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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGAgtgagtgatatcattgaagacatttctgcagttttcaaaatcataatattttatgcctttgtctttgctagtgattagtagtttgactttttattaattgtcatgtgtttttcag

Basic information

species Vitis vinifera
transcript Vv17s0000g09500.t01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g09500.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: LOC_Os12g27520.1 (Oryza sativa), 5'ss of exon 10
GGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGAgtgagt-gatatcattgaagacatttctgcagttttcaaaatcataatattttatgcctttgtctttgctagtgattagtagtttgactttttattaattgtcatgtgtttttcag
|||||||||||||||||||| ||||| ||  ||||||| ||||| |||||||| ||||| || |||||  ||||    |||||||| || || | |||||  || | | || ||||     |   |    || |||  |    |  |||    || || |   ||  |||  |||    || ||    ||| ||  |||| ||||         
GGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGAgtatgttgctgtccttga-----tccgtctcattgtcagta----agcattcacagcattggggattagtaggtatt----gtgtgctcatttgttgcttgt-atgtag-------

upper sequence: Vv17s0000g09500.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA17G13440.1 (Glycine max), 5'ss of exon 8
GGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGAgtgagtgatat-cattgaagacatttctgcagttttcaaaatcataatattttatgcctttgtctttgcta-gtgat-tagtagtttgactttttattaattgtcatgtgtttttcag
|| | ||| |||||||||||||| || ||| ||||||| ||||||||||||||||||||  | |||||| | || |||| |||| |||||||||| |||| ||||| || |  ||   || |     || ||     |  | ||| || | ||   |  || | |  |  || ||  |   ||||                               
GGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgacataccatgcgaacttaatctcaattgattgatccttaaaatatgataaataagtatgtattgtgtcatgcaaatgtttag-----------------------------

upper sequence: Vv17s0000g09500.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA06G18530.1 (Glycine max), 5'ss of exon 9
GGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGAgtgagtgatatcattgaagacatttctgcagttttcaaaatcataatattttatgcctttgtctttgctagtgattagtagtttgactttttattaattgtcatgtgtttttcag
|| ||||| ||||||||||||||||| ||| | ||||| || ||||||||||| |||||| | |||||  | || ||||| ||| | |||||||| |||| |||||| |   |       | | |  | |||  |  || || ||||| |   |  |||  |   || |    ||   |  ||  | |||     |  ||||||         
GGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCCATGATGGAGAGGGTGCTTGGTCCTATACCACAGCAGATGTTAAAGAGAGTTGAgtaagtgatttacct-------tgttttaactttctaccattatcatattat---caattgattgaacttgaacataaccgagtgtatcttttaccctgctcatgtag-------

upper sequence: Vv17s0000g09500.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA05G02740.1 (Glycine max), 5'ss of exon 9
GGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGAgtgagtgatat-cattgaagacatttctgcagttttcaaaatcataatattttatgcctttgtctttgctagtgattagtagtttgactttttattaattgtcatgtgtttttcag
|| ||||| ||||||||||||||||| ||| | ||||| ||||| ||||||||||||||  | ||| || | || |||  |||| |||||||||| |||| ||||   | |  ||   || |   | || ||     |  | ||| || | ||   |   | | |  ||     |  | ||   | | ||||                      
GGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTTGCAATGATGGAAAGGGTACTTGGTTCATTACCACAGACCATGATGAAGAGAGTCGAgtaagtggcttaccatgctaacttgatttcaattgattgatccttaaaatatgataaatgactatgtatta-----tgtttgtgcaaatgtttag---------------------

upper sequence: Vv17s0000g09500.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA04G36360.1 (Glycine max), 5'ss of exon 9
GGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGAgtgagtgatatcattgaagacatttctgcagttttcaaaatcataatattttatgcctttgtctttgctagtgattagtagtttgactttttattaattgtcatgtgtttttcag
|| ||||| ||||||||||||||||| ||| | ||||| || || |||||||| |||||| | |||||  | || ||||| ||| | |||||||| |||| |||||| |   |   ||  |||||    || ||||| | || | ||  |    |||   | |  |    || |     ||| ||| |       | |               
GGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCTATGATGGAGAGGGTGCTTGGTCCTATACCACAGCAGATGTTAAAGAGAGTTGAgtaagtgatttaccttgtgaattttctattattatcaaatttatcaaatgattgaacttgaacataacc---gagtgtatcttttactctgcccatgtag---------------

upper sequence: Vv17s0000g09500.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: EFJ32324 (Selaginella moellendorffii), 5'ss of exon 9
GGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGAgtgagtgatatc---attgaagacatttctgcagttttcaaaatcataatattttatgcctttgtctttgctagtgattagtagtttgactttttattaattgtcatgtgtttttcag
|||||  || ||||||||||||| || ||||| |||||||| || |||||||||||  |  | |||||  |  |    | |||  |  | |  ||||||| ||| | ||    | || |   ||       ||     |   ||   |  ||| |||                                                           
GGAGATCCACTGTTTCAGACTCACGAAAATCTCGAGCACCTGGCAATGATGGAAAGAATTCTCGGTCCCATTTCCAGACGCATAATCGATAACGTAGAgtaagtcagatttgtactggatctataaaccttgtggctcatcccacggtgctttgtgcag---------------------------------------------------------

upper sequence: Vv17s0000g09500.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: EFJ20929 (Selaginella moellendorffii), 5'ss of exon 7
GGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGAgtgagtgatatcattgaagacatttctgcagttttcaaaatcataatattttatgcctttgtctttgctagtgattagtagtttgactttttattaattgtcatgtgtttttcag
|||||  |||||||||||||||| || ||||| |||||||| || |||||||||||  |  | |||||  | ||    | |||  |  | |  ||||||| |||               |||| | | |  |  | || | |  |   | || ||   ||  || |||  |                                          
GGAGATCCATTGTTTCAGACTCACGAAAATCTCGAGCACCTGGCAATGATGGAAAGAATTCTCGGTCCCATTCCCAGACGCATAATCGATAACGTAGAgtaagtcgg------------atttgtactggatctataaaccttgtggctcatcccacggtgctttctacag------------------------------------------

upper sequence: Vv17s0000g09500.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: EFJ20930 (Selaginella moellendorffii), 5'ss of exon 8
GGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGAgtgagtgatatcattgaagacatttctgcagttttcaaaatcataatattttatgcctttgtctttgctagtgattagtagtttgactttttattaattgtcatgtgtttttcag
|||||  || ||||||||||||| || ||||| ||||||||||| |||||||||||  |  | |||||  | ||    | |||  |  | |  ||||||| |||   ||   |   |  || | |  |  ||       ||   |  ||| |||                                                           
GGAGATCCACTGTTTCAGACTCACGAAAATCTCGAGCACCTTGCAATGATGGAAAGAATTCTCGGTCCCATTCCCAGACGCATAATCGATAACGTAGAgtaagtcggatttctactgg-atctgtaaacctt------ccacggtgctttgtgcag---------------------------------------------------------

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|30133828|gb|CB919167.1|CB919167
EST:     ATGGAAAGGGTGTTGGGTCCACTACCGCAGCACATGCTGAAGAGAGTAGA                         CCGACATGCAGAGAAGTATGTACGAAGGGGTAGATTGGACTGGCCAGAAGG
genomic: ATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGAgtgagtgata ... tgtttttcagCCGACATGCAGAGAAGTATGTACGAAGGGGTAGATTGGACTGGCCAGAAGG
EST: gi|222357016|gb|GH717878.1|GH717878
EST:     ATGGAAAGGGTGTTGGGTCCACTACCGCAGCACATGCTGAAGAGAGTAGA                         CCGACATGCAGAGAAGTATGT
genomic: ATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGAgtgagtgata ... tgtttttcagCCGACATGCAGAGAAGTATGT
EST: gi|110373955|gb|EC938383.1|EC938383
EST:     ATGGAAAGGGTGTTGGGTCCACTACCGCAGCACATGCTGAAGAGAGTAGA                         CCGACATGCAGAGAAGTATGTACGAAGGGGTAGATTGGACTGGCCAGAAGG
genomic: ATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGAgtgagtgata ... tgtttttcagCCGACATGCAGAGAAGTATGTACGAAGGGGTAGATTGGACTGGCCAGAAGG
EST: gi|71886247|gb|DT035302.1|DT035302
EST:     ATGGAAAGGGTGTTGGGTCCACTACCGCAGCACATGCTGAAGAGAGTAGA                         CCGACATGCAGAGAAGTATGTA
genomic: ATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGAgtgagtgata ... tgtttttcagCCGACATGCAGAGAAGTATGTA
EST: gi|110362754|gb|EC926306.1|EC926306
EST:     ATGGAAAGGGTGTTGGGTCCACTACCGCAGCACATGCTGAAGAGAGTAGA                         CCGACATGCAGAGAAGTATGTACGAAGGGGTAGATTGGACTGGCCAGAAGG
genomic: ATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGAgtgagtgata ... tgtttttcagCCGACATGCAGAGAAGTATGTACGAAGGGGTAGATTGGACTGGCCAGAAGG
EST: gi|71889805|gb|DT038860.1|DT038860
EST:     ATGGAAAGGGTGTTGGGTCCACTACCGCAGCACATGCTGAAGAGAGTAGA                         CCGACATGCAGAGAAGTATGTACGAAGGGGTAGATTGGACTGGCCAGAAGG
genomic: ATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGAgtgagtgata ... tgtttttcagCCGACATGCAGAGAAGTATGTACGAAGGGGTAGATTGGACTGGCCAGAAGG
EST: gi|32268109|gb|CD717268.1|CD717268
EST:     ATGGAAAGGGTGTTGGGTCCACTACCGCAGCACATGCTGAAGAGAGTAGA                         CCGACATGCAG
genomic: ATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGAgtgagtgata ... tgtttttcagCCGACATGCAG
EST: gi|30255726|gb|CB971858.1|CB971858
EST:     ATGGAAAGGGTGTTGGGTCCACTACCGCAGCACATGCTGAAGAGAGTAGA                         CCGACATGCAGCGAAGTATGTACGAAGGGGTAGATTGGACTGGCCAGAAGG
genomic: ATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGAgtgagtgata ... tgtttttcagCCGACATGCAGAGAAGTATGTACGAAGGGGTAGATTGGACTGGCCAGAAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGAgtgagtgatatcattgaagacatttctgcagttttcaaaatcataatattttatgcctttgtctttgctagtgattagtagtttgactttttattaattgtcatgtgtttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA