Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattttagcttggtgtaataactgtggaagaataggttgttaggattagataaaaaattttaaattactgagttctgagcaatttgtatgttctttatagGCTGTTAGCAGGGAAATACGTAAGATATTGACAGAAAGGGCAGCCAATTTCAACATCGCTCTGGATGATGTGTCCATCACAAGCCTTACTTTTGGGAAGG

Basic information

species Vitis vinifera
transcript Vv15s0048g02350.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0048g02350.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os03g60000.1 (Oryza sativa), 3'ss of exon 3
--------------------------------------------------tattttagcttggtgtaataactgtggaagaataggttgttaggatta-gataaaaaattttaaattactgagttctgagcaatttgtatgttctttatagGCTGTTAGCAGGGAAATACGTAAGATATTGACAGAAAGGGCAGCCAATTTCAACATCGCTCTGGATGATGTGTCCATCACAAGCCTTACTTTTGGGAAGG
                                                  |||  ||   | || ||| | ||     | | |||| | ||  | ||| ||   || ||  ||   || |  | |   |   | |  | | | |   | ||||||| |||||||| ||  | |||||  ||||||| |||||   ||| |||||||| |||||||||||||||||||||||||| || |  ||||| || |
gtactgtcatcatatctatctgtgtttaaatatctaatatgtttccatggtatgctatgctagtttaagagcta--atatagtaggatatttagtttaagagttaatatagtaggata-tatgctaataattactcctttatccaacacagGCTGTGAGCAGGGAGATTAGGAAGATCCTGACAGAGAGGGCTAGCAACTTCAACATTGCTCTGGATGATGTGTCCATCACAAGTCTCAGCTTTGGAAAAG

upper sequence: Vv15s0048g02350.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os03g62490.1 (Oryza sativa), 3'ss of exon 3
----------------------------------------------------tattttagcttggtgtaataactg-tggaagaataggttgttaggatta-gataaaaaattttaaattactgagttctgagcaatttgtatgttctttatagGCTGTTAGCAGGGAAATACGTAAGATATTGACAGAAAGGGCAGCCAATTTCAACATCGCTCTGGATGATGTGTCCATCACAAGCCTTACTTTTGGGAAGG
                                                    |||  ||   | || ||| | ||  |  |  | || | | ||  | ||| ||   || ||  ||   ||    ||  | |  | ||  | | | |   | ||||||| |||||||| ||  | |||||  ||||||| |||||   ||| |||||||| |||||||||||||||||||||||||| || |  ||||| || |
gtactgtcttatcatatctatctgtgtttaaatatctaatatgtttccatggtatgctatgctagtttaagagctaatatagtagtatgatatttagtttaagagctaatatagtaggatatatggtaataatta-ttcctttatccaacacagGCTGTGAGCAGGGAGATTAGGAAGATCCTGACAGAGAGGGCTAGCAACTTCAACATTGCTCTGGATGATGTGTCCATCACAAGTCTCAGCTTTGGAAAAG

upper sequence: Vv15s0048g02350.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AC217358.3_FGT005 (Zea mays), 3'ss of exon 3
------------tattttagcttggtgtaataactgtggaagaatagg-ttgttaggattagataaaaa-attttaaattactgagttctgagcaatttgtatgttctttatagGCTGTTAGCAGGGAAATACGTAAGATATTGACAGAAAGGGCAGCCAATTTCAACATCGCTCTGGATGATGTGTCCATCACAAGCCTTACTTTTGGGAAGG
              | |   |  | |||  |  |  |  || ||  |  ||| ||||||| ||| | |  |   ||  |||     |  |       ||  || | |  |  ||||||| |||||||| ||  | |||||  |||| || |||||   ||| ||||| || ||||||||||||||||||||||||||||| |  ||||| || |
gtaccattcatgcgtctagacacgatgt--tccccatataacaactgtcttgctaggattggatgagattaggatatgttaacagttcattcatgcattcgat-tccgatgcagGCTGTGAGCAGGGAGATTAGGAAGATTCTGACTGAGAGGGCCAACAACTTCAATATTGCTCTGGATGATGTGTCCATCACAAGCCTCAGCTTTGGAAAAG

upper sequence: Vv15s0048g02350.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G30410.1 (Glycine max), 3'ss of exon 5
--tattttagcttggtgtaataactgtggaagaataggttgttaggat-tagataaaaaattttaaattactgagttctgagcaatttgtatgttctttatagGCTGTTAGCAGGGAAATACGTAAGATATTGACAGAAAGGGCAGCCAATTTCAACATCGCTCTGGATGATGTGTCCATCACAAGCCTTACTTTTGGGAAGG
  || ||        |||  |     |   || ||   ||  ||| |   ||   |     |||||| |      ||       |  |   |  ||||| |||||||||||  ||||||| || ||||| ||||| |||||||| || || ||||| || || || ||||||||||| || || || || |||||||| ||||
attagttccatgcaatgttttcttatttcgagtattcatttctagcacacaggagagtgtgtttaaacttaaacatttaacttgacct---taatctttgtagGCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTCAATATTGCCCTTGATGATGTGTCAATTACTAGTCTGACTTTTGGCAAGG

upper sequence: Vv15s0048g02350.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G36940.1 (Glycine max), 3'ss of exon 4
--tattttagcttggtgtaataactgtggaagaataggttgttaggattagataaaaaat-tttaaattactgagttctgagcaatttgtatgttctttatagGCTGTTAGCAGGGAAATACGTAAGATATTGACAGAAAGGGCAGCCAATTTCAACATCGCTCTGGATGATGTGTCCATCACAAGCCTTACTTTTGGGAAGG
  || ||        |||  |     |   || ||   ||  ||| |     || |   | ||| || |      ||       |  |   |  ||||| |||||||||||  ||||||| || |||||  |||| |||||||| || || ||||| || || || ||||||||||| || || || || |||||||| ||||
attagttccatgcaatgttttcttatttcgagtattcatttctagcacacagtagagtttgtttgaacttaaacatttaacttgacct---taatctttgtagGCTGTTAGTCGGGAAATCCGGAAGATTCTGACTGAAAGGGCTGCTAACTTCAATATTGCCCTTGATGATGTGTCAATTACTAGTCTGACTTTTGGCAAGG

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|110711108|gb|EE087281.1|EE087281
EST:     AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGGGAG                         GCTGTTAGTANGGAAATACGCAAGATATTGACAGAAAGGGCAGCCAATTTC
genomic: AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGGGAGgtaggtaacc ... ttctttatagGCTGTTAGCAGGGAAATACGTAAGATATTGACAGAAAGGGCAGCCAATTTC
EST: gi|161716355|gb|FC066866.1|FC066866
EST:     AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGGGAG                         GCTGTTAGCAGGGAAATACGTAAGATATTGAC
genomic: AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGGGAGgtaggtaacc ... ttctttatagGCTGTTAGCAGGGAAATACGTAAGATATTGAC
EST: gi|22013946|gb|BQ798980.1|BQ798980
EST:     AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGGGAG                         GCTGTTAGTAGGGAAATACGCAAGATATTGACAGAAAGGGCAGCCAATTTC
genomic: AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGGGAGgtaggtaacc ... ttctttatagGCTGTTAGCAGGGAAATACGTAAGATATTGACAGAAAGGGCAGCCAATTTC
EST: gi|110414101|gb|EC979926.1|EC979926
EST:     AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGGGAG                         GCTGTTAGTAGGGAAATACGCAAGATATTGACAGAAAGGGCAGCCAATTTC
genomic: AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGGGAGgtaggtaacc ... ttctttatagGCTGTTAGCAGGGAAATACGTAAGATATTGACAGAAAGGGCAGCCAATTTC
EST: gi|110708454|gb|EE086015.1|EE086015
EST:     AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGGGAG                         GCTGTTAGTAGGGAAATACGCAAGATATTGACAGAAAGGGCAGCCAATTTC
genomic: AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGGGAGgtaggtaacc ... ttctttatagGCTGTTAGCAGGGAAATACGTAAGATATTGACAGAAAGGGCAGCCAATTTC
EST: gi|30297423|gb|CB974217.1|CB974217
EST:     AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGGGAG                         GCTGTTAGCAGGGAAATACGTAAGATATTGACAGAAAGGGCAGCCAATTTC
genomic: AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGGGAGgtaggtaacc ... ttctttatagGCTGTTAGCAGGGAAATACGTAAGATATTGACAGAAAGGGCAGCCAATTTC
EST: gi|110421504|gb|EC987802.1|EC987802
EST:     AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGGGAG                         GCTGTTAGTAGGGAAATACGCAAGATATTGACAGAAAGGGCAGCCAATTTC
genomic: AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGGGAGgtaggtaacc ... ttctttatagGCTGTTAGCAGGGAAATACGTAAGATATTGACAGAAAGGGCAGCCAATTTC
EST: gi|110720744|gb|EE096932.1|EE096932
EST:     AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGGGAG                         GCTGTTAGTANGGAAATACGCAAGATATTGACAGAAAGGGCAGCCAATTTC
genomic: AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGGGAGgtaggtaacc ... ttctttatagGCTGTTAGCAGGGAAATACGTAAGATATTGACAGAAAGGGCAGCCAATTTC
EST: gi|18459675|gb|BM437953.1|BM437953
EST:     AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGGGAG                         GCTGTTAGCAGGGAAATACGTAAGATATTGACAGAAAGGGCAGCCAATTTC
genomic: AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGGGAGgtaggtaacc ... ttctttatagGCTGTTAGCAGGGAAATACGTAAGATATTGACAGAAAGGGCAGCCAATTTC
EST: gi|110699664|gb|EE076859.1|EE076859
EST:     AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGGGAG                         GCTGTTAGTAGGGAAATACGCAAGATATTGACAGAAAGGGCAGCCAATTTC
genomic: AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGGGAGgtaggtaacc ... ttctttatagGCTGTTAGCAGGGAAATACGTAAGATATTGACAGAAAGGGCAGCCAATTTC
EST: gi|161720129|gb|FC065124.1|FC065124
EST:     AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGGGAG                         GCTGTTAGCAGGGAAATACGTAAGATATTGACAGAAAGGGCAGCCAATTTT
genomic: AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGGGAGgtaggtaacc ... ttctttatagGCTGTTAGCAGGGAAATACGTAAGATATTGACAGAAAGGGCAGCCAATTT-
EST: gi|110729989|gb|EE106553.1|EE106553
EST:     AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGGGAG                         GCTGTTAGTANGGAAATACGCAAGATATTGACAGAAAGGGCAGCCAATTTC
genomic: AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGGGAGgtaggtaacc ... ttctttatagGCTGTTAGCAGGGAAATACGTAAGATATTGACAGAAAGGGCAGCCAATTTC
EST: gi|110367206|gb|EC931133.1|EC931133
EST:     AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGGGAG                         GCTGTTAGCAGGGAAATACGTAAGATATTGACAGAAAGGGCAGCCAATTTC
genomic: AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGGGAGgtaggtaacc ... ttctttatagGCTGTTAGCAGGGAAATACGTAAGATATTGACAGAAAGGGCAGCCAATTTC
EST: gi|110718347|gb|EE095076.1|EE095076
EST:     AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGGGAG                         GCTGTTAGTAGGGAAATACGCAAGATATTGACAGAAAGGGCAGCCAATTTT
genomic: AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGGGAGgtaggtaacc ... ttctttatagGCTGTTAGCAGGGAAATACGTAAGATATTGACAGAAAGGGCAGCCAATTT-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagataaaaaattttaaattactgagttctgagcaatttgtatgttctttatagGCTGTTAGCAGGGAAATACGTAAGATATTGACAGAAAGGGCAGCCAATTTCAACATCGCTCTGGATGATGTGTCCATCACAAGCCTTACTTTTGGGAAGG
                                           tgttcttt  CT-rich tract
     taaaaaattttaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattttagcttggtgtaataactgtggaagaataggttgttaggattagataaaaaattttaaattactgagttctgagcaatttgtatgttctttatagGCTGTTAGCAGGGAAATACGTAAGATATTGACAGAAAGGGCAGCCAATTTCAACATCGCTCTGGATGATGTGTCCATCACAAGCCTTACTTTTGGGAAGG

- - - agcttgg
- - - - - - - - - - - - -ggaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaat