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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAGgtaagtggtttgttcttctctgatcagtcaaattttcttgttttgtttaaattcttagtgctgtcaacttctttgtagagtcaattttcaaattttatttgttgatgttttttgcag

Basic information

species Vitis vinifera
transcript Vv14s0219g00120.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0219g00120.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G015869_T02 (Zea mays), 5'ss of exon 3
ATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAGgtaagtggtttgttcttctctgatcagtcaaattttcttgttttgtttaaattcttagtgctgtcaacttctttgtagagtcaattttcaaat-tttatttgttgatgttttttgcag
||||| ||||| |||||||||||||||||||| ||| | ||||||||    |||||||| |||||  | |||||| |    || ||||||||   | ||||| | |  | |   |  | |||||||||  |     |||    || | | ||   ||||  |||| |   || |     |||  | ||                    
ATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAGgt---tagtttgctatgttattgaccatgaaattttctcctagctgtta----ctgactccta--aactcttttgaattatccaaaccgaaacatatag-------------------

upper sequence: Vv14s0219g00120.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA16G07110.1 (Glycine max), 5'ss of exon 3
ATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAGgtaag--tggtttgttcttctctgatcagtcaaattttcttgttttgtttaaattcttagtgctgtcaacttctttgtagagtcaattttcaaattttatttgttgatgttttttgcag
||||||||||| ||||||||||||||||||||||| || ||||||||| |  |||||||| |||| ||||| || |||||||||||||| |||||  || | |||  ||||||  |     |  || |  | |||||||      ||  |  |||   | ||||   |   |   |  ||     ||  |||||||  |          
ATGATACCTGTTGCTGCAAATGATGTTGCTTTCTCGATCCATGCTGTTCTACTGACAGCAATTACATTGTTCCAGATTGCAATCTATGAAgtaagcatgatatgtatttctctagttgagaatgttgttcttttttgtt------ctgtggactg---aattctcgattttgctgaacttagtgattgttttgttgtag----------

upper sequence: Vv14s0219g00120.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA16G07090.1 (Glycine max), 5'ss of exon 1
ATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAGgtaag--tggtttgttcttctctgatcagtcaaattttcttgttttgtttaaattcttagtgctgtcaacttctttgtagagtcaattttcaaattttatttgttgatgttttttgcag
||||||||||| ||||||||||||||||||||||| || ||||||||| |  |||||||| |||| ||||| || |||||||||||||| |||||  || | |||  ||||||  |     |  || |  | |||||||      ||  |  |||   | ||||   |   |   |  ||     ||  |||||||  |          
ATGATACCTGTTGCTGCAAATGATGTTGCTTTCTCGATCCATGCTGTTCTGCTGACAGCAATTACATTGTTCCAGATTGCAATCTATGAAgtaagcatgatatgtatttctctagttgagaatgttgttcttttttgtt------ctgtggactg---aattctcgattttgctgaacttagtgattgttttgttgtag----------

upper sequence: Vv14s0219g00120.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA19G23610.1 (Glycine max), 5'ss of exon 3
ATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAGgtaagtggtttgttcttctctgatcagtcaaattttcttgttttgtttaaattcttagt-gctgtcaacttctttgtagagtcaattttcaaattttatttgttgatgttttttgcag
|||||||| ||||| |||||||||||||||||||||   ||||||||| | ||||||||| || | ||||| || |||||||||||||| || |||| |   |||   |    |  |   | | ||||||   ||  |  ||  |||         |  || ||| |   ||                                    
ATGATACCCGTGGCAGCAAATGATGTTGCTTTCTCAGCCCATGCTGTTCTGTTGACAGCAATTTCCTTGTTCCAGATTGCAATCTATGATgttagtgctacattccctttaattgggcttattgttcttgcaatgaatttatgattaaccaaaaagaggttatttttcatgtag----------------------------------

upper sequence: Vv14s0219g00120.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT5G40670.1 (Arabidopsis thaliana), 5'ss of exon 3
ATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAGgtaagtggtttgttcttctctgatcagtcaaattttcttgttttgtttaaattcttagtgctgtcaacttctttgtagag-tcaattttcaaattttatttgttgatgttttttgcag
||||||||||||||||||||||||||||| ||||| || ||||| ||| |  |||||||  ||||  |||| || ||    |||||||| || |||  |    | |  |  | |        | |  || |    |  || |  |   |  |  |   |  ||| ||| | |    | |||                           
ATGATACCTGTGGCTGCAAATGATGTTGCATTCTCGATCCATGCAGTTGTAATGACAGCTGTTACACTGTTCCAGATCTTTATCTATGAAgtgagtaatcaagtttcttaggcttgcctttgtctctttatcccatacaagtgttctttttttcctgatgatttctagtgatttgctctcag--------------------------

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|110723575|gb|EE101045.1|EE101045
EST:     ATGCTGTCATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAG                         CGTGGAACTCAGAAGGTTTCAAAGATTTCCATTGGAATTGTTTCTGCTGCA
genomic: ATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAGgtaagtggtt ... ttttttgcagCGTGGAACTCAGAAGGTTTCAAAGATTTCCATTGGAATTGTTTGTGCTGCA
EST: gi|351045861|gb|FQ441046.1|FQ441046
EST:     ATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAG                         CGTGGAACTCAGAGGGTTTCAAAGATTTCCATTGGAATTGTTTCTGCTGCA
genomic: ATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAGgtaagtggtt ... ttttttgcagCGTGGAACTCAGAAGGTTTCAAAGATTTCCATTGGAATTGTTTGTGCTGCA
EST: gi|351030795|gb|FQ438633.1|FQ438633
EST:     ATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAG                         CGTGGAACTCAGAGGGTTTCAAAGATTTCCATTGGAATTGTTTCTGCTGCA
genomic: ATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAGgtaagtggtt ... ttttttgcagCGTGGAACTCAGAAGGTTTCAAAGATTTCCATTGGAATTGTTTGTGCTGCA
EST: gi|349811028|gb|FQ406016.1|FQ406016
EST:     ATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAAGTGCAATCTATGAG                         CGTGGAACTCAGAGGGTTTCAAAGATTTCCATTGGAATTGTTTCTGCTGCA
genomic: ATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAGgtaagtggtt ... ttttttgcagCGTGGAACTCAGAAGGTTTCAAAGATTTCCATTGGAATTGTTTGTGCTGCA
EST: gi|110699274|gb|EE076127.1|EE076127
EST:     ATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAG                         CGTGGAACTCAGAAGGTTTCAAAGATTTCCATTGGAATTGTTTGTGCTGCA
genomic: ATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAGgtaagtggtt ... ttttttgcagCGTGGAACTCAGAAGGTTTCAAAGATTTCCATTGGAATTGTTTGTGCTGCA
EST: gi|294966259|gb|GW837510.1|GW837510
EST:     ATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAG                         CGTGGAACTCAGAAGGTTTCAAAGATTTCCATTGGAATTGTTTGTGCTGCA
genomic: ATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAGgtaagtggtt ... ttttttgcagCGTGGAACTCAGAAGGTTTCAAAGATTTCCATTGGAATTGTTTGTGCTGCA
EST: gi|349820300|gb|FQ403916.1|FQ403916
EST:     ATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAG                         CGTGGAACTCAGAGGGTTTCAAAGATTTCCATTGGAATTGTTTCTGCTGCA
genomic: ATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAGgtaagtggtt ... ttttttgcagCGTGGAACTCAGAAGGTTTCAAAGATTTCCATTGGAATTGTTTGTGCTGCA
EST: gi|349809992|gb|FQ398617.1|FQ398617
EST:     ATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAG                         CGTGGAACTCAGAGGGTTTCAAAGATTTCCATTGGAATTGTTTCTGCTGCA
genomic: ATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAGgtaagtggtt ... ttttttgcagCGTGGAACTCAGAAGGTTTCAAAGATTTCCATTGGAATTGTTTGTGCTGCA
EST: gi|110696243|gb|EE075180.1|EE075180
EST:     ATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAG                         CGTGGAACTCAGAAGGTTTCAAAGATTTCCATTGGAATTGTTTCTGCTGCA
genomic: ATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAGgtaagtggtt ... ttttttgcagCGTGGAACTCAGAAGGTTTCAAAGATTTCCATTGGAATTGTTTGTGCTGCA
EST: gi|110724366|gb|EE100141.1|EE100141
EST:     ATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAG                         CGTGGAACTCAGAAGGTTTCAAAGATTTCCATTGGAATTGTTTGTGCTGCA
genomic: ATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAGgtaagtggtt ... ttttttgcagCGTGGAACTCAGAAGGTTTCAAAGATTTCCATTGGAATTGTTTGTGCTGCA
EST: gi|34549515|gb|CF517747.1|CF517747
EST:     ATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAG                         CGTGGAACTCAGAAGGTTTCAAAGATTTCCATTGGAATTGTTTCTGCTGCA
genomic: ATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAGgtaagtggtt ... ttttttgcagCGTGGAACTCAGAAGGTTTCAAAGATTTCCATTGGAATTGTTTGTGCTGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAGgtaagtggtttgttcttctctgatcagtcaaattttcttgttttgtttaaattcttagtgctgtcaacttctttgtagagtcaattttcaaattttatttgttgatgttttttgcag

- - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - GCTGTT