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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgttttctaattctcttcagttatacctgctgcagttacttttggcactcagaaagaagatccaagcattaggaagtttgacagtaacgagggtttgattttgaattgtagGTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTGATGGAGCGTGATTCACTTCGGATGCGAGATGGAGGGCCATTTATCTTTG

Basic information

species Vitis vinifera
transcript Vv10s0003g03120.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g03120.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os05g49050.1 (Oryza sativa), 3'ss of exon 5
gtatgtgttttctaattctcttcagtt-------atacctgctgcagttacttttggcactcagaaagaagatccaagcattaggaagtttgacagtaacgagggtttgattttg--aattgtagGTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTGATGGAGCGTGATTCACTTCGGATGCGAGATGGAGGGCCATTTATCTTTG
|| |||  || ||   ||  ||| |||       |||||||   ||   || || |  | |    |      |  |  | || | |  |||  || |        ||  || ||    |    || | ||||||||||| ||||||||||||||||||||||||||| |||| || ||||| || ||| | ||||| ||||| || |||||||| ||| ||||||
gtgtgttattactttctccattctgttacgatgcatacctgtatcaaagacgtt-gatatttctgatatgcttgtacccttttgca--tttaccatttgatcaatttcaatctttctgaacacagATAATAAACAAGACAGACCTTGCACCAGCAGTTGGAGCTGACCTGGCTGTAATGGAACGAGATGCGCTTCGCATGCGGGAAGGAGGGCCTTTTGTCTTTG

upper sequence: Vv10s0003g03120.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G413652_T01 (Zea mays), 3'ss of exon 5
gtatgtgttttctaattctct----tcagttata-cctgctgcagtta----cttttggcactcagaaagaagatccaagcattaggaag--------------tttgacagtaacgagggtttga--ttttgaattgtagGTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTGATGGAGCGTGATTCACTTCGGATGCGAGATGGAGGGCCATTTATCTTTG
||  ||  |     |||| |     |||  |||| |||  |||| |||    | ||||   ||| | ||    ||     | || | |                || | | | |   |  || |||  || |||| |  |||| ||||||||||| ||||| ||||| || |||||||||||  || | || |||||||| ||  ||||||| ||||| || |||||||| ||| | ||||
gtgcgtcgtgctgtattcaccagcatcatctataaccttgtgcacttaacttcatttgtagctctgcaaacttattttgacttttgcacactggtcatattttattggccggcataaaatgtctgagtttctgaact-cagGTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTAATGGAGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTG

upper sequence: Vv10s0003g03120.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA08G08970.2 (Glycine max), 3'ss of exon 4
gtatgtgttttctaattctcttcagttatacctgctgcagttacttttggcactcagaaagaagatccaagcattaggaagtttgacagtaacga-gggtttgatt---ttgaattgtagGTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTGATGGAGCGTGATTCACTTCGGATGCGAGATGGAGGGCCATTTATCTTTG
    ||   | | | ||   |  || | |     |||  |||  ||   | |||||  || |  ||||  |    | ||  |||||   | |  | ||   |||||    |  |||  ||||||||||||||||||||||||| || ||| |||| ||||| |||||||| ||| |||| ||| | || |||||| ||||||||||||||||| ||||||
----gtaagtgccacttgcat--agctctttgcactgtggtt--ttcatggactcattaatacaatccttgttgcatgatttttgaatatgattatggaactgattggacttcattccagGTGATAAACAAGACTGACCTTGCTCCTGCAATTGGGGCTGATTTGGCAGTCATGCAGCGGGATGCTCTGCGGATGAGAGATGGAGGGCCATTTGTCTTTG

upper sequence: Vv10s0003g03120.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT2G34470.2 (Arabidopsis thaliana), 3'ss of exon 5
gtatgtgttttctaattctcttcagttatacctgctgcagttacttttggcactcagaaagaagatccaagcattaggaagtttgacagtaacgagggtttgattttg-aattgtagGTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTGATGGAGCGTGATTCACTTCGGATGCGAGATGGAGGGCCATTTATCTTTG
                    | |  ||||    |||||  | ||| ||  |||| |           ||||  |   | ||| ||| || | |    ||    ||||  || || |||||||||||||||||||||||||| |||| ||||| ||||||||  | || |||||  | |||||||| || ||||| ||||||||||||||| ||||||
-------------------gtgcgcttat----gctgccttaactctt--cacttactccttttgatcaagtctatagtagtgtgaaagaatctcttgtggatttttccaactgcagGTGATAAACAAGACTGACCTTGCAGCAGCTGTTGGGGCTGACTTATCGGTCATGGAAAGGGATTCACTACGCATGCGTGATGGAGGGCCATTTGTCTTTG

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|110396928|gb|EC962635.1|EC962635
EST:     ACAAAATTCCTCGGAAAGGAGGCCCAGGCATAACCCAAGCTGATCTCCTA                         GTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTG
genomic: ACAAAATTCCTCGGAAAGGAGGCCCAGGCATAACCCAAGCTGATCTCCTAgtatgtgttt ... tgaattgtagGTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTG
EST: gi|30297699|gb|CB974493.1|CB974493
EST:     ACAAAATTCCTCGGAAAGGAGGCCCAGGCATAACCCAAGCTGATCTCCTA                         GTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTG
genomic: ACAAAATTCCTCGGAAAGGAGGCCCAGGCATAACCCAAGCTGATCTCCTAgtatgtgttt ... tgaattgtagGTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTG
EST: gi|110377199|gb|EC942256.1|EC942256
EST:     ACAAAATTCCTCGGAAAGGAGGCCCAGGCATAACCCAAGCTGATCTCCTA                         GTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTG
genomic: ACAAAATTCCTCGGAAAGGAGGCCCAGGCATAACCCAAGCTGATCTCCTAgtatgtgttt ... tgaattgtagGTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTG
EST: gi|32459190|gb|CD800364.1|CD800364
EST:     ACAAAATTCCTCGGAAAGGAGGCCCAGGCATAACCCAAGCTGATCTCCTA                         GTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTG
genomic: ACAAAATTCCTCGGAAAGGAGGCCCAGGCATAACCCAAGCTGATCTCCTAgtatgtgttt ... tgaattgtagGTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTG
EST: gi|110370143|gb|EC934323.1|EC934323
EST:     ACAAAATTCCTCGGAAAGGAGGCCCAGGCATAACCCAAGCTGATCTCCTA                         GTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTG
genomic: ACAAAATTCCTCGGAAAGGAGGCCCAGGCATAACCCAAGCTGATCTCCTAgtatgtgttt ... tgaattgtagGTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTG
EST: gi|30297767|gb|CB974561.1|CB974561
EST:     ACAAAATTCCTCGGAAAGGAGGCCCAGGCATAACCCAAGCTGATCTCCTA                         GTGATAACCAAGACTGCCCTTGCACCACCAGTTGGAGCTGACTTGGCAGTG
genomic: ACAAAATTCCTCGGAAAGGAGGCCCAGGCATAACCCAAGCTGATCTCCTAgtatgtgttt ... tgaattgtagGTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTG
EST: gi|110389282|gb|EC954107.1|EC954107
EST:     ACAAAATTCCTCGGAAAGGAGGCCCAGGCATAACCCAAGCTGATCTCCTA                         GTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTG
genomic: ACAAAATTCCTCGGAAAGGAGGCCCAGGCATAACCCAAGCTGATCTCCTAgtatgtgttt ... tgaattgtagGTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTG
EST: gi|110695590|gb|EE073783.1|EE073783
EST:     ACAAAATTCCTCGGAAAGGAGGCCCAGGCATAACCCAAGCTGATCTCCTA                         GTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTG
genomic: ACAAAATTCCTCGGAAAGGAGGCCCAGGCATAACCCAAGCTGATCTCCTAgtatgtgttt ... tgaattgtagGTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTG
EST: gi|30297878|gb|CB974672.1|CB974672
EST:     ACAAAATTCCTCGGAAAGGAGGCCCAGGCATAACCCAAGCTGATCTCCTA                         GTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTG
genomic: ACAAAATTCCTCGGAAAGGAGGCCCAGGCATAACCCAAGCTGATCTCCTAgtatgtgttt ... tgaattgtagGTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTG
EST: gi|34320115|gb|CF372869.1|CF372869
EST:     ACAAAATTCCTCGGAAAGGAGGCCCAGGCATAACCCAAGCTGATCTCCTA                         GTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTG
genomic: ACAAAATTCCTCGGAAAGGAGGCCCAGGCATAACCCAAGCTGATCTCCTAgtatgtgttt ... tgaattgtagGTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTG
EST: gi|34363050|gb|CF404635.1|CF404635
EST:     ACAAAATTCCTCGGAAAGGAGGCCCAGGCATAACCCAAGCTGATCTCCTA                         GTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTG
genomic: ACAAAATTCCTCGGAAAGGAGGCCCAGGCATAACCCAAGCTGATCTCCTAgtatgtgttt ... tgaattgtagGTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTG
EST: gi|22014004|gb|BQ799038.1|BQ799038
EST:     ACAAAATTCCTCGGAAAGGAGGCCCAGGCATAACCCAAGCTGATCTCCTA                         GTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTG
genomic: ACAAAATTCCTCGGAAAGGAGGCCCAGGCATAACCCAAGCTGATCTCCTAgtatgtgttt ... tgaattgtagGTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTG
EST: gi|22012463|gb|BQ797497.1|BQ797497
EST:     ACAAAATTCCTCGGAAAGGAGGCCCAGGCATAACCCAAGCTGATCTCCTA                         GTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTG
genomic: ACAAAATTCCTCGGAAAGGAGGCCCAGGCATAACCCAAGCTGATCTCCTAgtatgtgttt ... tgaattgtagGTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTG
EST: gi|110703836|gb|EE081029.1|EE081029
EST:     ACAAAATTCCTCGGAAAGGAGGCCCAGGCATAACCCAAGCTGATCTCCTA                         GTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTG
genomic: ACAAAATTCCTCGGAAAGGAGGCCCAGGCATAACCCAAGCTGATCTCCTAgtatgtgttt ... tgaattgtagGTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTG
EST: gi|22015218|gb|BQ800252.1|BQ800252
EST:     ACAAAATTCCTCGGAAAGGAGGCCCAGGCATAACCCAAGCTGATCTCCTA                         GTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTG
genomic: ACAAAATTCCTCGGAAAGGAGGCCCAGGCATAACCCAAGCTGATCTCCTAgtatgtgttt ... tgaattgtagGTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagatccaagcattaggaagtttgacagtaacgagggtttgattttgaattgtagGTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTGATGGAGCGTGATTCACTTCGGATGCGAGATGGAGGGCCATTTATCTTTG
                                     tttgattttgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgttttctaattctcttcagttatacctgctgcagttacttttggcactcagaaagaagatccaagcattaggaagtttgacagtaacgagggtttgattttgaattgtagGTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTGATGGAGCGTGATTCACTTCGGATGCGAGATGGAGGGCCATTTATCTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG