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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCCAGAAGAGGAGGGCCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAGgtttgttatgatgcaatccctgtgtgttgctgtttaatttttcccatctctctacttaattttttgtggattcagactagaaccccactggaaatggcccaatctaatatatttgtttaatatgcatttgcag

Basic information

species Vitis vinifera
transcript Vv11s0118g00670.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0118g00670.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os02g40880.1 (Oryza sativa), 5'ss of exon 4
GTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCCAGAAGAGGAGGGCCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAGgtttgttatgatgcaatc--cctgtgtgttgctgtttaatttttcccatctctctac-ttaattttttgtggattcagactagaaccccactggaaatggcccaatctaatatatttgtttaatatgcatttgcag
|||||||||||| || |||||||  ||| | ||||||||||||||||| || || || ||||||||||| ||||||||| | |||||||| ||||| |||||  |  ||  |    ||     || |  | |||||||    | | ||      |||   ||| |||| || ||  | |                                                         
GTGGGAGAATAGCTCATGGGGCAAGAAGCTAATTGTCCAGAAGAGGAGAGCGTCACTCAATGACTTTGACAGGTTCAAGGTTATGTTGGCCAAGATCAAGgtcagacatcctattctcaattggtttactcctgtttataactactcactagcttacaccaatgttttctgtatgaacag--------------------------------------------------------

upper sequence: Vv11s0118g00670.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os04g43540.1 (Oryza sativa), 5'ss of exon 4
GTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCCAGAAGAGGAGGGCCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAGgtt-tgttatgatgcaatccctgtgtgttgctgtttaatttttcccatctctctacttaattttttgtggattcagactagaaccccactggaaatggcccaatctaatatatttgtttaatatgcatttgcag
||||||||| || || ||||| |  ||  ||||||||||||||||||| || || || || |||||||| ||||||||| | |||||||| ||||| |||||  |  |  | |  |  | ||  |  | |    || |||       | | |  |   |   | |  |  | || || | | |    |   |                                          
GTGGGAGAACAGCTCATGGGGTAAGAAACTGATTGTCCAGAAGAGGAGAGCATCCCTCAACGACTTTGACAGGTTCAAGGTTATGTTGGCGAAGATCAAGgtgatactccgctctacactct-cgaatagtacctttattgaaggt-tttgttcatacaccctctaat--actctgattggcatatgaacag------------------------------------------

upper sequence: Vv11s0118g00670.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G028883_T01 (Zea mays), 5'ss of exon 4
GTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCCAGAAGAGGAGGGCCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAGgtttgttatgatgcaatccctgtgtgttgctgtttaatttttcccatctctctacttaattttttgtggattcagactagaaccccactggaaatggcccaatctaatatatttgtttaatatgcatttgcag
|||||||||||| || |||||||  ||| ||||||| ||||||||||| || || || ||||||||||| ||||||||| |||||||||| ||||| ||||||||  ||      || |  | ||  |      |||||| ||| ||   ||| |||| ||  |  |  | |   |   |     || | |||  |                                     
GTGGGAGAATAGCTCATGGGGCAAGAAGCTGATTGTTCAGAAGAGGAGAGCATCACTCAATGACTTTGACAGGTTCAAGGTCATGTTGGCGAAGATCAAGgtttggcat------attctagagtaat------taatttatcc-attgttctgcttatttcctaatatactggtat--ggttgtcatttgaacag-------------------------------------

upper sequence: Vv11s0118g00670.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G140116_T01 (Zea mays), 5'ss of exon 4
GTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCCAGAAGAGGAGGGCCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAGgtttgttatgatgcaatccc-tgtgtgttgctgtttaatttttcccatctctcta-cttaattttttgtggattcagactagaaccccactggaaatggcccaatctaatatatttgtttaatatgcatttgcag
||||||||| || || |||||||  ||| ||||||||||||||||||| || || || ||||||||||||||||||||  ||||| |||| |||||||||||  |  |   | |  ||   ||| |  | |   || |   |  | || |  ||  || |   |||  |    |   |   ||||                                                  
GTGGGAGAACAGCTCATGGGGCAAGAAGCTGATTGTCCAGAAGAGGAGAGCATCGCTCAATGACTTTGATAGGTTCAAAGTCATGCTGGCGAAGATTAAGgtcaggaaccttcctgtcaaatgtctagttcctgttgacagtgtctatattgctggctcacactttctttttcttttatgtgaacag------------------------------------------------

upper sequence: Vv11s0118g00670.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G168330_T02 (Zea mays), 5'ss of exon 4
GTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCCAGAAGAGGAGGGCCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAGgtttgttatgatgcaatccctgtgtgttgctgtttaatttttcccatctctctacttaattttttgtggattcagac-tagaaccccactggaaatggcccaatctaatatatttgtttaatatgcatttgcag
|||||| || || || |||||||  ||| ||||||||||||||||||||||  | || | ||||||||| ||||||||| ||||| |||||| ||| |||||  |  |        |||||||       ||| || ||  |     |     ||| | | | |||     ||| || |    ||    || |||  |                                    
GTGGGAAAACAGCTCATGGGGCAAGAAGCTGATTGTCCAGAAGAGGAGGGCTGCGCTCAGTGACTTTGACAGGTTCAAGGTCATGCTGGCAAGGATCAAGgtcaggaacc------tccctgt---caaatgtctagttcctgttggc-----actgagtatattgcttgctcacacctttttcctttatgtaaacag------------------------------------

upper sequence: Vv11s0118g00670.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G163104_T01 (Zea mays), 5'ss of exon 2
-GTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCCAGAAGAGGAGGGCCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAGgtttgttatgatgcaatccctgtgtgttgctgtttaatttttcccatctctctacttaattttttgtggattcagactagaaccccactggaaatggcccaatctaatatatttgtttaatatgcatttgcag
 |||||||||  | || ||||||| || | ||||| || |||||||||| ||  | || ||| ||||||||||||||||  ||||| |||||||||| |||||  |  |     |||||            |||||||||  |     | || | ||  ||| |||||    ||| |||    |   | || |||  |                                    
AGTGGGAGAACGGCTCATGGGGCATAA-GCTGATTTTCTAGAAGAGGAGAGCAGCGCTCAATAACTTTGATAGGTTCAAAGTCATGCTGGCAAAGATCAAGgtcaggaacctcccaatca---------aatgtttaattcctgttggcactgt-ctatattgtttgt----tcacactttttcttta-tgtaaacag------------------------------------

upper sequence: Vv11s0118g00670.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT4G27090.1 (Arabidopsis thaliana), 5'ss of exon 4
GTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCCAGAAGAGGAGGGCCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAGgtttgttatgatgcaatccctgtgtgttgctgtttaatttttcccatctctctacttaattttttgtggattcagactagaaccccactggaaatggcccaatctaatatatttgtttaatatgcatttgcag
||||||||| || || ||||| || ||| | || || |||||  | |||||    ||||| ||||||||||||||||||||||||||||| ||||| |||||  ||               ||||     ||||  || |||   || ||| |  |        |||  |||||    |||||   | ||  |||||     | |  | | |                     
GTGGGAGAAAAGCTCATGGGGTAGGAAGCTTATCGTGCAGAAACGTAGGGCTAACCTTAACGACTTTGATAGGTTCAAGATCATGTTGGCCAAGATCAAGgtcagt---------------gtgttaaattgttagatgtttgaaat-tctgtggtag------tgttcattcatgtcagaactgaaatgttaatgggtttttttgctgtttgcag-----------------

upper sequence: Vv11s0118g00670.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT2G20450.1 (Arabidopsis thaliana), 5'ss of exon 4
GTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCCAGAAGAGGAGGGCCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAGgtttgttatgatgcaatccctgtgtgttgctgtttaatttttcccatctctctacttaattttttgtggattcagactaga--accccactggaaatggcccaatctaatatatttgtttaatatgcatttgcag
||||||||| ||||| ||||| || ||  | ||||| |||||||| || ||  | || ||||| ||||| |||||||||||||||||||| || || |||||| ||| |  |    ||  ||| |    |  | |  ||||   || ||||       | ||| ||   || ||||  ||    | |  ||  |  || ||  |  |    |                       
GTGGGAGAAGAGTTCATGGGGTAGGAAACTTATTGTGCAGAAGAGAAGAGCTGCCCTCAATGATTTTGACAGGTTCAAGATCATGTTGGCCAAAATCAAGgttggtt-tact----tctttgtatccaccaatgttgttttagtcaactct-------actttgtgcaaatgcagatgagttttcactgcttcatttgccctcactttcggt-----------------------

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|30134455|gb|CB919793.1|CB919793
EST:     CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAG                         AGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
genomic: CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAGgtttgttatg ... gcatttgcagAGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
EST: gi|37187972|gb|CF607323.1|CF607323
EST:     CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAG                         AGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
genomic: CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAGgtttgttatg ... gcatttgcagAGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
EST: gi|77580814|gb|DV219318.1|DV219318
EST:     CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAG                         AGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
genomic: CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAGgtttgttatg ... gcatttgcagAGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
EST: gi|110429198|gb|EC995687.1|EC995687
EST:     CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAG                         AGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
genomic: CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAGgtttgttatg ... gcatttgcagAGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
EST: gi|71869827|gb|DT018882.1|DT018882
EST:     CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAG                         AGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
genomic: CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAGgtttgttatg ... gcatttgcagAGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
EST: gi|34319412|gb|CF372166.1|CF372166
EST:     CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAG                         AGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
genomic: CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAGgtttgttatg ... gcatttgcagAGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
EST: gi|27581709|gb|CB004404.1|CB004404
EST:     CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAG                         AGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
genomic: CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAGgtttgttatg ... gcatttgcagAGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
EST: gi|110706377|gb|EE081851.1|EE081851
EST:     CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAG                         AGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
genomic: CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAGgtttgttatg ... gcatttgcagAGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
EST: gi|71865933|gb|DT014988.1|DT014988
EST:     CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAG                         AGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
genomic: CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAGgtttgttatg ... gcatttgcagAGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
EST: gi|34543799|gb|CF512031.1|CF512031
EST:     CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAG                         AGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
genomic: CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAGgtttgttatg ... gcatttgcagAGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
EST: gi|71880453|gb|DT029508.1|DT029508
EST:     CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAG                         AGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
genomic: CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAGgtttgttatg ... gcatttgcagAGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
EST: gi|110361702|gb|EC925195.1|EC925195
EST:     CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAG                         AGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
genomic: CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAGgtttgttatg ... gcatttgcagAGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
EST: gi|77577814|gb|DV217659.1|DV217659
EST:     CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAG                         AGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
genomic: CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAGgtttgttatg ... gcatttgcagAGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
EST: gi|352795130|gb|FQ477240.1|FQ477240
EST:     CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAG                         AGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
genomic: CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAGgtttgttatg ... gcatttgcagAGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
EST: gi|32460994|gb|CD802168.1|CD802168
EST:     CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAG                         AGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
genomic: CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAGgtttgttatg ... gcatttgcagAGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
EST: gi|351017039|gb|FQ424466.1|FQ424466
EST:     CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAG                         AGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
genomic: CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAGgtttgttatg ... gcatttgcagAGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
EST: gi|110428543|gb|EC995018.1|EC995018
EST:     CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAG                         AGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
genomic: CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAGgtttgttatg ... gcatttgcagAGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
EST: gi|110420972|gb|EC987259.1|EC987259
EST:     CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAG                         AGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
genomic: CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAGgtttgttatg ... gcatttgcagAGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
EST: gi|110424520|gb|EC990883.1|EC990883
EST:     CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAG                         AGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
genomic: CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAGgtttgttatg ... gcatttgcagAGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
EST: gi|110714507|gb|EE091492.1|EE091492
EST:     CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAG                         AGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA
genomic: CCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAGgtttgttatg ... gcatttgcagAGGGGTGGAGTGATCAGGCAAGAGCTGGCAAAGCTGAAAAAACAGACTGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGGAGAATAGTTCCTGGGGCAGAAAGTTGATTGTCCAGAAGAGGAGGGCCTCTCTTAATGACTTTGATAGGTTCAAGATCATGTTGGCAAAGATTAAGgtttgttatgatgcaatccctgtgtgttgctgtttaatttttcccatctctctacttaattttttgtggattcagactagaaccccactggaaatggcccaatctaatatatttgtttaatatgcatttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG