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

GTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAGgtagcaattgactctatcctctaacttcttaaggaattttactcaatagtgcatggtctgagatatgtcgggtttatgttgtcctgttttttcacaatag...

Basic information

species Vitis vinifera
transcript Vv16s0022g01770.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0022g01770.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: LOC_Os03g14450.1 (Oryza sativa), 5'ss of exon 11
GTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAGgtagcaattgactctatcctct--aacttcttaaggaattttactcaatagtgcatggtctgagatatgtcgggtttatgttgtcctgttttttcacaatag
||||| ||||||||||||||||||||||||||||||||   | |   |||  | ||||||||  | || |||||||||||||||    |    | | ||| ||  || || ||      ||| |  |     |  ||| |    | |   | |  ||||                        
GTTGTCATTGGGATGGATGTTGCTGCTTCAGAGTTCTACACTGA---GGACCAAACCTATGATCTTAACTTCAAGGAAGAGgtaaatgtcagttttttccccttgaaattttttgaagttttaatgcccccatttatgatgcttgtttccttg--tttag-----------------------

upper sequence: Vv16s0022g01770.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: LOC_Os10g08550.5 (Oryza sativa), 5'ss of exon 11
GTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAGgtag----caattgactctatcctc------------taacttcttaaggaattttactcaatagtgcatggt-ctg-agatatgtcgggtttatgttgtcctgttttttcacaatag
||||| ||||| ||||||||||||||||| || |||||  || ||||||| || ||||||||| | || |||||||| |||||||    ||||    |  ||  |             |  ||   |     || | |   |   ||  ||  | |||   |  | | |||   || ||||  | | ||||     |||
GTTGTCATTGGAATGGATGTTGCTGCTTCGGAATTCTACAATGACAAGGACAAAACCTATGACCTTAACTTCAAGGAGGAGgtaggtggcaatctgtttcatttttgatagtagggattggctcactgtttgatatcatgtagatgtatataatgctgtgaacttattgggaacat-ttgtgat-tctttttgttgtag

upper sequence: Vv16s0022g01770.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GRMZM2G133721_T01 (Zea mays), 5'ss of exon 2
GTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAGgtagcaattg--actc-----tatcctctaacttcttaaggaattttactcaatag--------tgcatggtctgagatatgtcgggtttatgttgtcctgttttttcacaatag-----------------------
|| || ||||||||||||||||||||||| |||||||  | | | || || ||||| |||||  | ||||||||||| ||||||  |||    |||      |||  | | |    || |   |  ||   | ||||        ||  |  |   | |   ||  |||      ||  |  || ||| | | ||                        
GTGGTCATTGGGATGGATGTTGCTGCTTCTGAGTTCTTCGGTGAGAAAGACAAGACTTATGATCTTAATTTCAAGGAGGAGgtaagaatcacaacttcttagtatgtttttatagtttcatttaccttgagctatagctattccttgtgttattctataggggtatggtaatacatgagcatttgttttatattaacgtgtagtcactttcttggccag

upper sequence: Vv16s0022g01770.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA09G28100.1 (Glycine max), 5'ss of exon 11
GTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAGgt-agcaatt--gactctatcctctaacttcttaaggaattttactcaatagtgcatggtctgagatatgtcgggtttatgttgtcctgttttttcacaatag--------
|||||||||||||||||||||||||||||||| || |||||||||||||| || ||||||||||||||||| |||||||||||   ||| |  ||  |  |   | || || |     | ||| | |       |    |    |  | | |      |   ||  |  | |   | || | |         
GTTGTAATTGGGATGGATGTTGCTGCTTCAGAATTTTATGATAACAAGGACAAAACCTATGACTTGAATTTTAAGGAAGAGgttgacaacttagaaacattttcccaatttttcttaaattttcattttgctccgttgagatatatttctttttcaaatgctttaactagataactgactacattattgcag

upper sequence: Vv16s0022g01770.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA16G32960.1 (Glycine max), 5'ss of exon 11
GTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAGgt-agcaatt---gactctatcctctaacttcttaagga-----attttactcaatagtg-catggtc-----tgagatatgtcgggtttatgttgtcctgttttttcacaatag
|||||||||||||||||||||||||||||||| || || |||||||||||||| ||||||||||||||||| |||||||||||   ||| |    |   | | | ||   |||||  | |     ||||| |||| | | |  ||  |      | ||||   |    |  ||      ||   || |  ||    
GTTGTAATTGGGATGGATGTTGCTGCTTCAGAATTTTACGATAACAAGGATAAAACCTATGACTTGAATTTTAAGGAAGAGgttgacaaattagaaacattttcccttttttcttttgaattttcatttttctcagttgagatatatttctttgtcagatgctttaactagataactgactaccttattgcag---

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|71890438|gb|DT039493.1|DT039493
EST:     GACCTATGACTTGAATTTCAAGGAAGAG                         AACAATG-TGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
genomic: GACCTATGACTTGAATTTCAAGGAAGAGgtagcaattg ... tctgctgcagAACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
EST: gi|22009325|gb|BQ794359.1|BQ794359
EST:     TTCAAGGAAGAG                         AACAATGATGGATCAC-AAAAATATCTGGAGACAGCTTGAAGAATG-TTAC
genomic: TTCAAGGAAGAGgtagcaattg ... tctgctgcagAACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
EST: gi|110716823|gb|EE092142.1|EE092142
EST:     AGTTCTATGATAACAAGGATAAGACGTATGACTTGAATTTCAAGGAAGAG                         AACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
genomic: AGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAGgtagcaattg ... tctgctgcagAACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
EST: gi|27586582|gb|CB009277.1|CB009277
EST:     AGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAG                         AACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
genomic: AGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAGgtagcaattg ... tctgctgcagAACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
EST: gi|30297237|gb|CB974031.1|CB974031
EST:     GAATTTCAAGGAAGAG                         AACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
genomic: GAATTTCAAGGAAGAGgtagcaattg ... tctgctgcagAACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
EST: gi|156732544|gb|EV236665.1|EV236665
EST:     AGTTCTATGATAACAAGGATAAGACGTATGACTTGAATTTCAAGGAAGAG                         AACAATGATGGATCACAAAAAATATCTGGAGACGGCTTGAAGAATGTTTAC
genomic: AGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAGgtagcaattg ... tctgctgcagAACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
EST: gi|26267083|gb|CA818146.1|CA818146
EST:     TAAGACCTATGAC-TGAATTTCAAGGAAGAG                         AACAATGATGGATCACAAAAAATATCTGGAGACAGCCTGAAGAATGTTTAC
genomic: TAAGACCTATGACTTGAATTTCAAGGAAGAGgtagcaattg ... tctgctgcagAACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
EST: gi|30297383|gb|CB974177.1|CB974177
EST:     TGACTTGAATTTCAAGGAAGAG                         AACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
genomic: TGACTTGAATTTCAAGGAAGAGgtagcaattg ... tctgctgcagAACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
EST: gi|110720665|gb|EE096796.1|EE096796
EST:     AGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAG                         AACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
genomic: AGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAGgtagcaattg ... tctgctgcagAACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
EST: gi|161719189|gb|FC069366.1|FC069366
EST:     AGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAG                         CACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
genomic: AGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAGgtagcaattg ... tctgctgcagAACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
EST: gi|110422151|gb|EC988464.1|EC988464
EST:     AGTTCTATGATAACAAGGATAAGACTTATGACTTGAATTTCAAGGAAGAG                         AACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
genomic: AGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAGgtagcaattg ... tctgctgcagAACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
EST: gi|27585372|gb|CB008067.1|CB008067
EST:     AGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAG                         AACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
genomic: AGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAGgtagcaattg ... tctgctgcagAACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
EST: gi|110405512|gb|EC971053.1|EC971053
EST:     AGTTCTATGATAACAAGGATAAGACGTATGACTTGAATTTCAAGGAAGAG                         AACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
genomic: AGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAGgtagcaattg ... tctgctgcagAACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
EST: gi|110700865|gb|EE077893.1|EE077893
EST:     AGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAG                         AACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
genomic: AGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAGgtagcaattg ... tctgctgcagAACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
EST: gi|27584827|gb|CB007522.1|CB007522
EST:     AGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAG                         AACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
genomic: AGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAGgtagcaattg ... tctgctgcagAACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
EST: gi|110715456|gb|EE093529.1|EE093529
EST:     AGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAG                         AACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
genomic: AGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAGgtagcaattg ... tctgctgcagAACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
EST: gi|30297175|gb|CB973969.1|CB973969
EST:     AGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAG                         AACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
genomic: AGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAGgtagcaattg ... tctgctgcagAACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
EST: gi|30297322|gb|CB974116.1|CB974116
EST:     AGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAG                         AACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
genomic: AGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAGgtagcaattg ... tctgctgcagAACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
EST: gi|30251837|gb|CB969570.1|CB969570
EST:     ATAAGACCTATGACTTGAATTTCAAGGAAGAG                         AACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
genomic: ATAAGACCTATGACTTGAATTTCAAGGAAGAGgtagcaattg ... tctgctgcagAACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
EST: gi|30125536|gb|CB910875.1|CB910875
EST:     ATTTCAAGGAAGAG                         AACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
genomic: ATTTCAAGGAAGAGgtagcaattg ... tctgctgcagAACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
EST: gi|71866289|gb|DT015344.1|DT015344
EST:     GACCTATGACTTGAATTTCAAGGAAGAG                         AACAATG-TGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
genomic: GACCTATGACTTGAATTTCAAGGAAGAGgtagcaattg ... tctgctgcagAACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
EST: gi|30301049|gb|CB977843.1|CB977843
EST:     AGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAG                         AACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
genomic: AGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAGgtagcaattg ... tctgctgcagAACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
EST: gi|30305158|gb|CB981952.1|CB981952
EST:     TATGACTTGAATTTCAAGGAAGAG                         AACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
genomic: TATGACTTGAATTTCAAGGAAGAGgtagcaattg ... tctgctgcagAACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
EST: gi|110418381|gb|EC984529.1|EC984529
EST:     AGTTCTATGATAACAAGGATAAGACGTATGACTTGAATTTCAAGGAAGAG                         AACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
genomic: AGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAGgtagcaattg ... tctgctgcagAACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
EST: gi|26265143|gb|CA816206.1|CA816206
EST:     GATAAGACCTATGAC-TGAATTTCAAGGAAGAG                         AACAATGATGGATCACAAAAAATATCTGGAGACAGCCTGAAGAATGTTTCC
genomic: GATAAGACCTATGACTTGAATTTCAAGGAAGAGgtagcaattg ... tctgctgcagAACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
EST: gi|110686170|gb|EE063531.1|EE063531
EST:     AGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAG                         AACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
genomic: AGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAGgtagcaattg ... tctgctgcagAACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
EST: gi|110358476|gb|EC922715.1|EC922715
EST:     ACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAG                         AACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
genomic: ACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAGgtagcaattg ... tctgctgcagAACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
EST: gi|161719251|gb|FC068252.1|FC068252
EST:     AGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAG                         AACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
genomic: AGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAGgtagcaattg ... tctgctgcagAACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
EST: gi|110377559|gb|EC942632.1|EC942632
EST:     ATTTCAAGGAAGAG                         AACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
genomic: ATTTCAAGGAAGAGgtagcaattg ... tctgctgcagAACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
EST: gi|110362047|gb|EC925554.1|EC925554
EST:     AGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAG                         AACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC
genomic: AGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAGgtagcaattg ... tctgctgcagAACAATGATGGATCACAAAAAATATCTGGAGACAGCTTGAAGAATGTTTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAGgtagcaattgactctatcctctaacttcttaaggaattttactcaatagtgcatggtctgagatatgtcgggtttatgttgtcctgttttttcacaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctatcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaggaat