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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGTTGGCTACACACCGGTGACATTGGCTATGTTGACGATGATGAAGAGGTGTTCATCGTAGATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAGgcatgtattcttatgctccattttccccttcaattactatcctactatttcgtagaagaacatcatatgttgacaccaagaggaagtttggaacggtgga...

Basic information

species Vitis vinifera
transcript Vv16s0039g02040.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0039g02040.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os02g46970.1 (Oryza sativa), 5'ss of exon 3
CGGTTGGCTACACACCGGTGACATTGGCTATGTTGACGATGATGAAGAGGTGTTCATCGTAGATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAGgcatgtattcttatgctccattttccccttcaattactatcctactatttcgtagaagaac-atcatatgttgacaccaagaggaagtttggaacggtgga
 || ||||| |||||||| ||||| ||||| || ||||| || || ||||| |||||||| ||  | || || || |||||||||||||| || ||||||| |  ||     | |    |   |   | ||| ||    | ||  || |||| |    ||| ||  | | || |  |                        
GGGGTGGCTGCACACCGGCGACATCGGCTACGTCGACGACGACGACGAGGTCTTCATCGTCGACCGTGTCAAGGAGCTCATCAAATTCAAGGGGTTCCAGgtaattaacagcagg----acacttagcatcagtt----ttctgataattcgcactgtaactattgtctattcatgcag----------------------

upper sequence: Vv16s0039g02040.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA11G01240.1 (Glycine max), 5'ss of exon 4
CGGTTGGCTACACACCGGTGACATTGGCTATGTTGACGATGATGAAGAGGTGTTCATCGTAGATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAGgcatgtattcttatgctccattttccccttcaattactatcctact------atttcgtagaagaacatcatatgttgacaccaagaggaagtttggaacggtgga
 |||||||| |||||||||||  |||||||||| || || ||||| ||  | ||||| || || || |||||||||||||||||||  ||||||||||||| || | | | | |     |||| || | |||  || | |  ||        |    ||   || |  | ||   || |    |        ||||    | | | 
GGGTTGGCTTCACACCGGTGATGTTGGCTATGTAGATGAAGATGATGAAATTTTCATTGTTGACAGGGTGAAAGAACTCATCAAATATAAAGGCTTCCAGgtatatttacatttaa---atttgcctcatcatgtagttttatagagagaaaacaatgtgacagcaagtaattaattaattatatttattcttttgttctgctag-

upper sequence: Vv16s0039g02040.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA01G44270.1 (Glycine max), 5'ss of exon 4
CGGTTGGCTACACACCGGTGACATTGGCTATGTTGACGATGATGAAGAGGTGTTCATCGTAGATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAGgcatgtattcttatgctccattttccccttcaattactatcctactatttcgtagaagaacatcatatgttgac-accaagaggaagtttggaacggtgga--
 |||||||| |||||||||||  ||||||| || || |||||||| ||  | ||||| || || || ||||| |||||||||||||  ||||||||||||| || |          |  | ||| ||   ||  ||   |  ||         |  |      ||    || |  |   | |   | | |      |||    
GGGTTGGCTTCACACCGGTGATGTTGGCTACGTAGATGATGATGACGAAATTTTCATTGTTGACAGGGTGAAGGAACTCATCAAATATAAAGGCTTCCAGgtatattaataggcatttaaatttgcctcacatatatagttttatagagagaaaacaatgtgacaagaattaattaattatatttattcttttgttgtgctag

upper sequence: Vv16s0039g02040.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT1G65060.1 (Arabidopsis thaliana), 5'ss of exon 4
CGGTTGGCTACACACCGGTGACATTGGCTATGTTGACGATGATGAAGAGGTGTTCATCGTAGATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAGgcatgtattcttatgctccattttccccttcaattactatcc-tactatttcgtagaagaacatcatatgttgacaccaagaggaagtt-tggaacggtgga------------------------------------------------------------------
 |||||||| ||||| || |||||||| |||||||| || ||||| ||| | ||||| || ||| || | |||||| ||||||| ||||||||||| |||||| ||    | ||  || ||| | |  || | ||   |    |  |    | || || |   | | ||  ||| |   | |   | |  |  ||   |                                                                     
AGGTTGGCTTCACACAGGAGACATTGGATATGTTGATGAAGATGATGAGATTTTCATTGTTGATCGACTTAAAGAAGTCATCAAGTTCAAAGGCTTTCAGgcaagtccattcatattc-attgttctttttatttttaacaagtgtttacacctaaaaaagatttacataatgatatagaaaattaatgatataatactattacttagttcaaaagataagatcatttcgaaatcgcggtatgatgatgatgagatgtgaaagaacag

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|352773444|gb|FQ472226.1|FQ472226
EST:     TGTTCATCGTAGATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAG                         GTACCGCCTGCTGAGCTTGAGGCCCTTCTGGTGAGTCACCCATCAATTGCT
genomic: TGTTCATCGTAGATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAGgcatgtattc ... tttcattcagGTACCGCCTGCTGAGCTTGAGGCCCTTCTGGTGAGTCACCCATCAATTGCT
EST: gi|110425483|gb|EC991868.1|EC991868
EST:     TGTTTATCGTAGATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAG                         GTACCGCCTGCTGAGCTTGAGGCCCTTCTGGTGAGCCACCCATCAATTGCC
genomic: TGTTCATCGTAGATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAGgcatgtattc ... tttcattcagGTACCGCCTGCTGAGCTTGAGGCCCTTCTGGTGAGTCACCCATCAATTGCT
EST: gi|110699052|gb|EE077254.1|EE077254
EST:     TGTTTATCGTAGATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAG                         GTACCGCCTGCTGAGCTTGAGGCCCTTCTGGTGAGCCACCCATCAATTGCC
genomic: TGTTCATCGTAGATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAGgcatgtattc ... tttcattcagGTACCGCCTGCTGAGCTTGAGGCCCTTCTGGTGAGTCACCCATCAATTGCT
EST: gi|110422395|gb|EC988717.1|EC988717
EST:     CGTAGATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAG                         GTACCGCCTGCTGAGCTTGAGGCCCTTCTGGTGAGCCACCCATCAATTGCC
genomic: CGTAGATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAGgcatgtattc ... tttcattcagGTACCGCCTGCTGAGCTTGAGGCCCTTCTGGTGAGTCACCCATCAATTGCT
EST: gi|33404900|gb|CF210527.1|CF210527
EST:     TGTTCATCGTAGATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAG                         GTACCGCCTGCTGAGCTTGAGGCCCTTCTGGTGAGCCACCCATCAATTGCC
genomic: TGTTCATCGTAGATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAGgcatgtattc ... tttcattcagGTACCGCCTGCTGAGCTTGAGGCCCTTCTGGTGAGTCACCCATCAATTGCT
EST: gi|110699199|gb|EE075988.1|EE075988
EST:     TGTTTATCGTAAATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAG                         GTACCGCCTGCTGAGCTTGAGGCCCTTCTGGTGAGCCACCCATCAATTGCC
genomic: TGTTCATCGTAGATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAGgcatgtattc ... tttcattcagGTACCGCCTGCTGAGCTTGAGGCCCTTCTGGTGAGTCACCCATCAATTGCT
EST: gi|110361934|gb|EC925440.1|EC925440
EST:     TGTTCATCGTAGATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAG                         GTACCGCCTGCTGAGCTTGAGGCCCTTCTGGTGAGCCACCCATCAATTGCC
genomic: TGTTCATCGTAGATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAGgcatgtattc ... tttcattcagGTACCGCCTGCTGAGCTTGAGGCCCTTCTGGTGAGTCACCCATCAATTGCT
EST: gi|110384288|gb|EC948716.1|EC948716
EST:     TGTTTATCGTAGATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAG                         GTACCGCCTGCTGAGCTTGAGGCCCTTCTGGTGAGCCACCCATCAATTGCC
genomic: TGTTCATCGTAGATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAGgcatgtattc ... tttcattcagGTACCGCCTGCTGAGCTTGAGGCCCTTCTGGTGAGTCACCCATCAATTGCT
EST: gi|110388697|gb|EC953474.1|EC953474
EST:     TGTTCATCGTAGATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAG                         GTACCGCCTGCTGAGCTTGAGGCCCTTCTGGTGAGCCACCCATCAATTGCC
genomic: TGTTCATCGTAGATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAGgcatgtattc ... tttcattcagGTACCGCCTGCTGAGCTTGAGGCCCTTCTGGTGAGTCACCCATCAATTGCT
EST: gi|352768957|gb|FQ468148.1|FQ468148
EST:     TGTTCATCGTAGATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAG                         GTACCGCCTGCTGAGCTTGAGGCCCTTCTGGTGAGTCACCCATCAATTGCT
genomic: TGTTCATCGTAGATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAGgcatgtattc ... tttcattcagGTACCGCCTGCTGAGCTTGAGGCCCTTCTGGTGAGTCACCCATCAATTGCT
EST: gi|33404985|gb|CF210612.1|CF210612
EST:     TGTTCATCGTAGATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAG                         GTACCGCCTGCTGAGCTTGAGGCCCTTCTGGTGAGCCACCCATCAATTGCC
genomic: TGTTCATCGTAGATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAGgcatgtattc ... tttcattcagGTACCGCCTGCTGAGCTTGAGGCCCTTCTGGTGAGTCACCCATCAATTGCT
EST: gi|110376549|gb|EC941609.1|EC941609
EST:     TGTTTATCGTAGATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAG                         GTACCGCCTGCTGAGCTTGAGGCCCTTCTGGTGAGCCACCCATCAATTGCC
genomic: TGTTCATCGTAGATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAGgcatgtattc ... tttcattcagGTACCGCCTGCTGAGCTTGAGGCCCTTCTGGTGAGTCACCCATCAATTGCT
EST: gi|110362812|gb|EC926367.1|EC926367
EST:     TGTTCATCGTAGATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAG                         GTACCGCCTGCTGAGCTTGAGGCCCTTCTGGTGAGCCACCCATCAATTGCC
genomic: TGTTCATCGTAGATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAGgcatgtattc ... tttcattcagGTACCGCCTGCTGAGCTTGAGGCCCTTCTGGTGAGTCACCCATCAATTGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGTTGGCTACACACCGGTGACATTGGCTATGTTGACGATGATGAAGAGGTGTTCATCGTAGATAGAGTGAAAGAACTCATCAAATTCAAAGGCTTCCAGgcatgtattcttatgctccattttccccttcaattactatcctactatttcgtagaagaacatcatatgttgacaccaagaggaagtttggaacggtgga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttcccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagagga