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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttgatgtctatattttaaattattttcatatttatttctgggcatatgcttggagataatggtgcgatggggcttctgacacttgagtcctttgcagATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGGGTTCTTCATCGAGATTTGAAGCCCCAGAACTTACTCATAGATCGTCGTA

Basic information

species Vitis vinifera
transcript Vv15s0045g00310.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g02680.1 (Oryza sativa), 3'ss of exon 2
tttttgatgtctatattttaaattattttcatatttatttctgggcatatgcttggagataatggt-gcgatggggcttctgacacttgagtccttt--gcagATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGGGTTCTTCATCGAGATTTGAAGCCCCAGAACTTACTCATAGATCGTCGTA
       |||||| |||     ||   |||||  ||    | |    | |  | |   ||  |||| ||     ||  | ||||  ||   | ||||   |||   |  ||  ||||||| ||||| ||  ||||||| |||||||||||||| |||||||||||||||||||| || ||||| ||| | |||||||| ||||
-aaaatgtgtctacattcctg-ttgcattcatgcttgac-cagaaagtgtattagtttattgtggttgcatcttggaatgtgactgttttcttctttctccagTCATATCTCTATCAGATACTCCGCGGCGTTGCTTACTGTCATTCTCATAGAGTTCTTCATCGAGATTTGAAACCTCAGAATTTATTGATAGATCGGCGTA

upper sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g01850.1 (Oryza sativa), 3'ss of exon 4
tttttgatgtctatattttaaattattttcatatttatttctgggcatatgcttggagataatggt-gcgatggggcttctgacacttgagtccttt--gcagATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGGGTTCTTCATCGAGATTTGAAGCCCCAGAACTTACTCATAGATCGTCGTA
   |   |||||| |||     ||   |||||  ||    | |    | |  | |   ||  |||| ||     ||  | ||||  ||   | ||||   |||   |  ||  ||||||| ||||| ||  ||||||| |||||||||||||| |||||||||||||||||||| || ||||| ||| | |||||||| ||||
-aatatgtgtctaaattcctg-ttgcattcatgcttgac-cagaaagtgtattagtttattgtggttgcatcttggaatgtgactgttttcttctttcgccagTCATATCTCTATCAGATACTCCGCGGCGTTGCTTACTGTCATTCTCATAGAGTTCTTCATCGAGATTTGAAACCTCAGAATTTATTGATAGATCGGCGTA

upper sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g03060.1 (Oryza sativa), 3'ss of exon 2
----------------------------------------------------------------tttttgatgtctatattttaaattattttcatatttatttctgggcatatgcttggagataatggtgcgatggggcttctgacacttgagtcc-tttgcagATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGGGTTCTTCATCGAGATTTGAAGCCCCAGAACTTACTCATAGATCGTCGTA
                                                                  || | ||    | |   |     |   |||   |     |  |   ||| ||   | | |    |  |  | | | ||| |  ||| | |  | |||||  ||||||  | ||||||||||| || ||||| || || || || ||  | ||||| || ||||||||||||||||||||| | || |||||||| ||||
gtaagatgttgaaactaacatcctcttttcattgatgcaagtatcacgccatttagtgatagtaacttcgctgaaagtgtgggatgagctagccattgcttccattttgtgcatggtttatgttgaaacgggaaatgtgatgctgtcctttgcgcctgtgtgcagTCGTTCCTCTACCAGATTCTCCGGGGCATTGCGTACTGCCACTCGCACCGTGTTCTCCACCGAGATTTGAAGCCCCAGAACCTGCTGATAGATCGGCGTA

upper sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G143213_T02 (Zea mays), 3'ss of exon 3
-tttttgatgtctatattttaaattattttcat--atttatttctgggc-atatgcttggagata-atggtgcgatggggcttctgacacttgagtcctttgcagATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGGGTTCTTCATCGAGATTTGAAGCCCCAGAACTTACTCATAGATCGTCGTA
 | ||||   |   |  |||  ||| | |  ||  |        ||    |  ||| ||  |||  ||  ||  ||| | ||  |     ||   |  | | |||   | |||  | ||||| ||||||||  |||| || || ||||||||||| |||||||| ||||||||||| || ||||||||  | |||||||| ||||
ttatttgcctttcctcatttccattgtatctattaaccagaaaatgaatgaggtgcctgtggatgcattttgaaatgtgactgtt-----ttctttgttctccagTCATACCTCTACCAGATACTCCGTGGCGTTGCGTACTGCCATTCTCATAGAGTTCTTCACCGAGATTTGAAACCTCAGAACTTGTTGATAGATCGGCGTA

upper sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G008327_T01 (Zea mays), 3'ss of exon 3
----tttttgatgtctatattttaaattattttcatatttatttctgggcatatgcttggagata-atggtgcgatggggcttctgacacttgagtcctttgcagATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGGGTTCTTCATCGAGATTTGAAGCCCCAGAACTTACTCATAGATCGTCGTA
    ||  | || || ||  | |    ||   | | | | | |   | |||  ||||||  | |  ||  ||  |||   ||  |  |   |      | | |||   | |||  | ||||| ||||  ||| |||| || || ||||||||||| |||||||||||||| ||||| || || |||||| | |||||||| || |
ccctttcctcatttccattatatctcataacctgaaaatgaatgaggtgcaggtgcttgtgggtgcattctgaaatgtaactattttcttct-----ttctccagTCATACCTCTACCAGATACTCCACGGTGTTGCGTACTGCCATTCTCATAGAGTTCTTCATCGAGACTTGAAACCTCAAAACTTATTGATAGATCGGCGCA

upper sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G14390.1 (Glycine max), 3'ss of exon 3
tttttgatgtctatattttaaattattttcatatttatttctgggcatatgcttggagataatggtgcgatggggcttctgacacttga--gtccttt--gcagATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGGGTTCTTCATCGAGATTTGAAGCCCCAGAACTTACTCATAGATCGTCGTA
| | |  |||| |   || | || |     ||  | ||||  | | | || |    || || |   |   |     ||      ||| |   ||||||  ||||||||||||  |||| |||||| |||| |||||||| |||||||| ||||| |||||||||||||| ||||| || ||||| ||  | |||||||| ||||
tctattttgtcaagggtt-atataagggagatgctaattttggtgaaaatacc---agttagtttggatttaaaatttgaattccttaatgatcctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGAGTTCTTCATCGAGACTTGAAACCACAGAATTTGTTGATAGATCGCCGTA

upper sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G03470.1 (Glycine max), 3'ss of exon 3
tttttgatgtctatattttaaattattttcatatttatttctgggcatatgcttggagataatggtgcga--tggggcttctgacacttgagtcctttgcagATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGGGTTCTTCATCGAGATTTGAAGCCCCAGAACTTACTCATAGATCGTCGTA
||| |  |||| ||   ||| ||||     ||  | ||||  | | | || |  |    |   | |   |  |  |  ||||   | |       | |||||||||||||  |||| |||||| |||| |||||||| |||||||| ||||| |||||||||||||| ||||| || ||||| ||  | |||||||| ||||
tttattttgtc-atgggttatattagggagatgctaattttggtgaaaataccagttagtttggatttaaattttgaattctt-taatgatcctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGAGTTCTTCATCGAGACTTGAAACCACAGAATTTGTTGATAGATCGCCGTA

upper sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G25320.1 (Glycine max), 3'ss of exon 2
tttttgatgtc-tatattttaaattattttcatatttatttctgggcatatgcttggag-ataatggtgcgatggggcttctgacacttgagtcctttgcagATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGGGTTCTTCATCGAGATTTGAAGCCCCAGAACTTACTCATAGATCGTCGTA
|      | || |  ||  | ||||   |   | ||||||| |     |    |   |  |  |||     ||     || | | | |   |   | |||||||||||||| | || |||||| |||| ||||| || |||||||| ||||| |||||||||||||| || || || ||||| ||  | ||||||||  | |
tccaccttatcatgcatcgttaattgaatatgt-tttattttttattgtggtttcaaaacaagatgagctaattaaaatttttaaa-tgatgctttctgcagATGTTCCTGTACCAAATTCTCTGTGGCATTGCATACTGTCATTCACATAGAGTTCTTCATCGAGACTTAAAACCACAGAATTTGTTGATAGATCGCAGCA

upper sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G08330.1 (Glycine max), 3'ss of exon 3
tttttgatgtctat--attttaaattattttcatatttatttctgggcatatgcttggagataatggtgcgatggggcttctgacacttgagtcctttgcagATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGGGTTCTTCATCGAGATTTGAAGCCCCAGAACTTACTCATAGATCGTCGTA
||     |   |||  ||  | ||||   | ||| ||||||| |       |      | |  |||     ||     || | | | |   |   | |||||||||||||| | || |||||| |||| || ||||| |||||||| | ||| |||||||||||||| || || || ||||| ||  | ||||||||  | |
ttccaccttattatggatcgttaattgaatacat-tttatttttatcgtggtttcaaaacaagatgagctaatttaaatttttaaa-tgatgctttctgcagATGTTCCTGTACCAAATTCTCTGTGGCATCGCTTACTGTCATTCACGTAGAGTTCTTCATCGAGACTTAAAACCACAGAATTTGTTGATAGATCGCAGCA

upper sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G48750.1 (Arabidopsis thaliana), 3'ss of exon 4
-tttttgatgtctatattttaaattattttcatatttatttctgggcatatgcttggagataatggtgcgatggggcttctgacacttgagtcctttgcagATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGGGTTCTTCATCGAGATTTGAAGCCCCAGAACTTACTCATAGATCGTCGTA
 |   || |    |  |||     |  ||| |||| | |   |   |  |    |  | ||||  |       | |||  | |  |   |    ||| ||||  |  ||  | |||||||||||||| ||||| ||||| || |||||||||||||| ||||| ||| ||||||| ||||| ||  | || ||||| || |
gtgagtgctaagaaactttaggcattgttttatatatgtgcttaaactcaatactcaatataa--gctgatcagagctgttcatccacta----ttttcagACATATCTTTACCAGATTCTCCGTGGAATTGCGTATTGCCACTCTCATAGGGTTCTCCATCGTGATCTGAAGCCACAGAATTTGTTGATTGATCGCCGCA

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|30132539|gb|CB917878.1|CB917878
EST:     AGCACATGGATTCATCTCCGGATTTTGCCAAAGATTTACGTCTGATAAAG                         ATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGG
genomic: AGCACATGGATTCATCTCCGGATTTTGCCAAAGATTTACGTCTGATAAAGgtgactctgc ... tcctttgcagATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGG
EST: gi|30128118|gb|CB913457.1|CB913457
EST:     AGCACATGGATTCATCTCCGGATTTTGCCAGAGATTTACGTCTGATATAG                         ATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATACG
genomic: AGCACATGGATTCATCTCCGGATTTTGCCAAAGATTTACGTCTGATAAAGgtgactctgc ... tcctttgcagATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGG
EST: gi|110732023|gb|EE106947.1|EE106947
EST:     AGCACATGGATTCATCTCCGGATTTTGCCAAAGATTTACGTCTGATAAAG                         ATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGG
genomic: AGCACATGGATTCATCTCCGGATTTTGCCAAAGATTTACGTCTGATAAAGgtgactctgc ... tcctttgcagATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGG
EST: gi|71875892|gb|DT024947.1|DT024947
EST:     AGCACATGGATTCATCTCCGGATTTTGCCAAAGATTTACGTCTGATAAAG                         ATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGG
genomic: AGCACATGGATTCATCTCCGGATTTTGCCAAAGATTTACGTCTGATAAAGgtgactctgc ... tcctttgcagATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGG
EST: gi|30127193|gb|CB912532.1|CB912532
EST:     AGCACATGGATTCATCTCCGGATTTTGCCAAAGATTTACGTCTGATAAAG                         ATGTTCCTGCATCAGATTCTCC
genomic: AGCACATGGATTCATCTCCGGATTTTGCCAAAGATTTACGTCTGATAAAGgtgactctgc ... tcctttgcagATGTTCCTGCATCAGATTCTCC
EST: gi|110716217|gb|EE091004.1|EE091004
EST:     AGCACATGGATTCATCTCCGGATTTTGCCAAAGATTTACGTCTGATAAAG                         ATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGG
genomic: AGCACATGGATTCATCTCCGGATTTTGCCAAAGATTTACGTCTGATAAAGgtgactctgc ... tcctttgcagATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGG
EST: gi|29781538|gb|CB346072.2|CB346072
EST:     AGCACATGGATTCATCTCCGGATTTTGCCAAAGATTTACGTCTGATAAAG                         ATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGG
genomic: AGCACATGGATTCATCTCCGGATTTTGCCAAAGATTTACGTCTGATAAAGgtgactctgc ... tcctttgcagATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGG
EST: gi|30126104|gb|CB911443.1|CB911443
EST:     AGCACATGGATTCATCTCCGGATTTTGCCAAAGATTTACGTCTGATAAAG                         ATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGG
genomic: AGCACATGGATTCATCTCCGGATTTTGCCAAAGATTTACGTCTGATAAAGgtgactctgc ... tcctttgcagATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGG
EST: gi|161706121|gb|FC056257.1|FC056257
EST:     AGCACATGGATTCATCTCCGGATTTTGCCAAAGATTTACGTCTGATAAAG                         ATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGG
genomic: AGCACATGGATTCATCTCCGGATTTTGCCAAAGATTTACGTCTGATAAAGgtgactctgc ... tcctttgcagATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGG
EST: gi|110702955|gb|EE079378.1|EE079378
EST:     AGCACATGGATTCATCTCCGGATTTTGCCAAAGATTTACGTCTGATAAAG                         ATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGG
genomic: AGCACATGGATTCATCTCCGGATTTTGCCAAAGATTTACGTCTGATAAAGgtgactctgc ... tcctttgcagATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGG
EST: gi|30126370|gb|CB911709.1|CB911709
EST:     AGCACATGGATTCATCTCCGGATTTTGCCAAAGATTTACGTCTGATAAAG                         ATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGG
genomic: AGCACATGGATTCATCTCCGGATTTTGCCAAAGATTTACGTCTGATAAAGgtgactctgc ... tcctttgcagATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatgcttggagataatggtgcgatggggcttctgacacttgagtcctttgcagATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGGGTTCTTCATCGAGATTTGAAGCCCCAGAACTTACTCATAGATCGTCGTA
                               ttctgac  putative branch site (score: 2)
                                             tcctttgc  putative PPT
           agataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttgatgtctatattttaaattattttcatatttatttctgggcatatgcttggagataatggtgcgatggggcttctgacacttgagtcctttgcagATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGGGTTCTTCATCGAGATTTGAAGCCCCAGAACTTACTCATAGATCGTCGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - tgatgtc
- - - - - - - - - - - - - - - - - - -tttctgg
- - - - - - - - - - - - - - - - - - - - - - -catatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atggtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacttga