gattatccagGCCAATTCTGCACAAATATGCCAACGAAGATGTGTCACTTGGTGCCTGGTT
EST: gi|110413181|gb|EC978958.1|EC978958
EST:     CAGATTTATGCCATCTCAAAGGATCTGGCCACATATATCTCTGTCAACCA                         GCCAATTCTGCACAAATATGCCAACGAAGATGTGTCACTTGGTGCCTGGTT
genomic: CAGATTTATGCCATCTCAAAGGATCTGGCCACATATATCTCTGTCAACCAgtaagaacag ... gattatccagGCCAATTCTGCACAAATATGCCAACGAAGATGTGTCACTTGGTGCCTGGTT
EST: gi|110361463|gb|EC924936.1|EC924936
EST:     CAGATTTATGCCATCTCAAAGGATCTGGCCACATATATCTCTGTCAACCA                         GCCAATTCTGCACAAATATGCCAACGAAGATGTGTCACTTGGTGCCTGGTT
genomic: CAGATTTATGCCATCTCAAAGGATCTGGCCACATATATCTCTGTCAACCAgtaagaacag ... gattatccagGCCAATTCTGCACAAATATGCCAACGAAGATGTGTCACTTGGTGCCTGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatatcttattcagacttgttaaccttggagatttggctattttgattatccagGCCAATTCTGCACAAATATGCCAACGAAGATGTGTCACTTGGTGCCTGGTTTATTGGTCTCGAAGTTGAGCACATAGATGATCGCAACTTATGTTGTGGG
                                       tattttgattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatgctttgaatgatcagaaaaggtttgatgtttgattgatcgttaatatcttattcagacttgttaaccttggagatttggctattttgattatccagGCCAATTCTGCACAAATATGCCAACGAAGATGTGTCACTTGGTGCCTGGTTTATTGGTCTCGAAGTTGAGCACATAGATGATCGCAACTTATGTTGTGGG

- -tgctttg
- - - - - - - - cagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggctat