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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAGGAAAAAGGATTACAAGGATGGCAGATATTCTCAGGTGGTTTCAAATGCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAGgttattatttcccatgttatccttaatgattattctatttgaacacagatccaggtctctttcttgttacatgaatccattggtttctgtcaacctgcag...

Basic information

species Vitis vinifera
transcript Vv18s0072g00060.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0072g00060.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA20G30730.1 (Glycine max), 5'ss of exon 3
ATAGGAAAAAGGATTACAAGGATGGCAGATATTCTCAGGTGGTTTCAAATGCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAGgttatta--tttcccatgttatccttaatgattattctatttgaacacagatccaggtctctttcttgt-tacatgaatccattggtttctgtcaacctgcag
| || || ||||| |||||||||||||  |||||||||||||| ||||||||| |||||||||||||||| |||||||||||| || | ||||||||||||| ||||   ||   ||  |    |||      |   | |||  | | |  |     || || | ||||  | || || |  ||  ||  ||  |   |    
ACAGAAAGAAGGACTACAAGGATGGCAAGTATTCTCAGGTGGTGTCAAATGCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAGgtaattaagattttgattgtggatttatacgggaaaatgtttagatataactgatcctcactgttttgtgcaaatcaacctgtttattcttgcaatggtt---

upper sequence: Vv18s0072g00060.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA02G08690.1 (Glycine max), 5'ss of exon 3
ATAGGAAAAAGGATTACAAGGATGGCAGATATTCTCAGGTGGTTTCAAATGCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAGgttattatttcccatgttatc--cttaatgatta-ttctatttgaacacagatccaggtctctttcttgttacatgaatccattggtttctgtcaacctgcag--
||||||| || || ||||||||||| |  |||||||||||||| ||||||||| |||||||||||||||| ||||| |||||||| |||||||||||||||| |||  ||  | | ||     ||| ||| | | || || | |||   |  |  | || |  | || |     ||  | | ||   || | |     |      
ATAGGAAGAAAGACTACAAGGATGGGAAGTATTCTCAGGTGGTGTCAAATGCACTGGATATGAAGTTGAGGGATGATTTGGAGCGCTTGAAGAAAATCAGgtgattcattgtcgtatttgtatcttgatgttgaattttaatagaattaaattaaaagtttggtactag--gagtggtttcttt---ttttattggattatgaat

upper sequence: Vv18s0072g00060.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT1G22780.1 (Arabidopsis thaliana), 5'ss of exon 3
ATAGGAAAAAGGATTACAAGGATGGCAGATATTCTCAGGTGGTTTCAAATGCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAGgttattatttcc-catgttatccttaatgattattctatttgaacacagatccaggtctctttcttgttacatgaatccattggtttctgtcaacctgcag----
| ||  ||||||||||||||||||| | ||| || || || ||||| |||||  | || |||||||||||||||||  | |||||  | ||||| ||||||| |  |    | |||     |  |      | |  | |||  | ||      |      | |  || | |       |||   ||||| |      | ||    
ACAGACAAAAGGATTACAAGGATGGGAAATACTCCCAAGTTGTTTCCAATGCTCTTGACATGAAGTTGAGAGATGATCTTGAGCGTCTCAAGAAGATCAGgtaacaaacaacacatacagacactctcctctgtagtttttagataccatgttaa--tagtataatgatgccca---tcataactttctatatggaagaagctaa

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|110700267|gb|EE078111.1|EE078111
EST:     GCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAG                         GAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCAGCA
genomic: GCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAGgttattattt ... tgttatgcagGAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCAGCA
EST: gi|110732426|gb|EE107700.1|EE107700
EST:     GCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAG                         GAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCAGCA
genomic: GCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAGgttattattt ... tgttatgcagGAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCAGCA
EST: gi|110387218|gb|EC951868.1|EC951868
EST:     GCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAG                         GAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCAGCA
genomic: GCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAGgttattattt ... tgttatgcagGAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCAGCA
EST: gi|110371313|gb|EC935234.1|EC935234
EST:     GCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAG                         GAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCAGCA
genomic: GCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAGgttattattt ... tgttatgcagGAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCAGCA
EST: gi|110730467|gb|EE107583.1|EE107583
EST:     GCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAG                         GAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCAGCA
genomic: GCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAGgttattattt ... tgttatgcagGAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCAGCA
EST: gi|110391677|gb|EC956670.1|EC956670
EST:     GCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAG                         GAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCAGCA
genomic: GCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAGgttattattt ... tgttatgcagGAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCAGCA
EST: gi|351016436|gb|FQ423863.1|FQ423863
EST:     GCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAG                         GAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCAGCA
genomic: GCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAGgttattattt ... tgttatgcagGAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCAGCA
EST: gi|77579580|gb|DV218639.1|DV218639
EST:     GCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAG                         GAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCAGCA
genomic: GCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAGgttattattt ... tgttatgcagGAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCAGCA
EST: gi|71872730|gb|DT021785.1|DT021785
EST:     GCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAG                         GAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCAGCA
genomic: GCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAGgttattattt ... tgttatgcagGAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCAGCA
EST: gi|110419379|gb|EC985599.1|EC985599
EST:     GCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAG                         GAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCAGCA
genomic: GCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAGgttattattt ... tgttatgcagGAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCAGCA
EST: gi|110689883|gb|EE066499.1|EE066499
EST:     GCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAG                         GAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCAGCA
genomic: GCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAGgttattattt ... tgttatgcagGAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCAGCA
EST: gi|110700974|gb|EE078100.1|EE078100
EST:     GCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAA                         GAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCATCA
genomic: GCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAGgttattattt ... tgttatgcagGAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCAGCA
EST: gi|110420043|gb|EC986304.1|EC986304
EST:     GCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAG                         GAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCAGCA
genomic: GCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAGgttattattt ... tgttatgcagGAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCAGCA
EST: gi|110360370|gb|EC923419.1|EC923419
EST:     GCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAG                         GAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCAGCA
genomic: GCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAGgttattattt ... tgttatgcagGAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCAGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAGGAAAAAGGATTACAAGGATGGCAGATATTCTCAGGTGGTTTCAAATGCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAGgttattatttcccatgttatccttaatgattattctatttgaacacagatccaggtctctttcttgttacatgaatccattggtttctgtcaacctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaacaca