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'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttttgtaatcgtgccttgatatatccatatgcaaagttgttccttcatgtggataacaaatttcctttttctattttggctacctaaatgttattccagTACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATG

Basic information

species Vitis vinifera
transcript Vv15s0021g02230.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os04g46620.1 (Oryza sativa), 3'ss of exon 10
gttttgtaatcgtgccttgatatatccatatgca--aagttgttccttcatgtggataacaaatttcctttttctatt-ttggctacctaaatgttattccagTACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATG
   | ||  | |||  || || | |  ||||| |  | |||| |  ||| ||   |       |     |  | |||   ||   |    ||| | ||| |||||||| || |||||||| ||||||||||| |||||||| || || || ||  ||||||||||||||||||| |||||||||||||||
---tggtgtttgtgtgttaatctttgtatatgtatgatgttgatgattcctggctactgtctttaaatctgctttatgactgttcaatggaatatcatttcagTACTTCGTTGAGGCTGGAGCAATTGCTGTAAGGCGTGTGCGTAAGGAGGATTTGCGCCATGTTGCCAAGGCTACTGGTGCAACTATG

upper sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G110626_T01 (Zea mays), 3'ss of exon 10
---------------------------------------------------gttttgtaatcgtgccttgatatatccatatgcaaagttgttcc-----ttcatgtggataacaa--atttcctttttctattttggctacctaaatgttattccagTACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATG
                                                     | | |        |||||| |  ||||      |  ||| |       ||||   ||| ||    |||   |   | | || | |   | |  |   |||| ||||||||||| |||||||| || ||||| || |||||||| || || || ||  |||||||||||||||| || |||||||||||||||
gtatgtttttcatcattcaagcagaaagtgattctgatgatgtccttttaacatctattgagaactcttgatcttcccatgctagtatctgtacaggcaactcatcctgatgactgtcattgaatcactttgttattgtgtcatggaacatatttcagTACTTTGTTGAGGCTGGAGCTATTGCAGTAAGGCGTGTGCGCAAGGAAGATTTGCGCCATGTTGCCAAAGCCACTGGTGCAACTATG

upper sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G039263_T01 (Zea mays), 3'ss of exon 10
----gttttgtaatcgtgccttgata-tatccatatgcaaagttgttccttcatgtggataacaaatttcctttttctattttggctacctaaatgttattccagTACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATG
    |   | | ||| | || || || |||   ||   |||  |  ||||  |||    | ||  | |  ||   | |||| || |||   ||   || || ||||||||||| |||||||| || ||||| || |||||||| || || || ||  |||| ||||||||||| || |||||||||||||||
attaggactttgatctttccgtgctaatatttgtacagaaatctcatcctg-atgactgtcactgaatcactccat-tattgtg-ctatgcaa-catt-tttcagTACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG

upper sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA05G29870.1 (Glycine max), 3'ss of exon 10
gttttgtaatcgtgcctt---gatatatccatatgcaaagttgttccttcatgtggataacaaatttcctttttctattttggctacctaaatgttattccagTACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATG
 ||||||  |  ||  ||   |||||   | | | |  | |  |  | | |   |  | |  |||||     || | || || |||  ||  | || || ||||||||||| |||||||||||||||||||| || ||||| |||||||| ||||||||||||||||||||||| |||||||||||  ||
attttgtggttctgtgtttaagatatgctcttttactgattaatggcataaaaag--tcatgaatttatgcatttttttctgactatttat-tcttgtttcagTACTTTGTTGAGGCTGGGGCAATTGCTGTAAGACGTGTGCGGAAAGAGGACATGCGCCATGTTGCCAAGGCTACTGGTGCAACATTG

upper sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA08G12970.1 (Glycine max), 3'ss of exon 10
gttttgtaatcgtgcctt-gatatatccatatgcaaagttgttccttcatgtggataacaaatttcctttttctattttggctacctaaatgttattccagTACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATG
 ||||||  | |||  |  |||| ||     |  |  | ||              | |  |||||     || | || || |||  ||| | || || ||||||||||| |||||||||||||||||||| || ||||| |||||||| ||||||||||||||||||||||| |||||||||||  ||
-ttttgtggttgtgtttaagatacatgttcttttactgatgaatgacataaaaagtcatgaatttatgcattttgttctgactatttaattcttgtttcagTACTTTGTTGAGGCTGGGGCAATTGCTGTAAGACGTGTGCGGAAAGAGGACATGCGCCATGTTGCCAAGGCTACTGGTGCAACATTG

upper sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT3G20050.1 (Arabidopsis thaliana), 3'ss of exon 10
--------------------gttttgtaatcgtgccttgatatatccatatgcaaagtt-----gttccttcatgtggataacaaattt-cctttttctattttggctac-ctaaatgttattccagTACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATG
                     |||    |||||      |||  |   | |   ||||      |||   |   ||  ||      ||  || |  |  ||| |   | | ||   | ||||| ||||||||||| ||||| || || |||||||| |||||||| || ||||| |||||||| |||||||||||||| || || || ||| ||
gtgagaatgaaaaccaatgattttctctatcgtttacacataacttagtttttgaagtattcaagtttagttgcgtttatgtttggttcaccgtaatggattctcatttctcttgtttttatttcagTACTTTGTAGAGGCAGGAGCTATTGCTGTTAGGCGTGTGCGCAAAGAAGACATGCGTCATGTTGCCAAGGCGACAGGAGCGACTCTG

upper sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: EFJ12438 (Selaginella moellendorffii), 3'ss of exon 10
gttttgtaatcgtgccttgatatatccatatgcaaagttgttccttcatgtggataacaaatttcctttttctattttggctacctaaatgttattccagTACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATG
                                                | ||| | |   |||  |||||   |    | |||   |  ||| ||  ||||| ||||| || || || ||||| |||||  | ||||||||||| || ||| |||| ||||| ||||||||||||||||| || |||
-----------------------------------------------gtatggctcagcgattctcttttgaaacga-gactaaggatctgtgatctcagTATTTTGTAGAAGCAGGAGCAATAGCTGTACGCCGTGTTCGGAAGGAGGACCTGCGGCATGTGGCCAAGGCAACTGGTGCTACAATG

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|110719721|gb|EE095097.1|EE095097
EST:     GAGCCAATGTTGTTTTAACTACAAAAGGGATTGATGACATGGCACTTAAG                         TACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGACGAC
genomic: GAGCCAATGTTGTTCTAACTACAAAAGGGATTGATGACATGGCACTTAAGgcaagtttct ... gttattccagTACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGAC
EST: gi|26264285|gb|CA815348.1|CA815348
EST:     GAGCCAATGTTGTTCTAACTACAAAAGGGATTGATGACATGGCACTTAAG                         TACTTTGTGGTGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGACGAC
genomic: GAGCCAATGTTGTTCTAACTACAAAAGGGATTGATGACATGGCACTTAAGgcaagtttct ... gttattccagTACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGAC
EST: gi|351037610|gb|FQ462593.1|FQ462593
EST:     GAGCCAATGTTGTTCTAACTACAAAAGGGATTGATGACATGGCACTTAAG                         TACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGACGAC
genomic: GAGCCAATGTTGTTCTAACTACAAAAGGGATTGATGACATGGCACTTAAGgcaagtttct ... gttattccagTACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGAC
EST: gi|110701345|gb|EE078813.1|EE078813
EST:     AATGTTGTTTTAACTACAAAAGGGATTGATGACATGGCACTTAAG                         TACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGACGAC
genomic: AATGTTGTTCTAACTACAAAAGGGATTGATGACATGGCACTTAAGgcaagtttct ... gttattccagTACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGAC
EST: gi|351017726|gb|FQ436079.1|FQ436079
EST:     GAGCCAATGTTGTTCTAACTACAAAAGGGATTGATGACATGGCACTTAAG                         TACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGACGAC
genomic: GAGCCAATGTTGTTCTAACTACAAAAGGGATTGATGACATGGCACTTAAGgcaagtttct ... gttattccagTACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGAC
EST: gi|37187670|gb|CF607023.1|CF607023
EST:     GAGCCAATGTTGTTCTAACTACAAAAGGGATTGATGACATGGCACTTAAG                         TACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGACGAC
genomic: GAGCCAATGTTGTTCTAACTACAAAAGGGATTGATGACATGGCACTTAAGgcaagtttct ... gttattccagTACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGAC
EST: gi|33403784|gb|CF209411.1|CF209411
EST:     TGTTGTTCTAACTA-AAAAGGGATTGATGACATGGCACTTAAG                         TACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGACGAC
genomic: TGTTGTTCTAACTACAAAAGGGATTGATGACATGGCACTTAAGgcaagtttct ... gttattccagTACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGAC
EST: gi|71882935|gb|DT031990.1|DT031990
EST:     GAGCCAATGTTGTTCTAACTACAAAAGGGATTGATGACATGGCACTTAAG                         TACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGACGAC
genomic: GAGCCAATGTTGTTCTAACTACAAAAGGGATTGATGACATGGCACTTAAGgcaagtttct ... gttattccagTACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGAC
EST: gi|30322269|gb|CD005531.1|CD005531
EST:     GAGCCAATGTTGTTCTAACTACAAAAGGGATTGATGACATGGCACTTAAG                         TACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGACGAC
genomic: GAGCCAATGTTGTTCTAACTACAAAAGGGATTGATGACATGGCACTTAAGgcaagtttct ... gttattccagTACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGAC
EST: gi|110688105|gb|EE066273.1|EE066273
EST:     GAGCCAATGTTGTTCTAACTACAAAAGGGATTGATGACATGGCACTTAAG                         TACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGACGAC
genomic: GAGCCAATGTTGTTCTAACTACAAAAGGGATTGATGACATGGCACTTAAGgcaagtttct ... gttattccagTACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGAC
EST: gi|351048864|gb|FQ431529.1|FQ431529
EST:     GAGCCAATGTTGTTCTAACTACAAAAGGGATTGATGACATGGCACTTAAG                         TACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGACGAC
genomic: GAGCCAATGTTGTTCTAACTACAAAAGGGATTGATGACATGGCACTTAAGgcaagtttct ... gttattccagTACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgtggataacaaatttcctttttctattttggctacctaaatgttattccagTACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATG
                                     acctaaa  putative branch site (score: 3)
                                              ttattcc  putative PPT
                     tttttctatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttgtaatcgtgccttgatatatccatatgcaaagttgttccttcatgtggataacaaatttcctttttctattttggctacctaaatgttattccagTACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - tgccttg
- - - - - - - - - - - - -ccatatg
- - - - - - - - - - - - - - - - - - - - - - - catgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - -ataacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acctaaa