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'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttttatacttcaactgtgtttcttggttcactaggaggttgtaaacttgctattgaatacgtggttctcttcagGCACTTGTAGAGTTCTTTGGTACGCTTTCACGAGAATGGGCTTTGGAGTGCATGAAGGACCTTCTTCTGGTCAATCTAAGAGGCAACCTTCAGATAATTG

Basic information

species Vitis vinifera
transcript Vv13s0067g01290.t01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 18
gtttttatacttcaactgtgtttcttggttcactaggaggttgtaaacttgctattgaatacgtggttctctt---cagGCACTTGTAGAGTTCTTTGGTACGCTTTCACGAGAATGGGCTTTGGAGTGCATGAAGGACCTTCTTCTGGTCAATCTAAGAGGCAACCTTCAGATAATTG
|||| |   ||| |  | || ||  | |            |  |      | |  |  ||         | ||   ||||||||||| ||||||||||| || |||||| |||| ||||||||||||||||||||||||||||| ||||||||||||||||| || ||||| ||  |||
gtttgttatcttaagttatgctttgttgcctgtctattattactggctggggtggtccatttacaccattattgaacagGCACTTGTTGAGTTCTTTGGCACTCTTTCAAGAGAGTGGGCTTTGGAGTGCATGAAGGACCTTCTGCTGGTCAATCTAAGAGGGAATCTTCAAATTGTTG

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 18
gtttttatacttcaactgtgtttcttggttcactaggaggttgtaaacttgctattgaatacgtggttctctt---cagGCACTTGTAGAGTTCTTTGGTACGCTTTCACGAGAATGGGCTTTGGAGTGCATGAAGGACCTTCTTCTGGTCAATCTAAGAGGCAACCTTCAGATAATTG
|||| |   ||| |  | || ||  | |            |  |      | |  |  ||         | ||   ||||||||||| ||||||||||| || |||||| |||| ||||||||||||||||||||||||||||| ||||||||||||||||| || ||||| ||  |||
gtttgttatcttaagttatgctttgttgcctgtctattattactggctggggtggtctatttacaccattattgaacagGCACTTGTTGAGTTCTTTGGCACTCTTTCAAGAGAGTGGGCTTTGGAGTGCATGAAGGACCTTCTGCTGGTCAATCTAAGAGGGAATCTTCAAATTGTTG

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 16
gtttttatacttcaactgtgtttcttggttcactaggaggttgtaaacttgctattgaatacgtggttctcttcagGCACTTGTAGAGTTCTTTGGTACGCTTTCACGAGAATGGGCTTTGGAGTGCATGAAGGACCTTCTTCTGGTCAATCTAAGAGGCAACCTTCAGATAATTG
|||| |    ||||  | ||||  |    |   |  |  ||| |   |||| |  | || |  |   |  |  ||||||||||| ||||||||||| || |||||| | || |||||  | |||||||||||||||||||| ||||| ||||| || || || ||||||||  |||
gtttgtggtgttcagttatgttcttgaaatgtatctgttgtttt---cttgtttattaacaacttccttgca-cagGCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGCATGAAGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTG

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 4
-----------------------------------------gtttttatacttcaactgtgttt-cttggttcactaggaggttgtaaacttgctattga---atacgtggttctctt---cagGCACTTGTAGAGTTCTTTGGTACGCTTTCACGAGAATGGGCTTTGGAGTGCATGAAGGACCTTCTTCTGGTCAATCTAAGAGGCAACCTTCAGATAATTG
                                         ||  ||  ||   |  | |||   |||   | | |   || |  |    ||    ||     ||       |  |||   ||||||||||| ||||||||||| ||  | ||| |||| ||||||||||| |||||||| |||||||| ||||| ||||                        
cagagttgcctgatatcaagcgtgccattgcaaatacccatgtcattgaaccataggtttgtcgacttcagttattttcagatattttttttatgtttagCCCATTAACAACTTCCTTGGACAGGCACTTGTTGAGTTCTTTGGCACATTGTCAAGAGAGTGGGCTTTGGAATGCATGAAAGACCTTCTACTGGTTAATC------------------------

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GRMZM2G352837_T01 (Zea mays), 3'ss of exon 5
gtttttatacttcaactgtgtttcttggttcactaggaggttgtaaacttgctattgaatacgtggttctcttcagGCACTTGTAGAGTTCTTTGGTACGCTTTCACGAGAATGGGCTTTGGAGTGCATGAAGGACCTTCTTCTGGTCAATCTAAGAGGCAACCTTCAGATAATTG
|||| |  ||||||  | |   | |  | |  ||      |  |    |  | ||| |  || |     |   ||| ||||||| ||||||||||| ||  | ||| |||| ||||||||||| |||||||| |||||||| ||||| ||||| || || || ||||||||  |||
gtttgtcgacttcagttat---tttcagatatcttttttttaatgttttgcccattaacaactt--ccttggacagACACTTGTTGAGTTCTTTGGCACATTGTCAAGAGAGTGGGCTTTGGAATGCATGAAAGACCTTCTACTGGTTAATCTGAGGGGAAATCTTCAGATTGTTG

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GRMZM2G591258_T01 (Zea mays), 3'ss of exon 9
----------------gtttttatacttcaactgtgttt-cttggttcactaggaggttgtaaacttgctattgaatacgt----ggttctctt---cagGCACTTGTAGAGTTCTTTGGTACGCTTTCACGAGAATGGGCTTTGGAGTGCATGAAGGACCTTCTTCTGGTCAATCTAAGAGGCAACCTTCAGATAATTG
                ||  ||  ||  ||  | |||   |||   | | |   || |       ||  | ||     | |       |  |||   ||| ||||||| ||||||||||| ||  | ||| |||| ||||||||||| |||||||| |||||||| ||||| ||||| || || || ||||||||  |||
cattgtaaatacccatgtcattgaaccacaggtttgtcgacttcagttattttcagatatctttttttatgttttgcccattaacaacttccttggacagACACTTGTTGAGTTCTTTGGCACATTGTCAAGAGAGTGGGCTTTGGAATGCATGAAAGACCTTCTACTGGTTAATCTGAGGGGAAATCTTCAGATTGTTG

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 17
--------gtttttatacttcaac--tgtgtttcttggttcacta-ggaggttgtaaacttgctattgaatacgtggttctcttcagGCACTTGTAGAGTTCTTTGGTACGCTTTCACGAGAATGGGCTTTGGAGTGCATGAAGGACCTTCTTCTGGTCAATCTAAGAGGCAACCTTCAGATAATTG
        |||    | |||  |   | | | | |||   ||  | |   ||| |||| |   || | | |    |||||| | ||| |||| || || || |||||||| || |||||||||||||| || ||||||||||| || ||  | ||||||||||| ||||||||||| ||||| ||||
gtttgtgtgttccattgcttttataatttatctattgtaacatcatgctagttttaaaatacttagtcattgttcggttct-tgcagTCACTCGTTGAATTTTTTGGTACTCTGTCACGAGAATGGGCATTAGAGTGCATGAAAGATCTATTGCTGGTCAATCTTAGAGGCAACCTACAGATTATTG

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 18
----------------gtttttatacttcaactgtgtttcttggttcac--------taggaggttgtaaacttgctattgaatacgtggttctcttcagGCACTTGTAGAGTTCTTTGGTACGCTTTCACGAGAATGGGCTTTGGAGTGCATGAAGGACCTTCTTCTGGTCAATCTAAGAGGCAACCTTCAGATAATTG
                | |||||  ||      ||||||     || |         |  ||| || |||| |  ||| | | || |||||| | | ||| ||||||||||||| |||||||| || |||  ||||||||| || ||||||||||| ||| | || |||| |||||| || |||||||| ||||| ||||
gtttatgtgctgttctgcttttaatctattttagtgtttaacaattaaaacccattgtgtgagcttttaaaatacctactcattatgtggttgt-tacagTCACTTGTAGAGTTTTTTGGTACACTGTCAAAAGAATGGGCATTAGAGTGCATGAAAGACTTACTGCTGGCCAATCTTAGGGGCAACCTACAGATCATTG

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 17
----------gtttttatacttcaactgtgtttcttggttcacta-ggaggttgtaaacttgctattgaatacgtggttctcttcagGCACTTGTAGAGTTCTTTGGTACGCTTTCACGAGAATGGGCTTTGGAGTGCATGAAGGACCTTCTTCTGGTCAATCTAAGAGGCAACCTTCAGATAATTG
              ||    ||  | | | | | |||   || || |   ||| | || ||  || | | |      |||| | ||| |||| || || || |||||||| || ||| |||||||||| || ||||| ||||| |||||  | ||||||||||| ||||||||||| ||||| ||||
gtttgtgtgatccattgcttttataatttatctattgtaacattatgctagtttttaaattcttagtcattgttcaattct-tgcagTCACTCGTTGAATTTTTTGGTACTCTGTCAAGAGAATGGGCATTAGAGTGTATGAAAGACCTATTGCTGGTCAATCTTAGAGGCAACCTACAGATTATTG

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 18
gtttttatacttcaactg--tgtttcttggttcactaggaggttgtaaacttgctattgaatacgtggttc---tcttcagGCACTTGTAGAGTTCTTTGGTACGCTTTCACGAGAATGGGCTTTGGAGTGCATGAAGGACCTTCTTCTGGTCAATCTAAGAGGCAACCTTCAGATAATTG
  | |||    | ||||   ||||  ||| |  || |   | |  | || |||||    |   |     ||   | | ||||| ||||| ||||| |||||||| |||||  | || |||||  ||||||||||||| || || ||  ||||||| || |||||||||||||||||||| |
-gtattacctctgaactaattgttggttgctaaacaactcgatgttcaagttgctgaatatccctctactcaaatttgcagGCTCTTGTCGAGTTTTTTGGTACTCTTTCTAGCGAGTGGGCAATGGAGTGCATGAAAGATCTCCTGTTGGTCAACCTGAGAGGCAACCTTCAGATAATCG

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 18
-----gtttttatacttcaactgtgtttcttggttcactaggaggttgtaaacttgctattgaatacgtggttc--tcttcagGCACTTGTAGAGTTCTTTGGTACGCTTTCACGAGAATGGGCTTTGGAGTGCATGAAGGACCTTCTTCTGGTCAATCTAAGAGGCAACCTTCAGATAATTG
     |  | |  | |  |  |  |||  |      |||| | |||    || ||| |    || ||   | ||  | | ||||| ||||| ||||| ||||| || |||||  | || |||||| |||||||||||||||| ||  | |||||||| || |||||||| || ||||||||||
gtagtgcctctgaaatatattttggttgttaaacctactaagtggtc---aagttgttgcataacactctgctccatatgcagGCTCTTGTTGAGTTTTTTGGCACTCTTTCTAGCGAGTGGGCTATGGAGTGCATGAAGGATCTGTTGCTGGTCAACCTGAGAGGCAATCTGCAGATAATTG

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|122689653|gb|EC942290.1|EC942290
EST:     TGCCAGATATAAAACGCGTCATTGTGAATACACATGCAATTGAGCCACAG                         GCACTTGTAGAGTTCTTTGGTACGCTTTCACGAGAATGGGCTTTGGAGTGC
genomic: TGCCAGATATAAAACGCGTCATTGTGAATACACATGCAATTGAGCCACAGgtttttatac ... ttctcttcagGCACTTGTAGAGTTCTTTGGTACGCTTTCACGAGAATGGGCTTTGGAGTGC
EST: gi|122690707|gb|EC956547.1|EC956547
EST:     GTGAATACACATGCAATTGAGCCACAG                         GCACTTGTAGAGTTCTTTGGTACGCTTTCACGAGAATGGGCTTTGGAGTGC
genomic: GTGAATACACATGCAATTGAGCCACAGgtttttatac ... ttctcttcagGCACTTGTAGAGTTCTTTGGTACGCTTTCACGAGAATGGGCTTTGGAGTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttggttcactaggaggttgtaaacttgctattgaatacgtggttctcttcagGCACTTGTAGAGTTCTTTGGTACGCTTTCACGAGAATGGGCTTTGGAGTGCATGAAGGACCTTCTTCTGGTCAATCTAAGAGGCAACCTTCAGATAATTG
                                             ttctcttc  CT-rich tract
                               tattgaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttttatacttcaactgtgtttcttggttcactaggaggttgtaaacttgctattgaatacgtggttctcttcagGCACTTGTAGAGTTCTTTGGTACGCTTTCACGAGAATGGGCTTTGGAGTGCATGAAGGACCTTCTTCTGGTCAATCTAAGAGGCAACCTTCAGATAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG