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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATATATGGTATGCCCTTTCGGGATATGCAATTGGACTTGTAACTGCTTTGGCAGCTGGTGTTTTGACTCACTCACCTCAACCTGCACTTCTTTATCTGgtatgtatttgttgaaatcttattgctattttattaacctgaacatgtggatgaattagttttcttatggaaagtcaaagtgttaggaatattttctctt...

Basic information

species Vitis vinifera
transcript Vv16s0050g00580.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g00580.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA10G37870.3 (Glycine max), 5'ss of exon 3
ATATATATGGTATGCCCTTTCGGGATATGCAATTGGACTTGTAACTGCTTTGGCAGCTGGTGTTTTGACTCACTCACCTCAACCTGCACTTCTTTATCTGgtatgtatttgttgaaat--cttattgctattttattaacctgaacatgtggatgaattagttttcttatggaaagtcaaagtgttaggaatattttctctt-
||| ||||||||||| ||  | || ||||| ||||| || ||||||||||||||||||||||| ||||| |||||||||||||||||||||||||||||||||   |||| ||   ||  ||| |||  ||  || |    |   | | |  |    |   || | | |     | |||   | |     | | ||||| || 
ATACATATGGTATGCGCTACCCGGGTATGCCATTGGCCTGGTAACTGCTTTGGCAGCTGGTGTCTTGACCCACTCACCTCAACCTGCACTTCTTTATCTGgtactaatttatttctatttcttcttgtcataatactggttt---cttttatacctctactttctttgacctttattcatcatttattccagaatttctgttc

upper sequence: Vv16s0050g00580.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA20G29950.1 (Glycine max), 5'ss of exon 3
ATATATATGGTATGCCCTTTCGGGATATGCAATTGGACTTGTAACTGCTTTGGCAGCTGGTGTTTTGACTCACTCACCTCAACCTGCACTTCTTTATCTGgtatgtatttgttgaaatcttattgctattttattaacctgaacatgtggatgaattagttttctt--atggaaagtcaaagtgttaggaatattttctctt-
||| ||||||||||| ||  | || ||||| ||||| || |||||||||||||| |||||||| |||||||||||||||||||||||||||||||||||||||  | | | ||   || || ||  | |  || ||  |||      | | |   ||   |||||   |     | |||   | |     | | ||||| || 
ATACATATGGTATGCGCTACCCGGGTATGCCATTGGCCTGGTAACTGCTTTGGCTGCTGGTGTCTTGACTCACTCACCTCAACCTGCACTTCTTTATCTGgtacttctgtttttctat-ttgttcttgtcataata--ctggtttctttgctacctttactttctccaacctttattcatcatttataccagaatttctgttc
















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|110688147|gb|EE066363.1|EE066363
EST:     TGGCAGCTGGTGTTTTGACTCACTCACCTCAACCTGCACTTCTTTATCTG                         GTGCCTGCTACATTGGGACCCATCATATTCGTATCTTGGATAAGGAAGGAG
genomic: TGGCAGCTGGTGTTTTGACTCACTCACCTCAACCTGCACTTCTTTATCTGgtatgtattt ... gtgcttgtagGTGCCTGCTACATTGGGACCCATCATATTCGTATCTTGGATAAGGAAGGAG
EST: gi|110367682|gb|EC931629.1|EC931629
EST:     TGGCAGCTGGTGTTTTGACTCACTCACCTCAACCTGCACTTCTTTATCTG                         GTGCCTGCTACATTGGGACCCATCATATTCGTATCTTGGATAAGGAAGGAG
genomic: TGGCAGCTGGTGTTTTGACTCACTCACCTCAACCTGCACTTCTTTATCTGgtatgtattt ... gtgcttgtagGTGCCTGCTACATTGGGACCCATCATATTCGTATCTTGGATAAGGAAGGAG
EST: gi|30300064|gb|CB976858.1|CB976858
EST:     TGGCAGCTGGTGTTTTGACTCACTCACCTCAACCTGCACTTCTTTATCTG                         GTGCCTGCTACATTGGGACCCATCATATTCGTATCTTGGATAAGGAAGGAG
genomic: TGGCAGCTGGTGTTTTGACTCACTCACCTCAACCTGCACTTCTTTATCTGgtatgtattt ... gtgcttgtagGTGCCTGCTACATTGGGACCCATCATATTCGTATCTTGGATAAGGAAGGAG
EST: gi|34543123|gb|CF511355.1|CF511355
EST:     TGGCAGCTGGTGTTTTGACTCACTCACCTCAACCTGCACTTCTTTATCTG                         GTGCCTGCTACATTGGGACCCATCATATTCGTATCTTGGATAAGGAAGGAG
genomic: TGGCAGCTGGTGTTTTGACTCACTCACCTCAACCTGCACTTCTTTATCTGgtatgtattt ... gtgcttgtagGTGCCTGCTACATTGGGACCCATCATATTCGTATCTTGGATAAGGAAGGAG
EST: gi|83274884|gb|DV938980.1|DV938980
EST:     TGGCAGCTGGTGTTTTGACTCACTCACCTCAACCTGCACTTCTTTATCTG                         GTGCCTGCTACATTGGGACCCATCATATTCGTATCTTGGATAAGGAAGGAG
genomic: TGGCAGCTGGTGTTTTGACTCACTCACCTCAACCTGCACTTCTTTATCTGgtatgtattt ... gtgcttgtagGTGCCTGCTACATTGGGACCCATCATATTCGTATCTTGGATAAGGAAGGAG
EST: gi|30296886|gb|CB973680.1|CB973680
EST:     TGGCAGCTGGTGTTTTGACTCACTCACCTCAACCTGCACTTCTTTATCTG                         GTGCCTGCTACATTGGGACCCATCATATTCGTATCTTGGATAAGGAAGGAG
genomic: TGGCAGCTGGTGTTTTGACTCACTCACCTCAACCTGCACTTCTTTATCTGgtatgtattt ... gtgcttgtagGTGCCTGCTACATTGGGACCCATCATATTCGTATCTTGGATAAGGAAGGAG
EST: gi|110426826|gb|EC993249.1|EC993249
EST:     TGGCAGCTGGTGTTTTGACTCACTCACCTCAACCTGCACTTCTTTATCTG                         GTGCCTGCTACATTGGGACCCATCATATTCGTATCTTGGATAAGGAAGGAG
genomic: TGGCAGCTGGTGTTTTGACTCACTCACCTCAACCTGCACTTCTTTATCTGgtatgtattt ... gtgcttgtagGTGCCTGCTACATTGGGACCCATCATATTCGTATCTTGGATAAGGAAGGAG
EST: gi|34543206|gb|CF511438.1|CF511438
EST:     TGGCAGCTGGTGTTTTGACTCACTCACCTCAACCTGCACTTCTTTATCTG                         GTGCCTGCTACATTGGGACCCATCATATTCGTATCTTGGATAAGGAAGGAG
genomic: TGGCAGCTGGTGTTTTGACTCACTCACCTCAACCTGCACTTCTTTATCTGgtatgtattt ... gtgcttgtagGTGCCTGCTACATTGGGACCCATCATATTCGTATCTTGGATAAGGAAGGAG
EST: gi|34363637|gb|CF405222.1|CF405222
EST:     TGGCAGCTGGTGTTTTGACTCACTCACCTCAACCTGCACTTCTTTATCTG                         GTGCCTGCTACATTGGGACCCATCATATTCGTATCTTGGATAAGGAAGGAG
genomic: TGGCAGCTGGTGTTTTGACTCACTCACCTCAACCTGCACTTCTTTATCTGgtatgtattt ... gtgcttgtagGTGCCTGCTACATTGGGACCCATCATATTCGTATCTTGGATAAGGAAGGAG
EST: gi|30300134|gb|CB976928.1|CB976928
EST:     TGGCAGCTGGTGTTTTGACTCACTCCCCTCAACCTGCACTTCTTTATTTG                         GTGCCTGCTACATTGGGACCCATCATATTCGGATCTTGGATAAGGAAGGAG
genomic: TGGCAGCTGGTGTTTTGACTCACTCACCTCAACCTGCACTTCTTTATCTGgtatgtattt ... gtgcttgtagGTGCCTGCTACATTGGGACCCATCATATTCGTATCTTGGATAAGGAAGGAG
EST: gi|110368481|gb|EC932461.1|EC932461
EST:     TGGCAGCTGGTGTTTTGACTCACTCACCTCAACCTGCACTTCTTTATCTG                         GTGCCTGCTACATTGGGACCCATCATATTCGTATCTTGGATAAGGAAGGAG
genomic: TGGCAGCTGGTGTTTTGACTCACTCACCTCAACCTGCACTTCTTTATCTGgtatgtattt ... gtgcttgtagGTGCCTGCTACATTGGGACCCATCATATTCGTATCTTGGATAAGGAAGGAG
EST: gi|110405949|gb|EC971507.1|EC971507
EST:     TGGCAGCTGGTGTTTTGACTCACTCACCTCAACCTGCACTTCTTTATCTG                         GTGCCTGCTACATTGGGACCCATCATATTCGTATCTTGGATAAGGAAGGAG
genomic: TGGCAGCTGGTGTTTTGACTCACTCACCTCAACCTGCACTTCTTTATCTGgtatgtattt ... gtgcttgtagGTGCCTGCTACATTGGGACCCATCATATTCGTATCTTGGATAAGGAAGGAG
EST: gi|110363902|gb|EC927533.1|EC927533
EST:     TGGCAGCTGGTGTTTTGACTCACTCACCTCAACCTGCACTTCTTTATCTG                         GTGCCTGCTACATTGGGACCCATCATATTCGTATCTTGGATAAGGAAGGAG
genomic: TGGCAGCTGGTGTTTTGACTCACTCACCTCAACCTGCACTTCTTTATCTGgtatgtattt ... gtgcttgtagGTGCCTGCTACATTGGGACCCATCATATTCGTATCTTGGATAAGGAAGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATATATGGTATGCCCTTTCGGGATATGCAATTGGACTTGTAACTGCTTTGGCAGCTGGTGTTTTGACTCACTCACCTCAACCTGCACTTCTTTATCTGgtatgtatttgttgaaatcttattgctattttattaacctgaacatgtggatgaattagttttcttatggaaagtcaaagtgttaggaatattttctctt

- - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atggaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggaata