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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGATCTTCCTGTTGTGATATCATGTGCTAGTCTTGCCTTGGCAGATGCTGGGATTATGATGTATGACCTGGTTGCCTCAGTTTCTGTGgtatgcgcacacatgctgatgcacatcagttctcactttccttatttgagataagttatatggagtaagctccatatgcatataaacagtcattcaccaa...

Basic information

species Vitis vinifera
transcript Vv06s0004g02660.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g02660.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os03g62720.2 (Oryza sativa), 5'ss of exon 5
GTGATCTTCCTGTTGTGATATCATGTGCTAGTCTTGCCTTGGCAGATGCTGGGATTATGATGTATGACCTGGTTGCCTCAGTTTCTGTGgtatgcgcacacatgctgatgcacatcagttctcactttccttatttgagataagttatatggagtaagctccatatgcatataaacagtcattcaccaa
||||||||||  |  | || || |||||||||||||| ||||| |||||||| || |||||||||||||| ||| | ||||| |||||||||||  | ||||| ||      |     ||  |  | |   || || | |   |  || || | |      || || ||  |   |  |  ||   || 
GTGATCTTCCCATCATTATTTCTTGTGCTAGTCTTGCGTTGGCTGATGCTGGAATCATGATGTATGACCTTGTTACATCAGTATCTGTGgtatggcctcacattct------ctctcctttaccatgtgtgtacttaaaactcgacatttgaatttgaagaca-atccacctgtgc--ttctttgtcag

upper sequence: Vv06s0004g02660.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os03g62720.3 (Oryza sativa), 5'ss of exon 4
-----------GTGATCTTCCTGTTGTGATATCATGTGCTAGTCTTGCCTTGGCAGATGCTGGGATTATGATGTATGACCTGGTTGCCTCAGTTTCTGTGgtatgcgcacacatgctgatgcacatcagttctcactttccttatttgagataagttatatggagtaagctccatatgcatataaacagtcattcaccaa
           ||||||||||  |  | || || |||||||||||||| ||||| |||||||| || |||||||||||||| ||| | ||||| |||||||||||  | ||||| ||      |     ||  |  | |   || || | |   |  || || | |      || || ||  |   |  |  ||   || 
TTTGATTTCAGGTGATCTTCCCATCATTATTTCTTGTGCTAGTCTTGCGTTGGCTGATGCTGGAATCATGATGTATGACCTTGTTACATCAGTATCTGTGgtatggcctcacattct------ctctcctttaccatgtgtgtacttaaaactcgacatttgaatttgaagaca-atccacctgtgc--ttctttgtcag

upper sequence: Vv06s0004g02660.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os08g02360.1 (Oryza sativa), 5'ss of exon 5
GTGATCTTCCTGTTGTGATATCATGTGCTAGTCTTGCCTTGGCAGATGCTGGGATTATGATGTATGACCTGGTTGCCTCAGTTTCTGTGgtatgcgcacacatgctgat-gcacatcagttctcactttccttatttgagataagttatatggagtaagctccatatgcatataaacagtcattcaccaa
||||||||||  |  | || || |||||||||||||| ||||| ||||| || || ||||| |||||||| ||| | || || |||||||||||  ||||||| ||    ||    |||| |  ||  |    |  |  || |  | |  | ||  |   ||||        |     ||||        
GTGATCTTCCCATCATTATTTCTTGTGCTAGTCTTGCGTTGGCTGATGCCGGAATCATGATATATGACCTTGTTACATCGGTATCTGTGgtatggccacacattctctccgctttacagtgcgtacacttaaaaactc-gacatttgaatttgaagacaatccactctttgcttctttgtcag-------

upper sequence: Vv06s0004g02660.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G158789_T01 (Zea mays), 5'ss of exon 5
GTGATCTTCCTGTTGTGATATCATGTGCTAGTCTTGCCTTGGCAGATGCTGGGATTATGATGTATGACCTGGTTGCCTCAGTTTCTGTGgtatgcgcacacatgctgatgcacatcagttctcactttccttatttgagataagttatatggagtaagctccat-atg--catataaacagtcattcaccaa
||||||||||  |  | |||||||| ||||||||||| |||||||||||||| || |||||||||||||| ||| | || || || ||||||||| | | ||||||| | |   ||  |  | |||| |   |  | |   |     |||    ||||||  || |||  || ||      || ||  ||| 
GTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTGGAATCATGATGTATGACCTTGTTACATCTGTATCCGTGgtatgccccc-catgctgtttctgctctatgat-acttgc---acctaaaccatcagttatcagttaagcttgatgatgaccagattttacttccttgcccag

upper sequence: Vv06s0004g02660.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA11G20420.1 (Glycine max), 5'ss of exon 5
GTGATCTTCCTGTTGTGATATCATGTGCTAGTCTTGCCTTGGCAGATGCTGGGATTATGATGTATGACCTGGTTGCCTCAGTTTCTGTGgtatgcg-cacacatgctgatgcacatcagttctcactttccttatttgagataagttatatggagtaagctccatatgcat-ataaacagtcattcaccaa
||||||| || ||||| |||||||||||||| |||||| | ||||||||||| || |||||||||||  | |||||||||||||||||||||||   |   |   |   |||||   | |  |||||    |   |  |  |   || || || | | | ||  | |     ||    |||   |    | 
GTGATCTCCCAGTTGTCATATCATGTGCTAGCCTTGCCCTTGCAGATGCTGGAATAATGATGTATGATATAGTTGCCTCAGTTTCTGTGgtatggatcttgctcacatttgcactctaatg-tcactaatatatatgtacttgctttgtagggtgcacgatctgtttaagccattttaagtttattttga-

upper sequence: Vv06s0004g02660.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA12G08170.1 (Glycine max), 5'ss of exon 5
GTGATCTTCCTGTTGTGATATCATGTGCTAGTCTTGCCTTGGCAGATGCTGGGATTATGATGTATGACCTGGTTGCCTCAGTTTCTGTGgtatgcg-cacacatgctgatgcacatcagttctcactttccttatttgagataagttatatggagtaagctccatatgcatataaacagtcattcaccaa-
||||||| || ||||| ||||||||||| || |||||| | |||||||| || || ||||||||||| || |||||||||||||||||||||||   |   |   |   |||||   | |  |||||     | |    | |  ||   ||| | ||| ||   | | |   |  |   | |||    || 
GTGATCTCCCAGTTGTCATATCATGTGCAAGCCTTGCCCTTGCAGATGCGGGAATAATGATGTATGATCTTGTTGCCTCAGTTTCTGTGgtatgaatcttgctcacatttgcactctaatg-tcactaaatatgtacttgctttgtaggatgca-taatctgtttctaccattttaagtttattttgaaat

upper sequence: Vv06s0004g02660.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT4G27490.1 (Arabidopsis thaliana), 5'ss of exon 6
GTGATCTTCCTGTTGTGATATCATGTGCTAGTCTTGCCTTGGCAGATGCTGGGATTATGATGTATGACCTGGTTGCCTCAGTTTCTGTGgtatgcgcacac----------atgctgatgcacatcagttctcactt-tccttatttgagataagttatatggagtaagctccatatgcatataaacagtcattcaccaa--------------------------------------------------------------------------------
|||| ||  ||||| |||||||||||||||||||||| || || ||||| || |||||||||||||||||  |  |  | ||||| |||||||| | |                 |||| |   |  ||| || ||| |  ||||| |   ||||| |    ||        ||||     | | | |    | |||||                                                                                 
GTGACCTCTCTGTTTTGATATCATGTGCTAGTCTTGCTTTAGCTGATGCCGGAATTATGATGTATGACCTTATCACAGCTGTTTCAGTGgtatgtgtatgttacaatagttgcattgattcctctgcgttatctcttatgtttattagcattaagtgaagaagaaagtaacacatacattgacatatacaagtgcaccatagtctgagacatgtaaaacgtatagatatctgttaattctttattttgatacactgaaattatgcctgcaattttcgaag

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|29783231|gb|CB349270.2|CB349270
EST:     TGGCAGATGCTGGGATTATGATGTATGACCTGGTTGCCTCAGTTTCTGTG                         TCTTGTCTTGGTAAGAACCTTGTCATCGACCCTATTTTGGAAGAGGAAAGC
genomic: TGGCAGATGCTGGGATTATGATGTATGACCTGGTTGCCTCAGTTTCTGTGgtatgcgcac ... ttgtgcccagTCTTGTCTTGGTAAGAACCTTGTCATCGACCCTATTTTGGAAGAGGAAAGC
EST: gi|110726802|gb|EE102900.1|EE102900
EST:     TGGCAGATGCTGGGATTATGATGTATGACCTGGTTGCCTCAGTTTCTGTG                         TCTTGTCTTGGTAAGAACCTTGTCATCGACCCTATTTTGGAAGAGGAAAGC
genomic: TGGCAGATGCTGGGATTATGATGTATGACCTGGTTGCCTCAGTTTCTGTGgtatgcgcac ... ttgtgcccagTCTTGTCTTGGTAAGAACCTTGTCATCGACCCTATTTTGGAAGAGGAAAGC
EST: gi|28970321|gb|CB349354.1|CB349354
EST:     TGGCAGATGCTGGGATTATGATGTATGACCTGGTTGCCTCAGTTTCTGTG                         TCTTGTCTTGGTAAGAACCTTGTCATCGACCCTATTTTGGAAGAGGAAAGC
genomic: TGGCAGATGCTGGGATTATGATGTATGACCTGGTTGCCTCAGTTTCTGTGgtatgcgcac ... ttgtgcccagTCTTGTCTTGGTAAGAACCTTGTCATCGACCCTATTTTGGAAGAGGAAAGC
EST: gi|110428655|gb|EC995132.1|EC995132
EST:     TGGCAGATGCTGGGATTATGATGTATGACCTGGTTGCCTCAGTTTCTGTG                         TCTTGTCTTGGTAAGAACCTTGTCATCGACCCTATTTTGGAAGAGGAAAGC
genomic: TGGCAGATGCTGGGATTATGATGTATGACCTGGTTGCCTCAGTTTCTGTGgtatgcgcac ... ttgtgcccagTCTTGTCTTGGTAAGAACCTTGTCATCGACCCTATTTTGGAAGAGGAAAGC
EST: gi|32459062|gb|CD800236.1|CD800236
EST:     TGGCAGATGCTGGGATTATGATGTATGACCTGGTTGCCTCAGTTTCTGTG                         TCTTGTCTTGGTAAGAACCTTGTCATCGACCCTATTTTGGAAGAGGAAAGC
genomic: TGGCAGATGCTGGGATTATGATGTATGACCTGGTTGCCTCAGTTTCTGTGgtatgcgcac ... ttgtgcccagTCTTGTCTTGGTAAGAACCTTGTCATCGACCCTATTTTGGAAGAGGAAAGC
EST: gi|351026098|gb|FQ428110.1|FQ428110
EST:     TGGCAGACGCTGGGATTATGATGTATGACCTGGTTGCCTCAGTTTCTGTG                         TCTTGTCTTGGTAAGAACCTTGTCATCGACCCTATTTTGGAAGAGGAAAGC
genomic: TGGCAGATGCTGGGATTATGATGTATGACCTGGTTGCCTCAGTTTCTGTGgtatgcgcac ... ttgtgcccagTCTTGTCTTGGTAAGAACCTTGTCATCGACCCTATTTTGGAAGAGGAAAGC
EST: gi|32457906|gb|CD799080.1|CD799080
EST:     TGGCAGATGCTGGGATTATGATGTATGACCTGGTTGCCTCAGTTTCTGTG                         TCTTGTCTTGGTAAGAACCTTGTCATCGACCCTATTTCGGAAGAGGAAAGC
genomic: TGGCAGATGCTGGGATTATGATGTATGACCTGGTTGCCTCAGTTTCTGTGgtatgcgcac ... ttgtgcccagTCTTGTCTTGGTAAGAACCTTGTCATCGACCCTATTTTGGAAGAGGAAAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGATCTTCCTGTTGTGATATCATGTGCTAGTCTTGCCTTGGCAGATGCTGGGATTATGATGTATGACCTGGTTGCCTCAGTTTCTGTGgtatgcgcacacatgctgatgcacatcagttctcactttccttatttgagataagttatatggagtaagctccatatgcatataaacagtcattcaccaa

- - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataaaca