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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTTACCTTGCATGAAATGCTGCCATTGGCATTTGACTATGCTGGGCCGAAGCAAGCTGTCAAGGCAGTCTTCTTTGGAATGGCTTTCATGTCTGCAAGgtaaaatcaactcctagcaggacactctttcagaagccatttaaaaagtttctggtaatttcaatgattttggtagccctacaacctggaagaaaaaaaa...

Basic information

species Vitis vinifera
transcript Vv06s0004g01860.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: LOC_Os02g10230.1 (Oryza sativa), 5'ss of exon 11
TTCTTACCTTGCATGAAATGCTGCCATTGGCATTTGACTATGCTGGGCCGAAGCAAGCTGTCAAGGCAGTCTTCTTTGGAATGGCTTTCATGTCTGCAAGgtaaaatca-actcctagcaggacactctttcagaagccatttaaaaagtttctggtaatttcaatgattttggtagccctacaacctggaagaaaaaaaa--
| || || |||||||||||| | ||  | ||||||||||||||||| |  || || |||||||| ||||||||  |||| ||||| ||||||||||||||||    | |   | | |  |    |||| |    |     || | |   |   | || | |    ||  ||||    |  || |   |       | |     
TCCTCACTTTGCATGAAATGTTACCTCTAGCATTTGACTATGCTGGTCAAAAACAGGCTGTCAAAGCAGTCTTTGTTGGCATGGCCTTCATGTCTGCAAGgtttgttgatgtttcaaataaagtactcct---aatatgtttcagatcatccattgtgactaatgtggatttgcattcagtaaagattttcctttatattttt

upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GRMZM2G050484_T01 (Zea mays), 5'ss of exon 11
TTCTTACCTTGCATGAAATGCTGCCATTGGCATTTGACTATGCTGGGCCGAAGCAAGCTGTCAAGGCAGTCTTCTTTGGAATGGCTTTCATGTCTGCAAGgtaaaatcaactcct-------agcag-gacactctttcagaagccatttaaaaagtttctggtaatttcaatgattttggtagccctacaacctggaagaaaaaaaa
| || || |||||||||||||||||  | ||||||||||||  ||| | ||||||||||||||| || |||||  | || ||||| | ||||||||||||||    || | || |       ||||  |  | || || || |  |||||       |  |  | |     |||  |||| |  ||||    |    ||||     | 
TCCTCACTTTGCATGAAATGCTGCCTCTTGCATTTGACTATTGTGGCCAGAAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAGgtttg-tcgattcttcaaattaagcaaagggattccttgagtaaacattttg-----tcttaatgaccagtatggatttgctttccctttc-cgcaaaagactcgta-

upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA15G03820.2 (Glycine max), 5'ss of exon 11
TTCTTACCTTGCATGAAATGCTGCCATTGGCATTTGACTATGCTGGGCCGAAGCAAGCTGTCAAGGCAGTCTTCTTTGGAATGGCTTTCATGTCTGCAAGgtaaaa--tcaactcctagcaggacactctttcagaagccatttaaaaagtttctggtaatttcaatgattttggtagccctacaacctggaagaaaaaaaa
|||| ||| | |||||||||||||||||||| ||||| ||||| || | ||||||| |||| ||||| ||||| || || |||||||||||||||||||||||| |     | | |||     | | | |||||  |||   | | | || ||||     | |   |  ||| |  ||   |  ||       ||       
TTCTGACCCTTCATGAAATGCTGCCATTGGCTTTTGATTATGCGGGACAGAAGCAATCTGTTAAGGCTGTCTTTTTGGGGATGGCTTTCATGTCTGCAAGgtaagaatctcattgctaatcaaatagtttttcaagagctgatgatatagcttctttctttattgctactttggtaagatatttaatgcatttgagtgtc--

upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA13G41580.1 (Glycine max), 5'ss of exon 11
TTCTTACCTTGCATGAAATGCTGCCATTGGCATTTGACTATGCTGGGCCGAAGCAAGCTGTCAAGGCAGTCTTCTTTGGAATGGCTTTCATGTCTGCAAGgt-aaaatca-actcctagcaggacactctttcagaagccatttaaaaagtttctggtaatttcaatgattttggtagccctacaacctggaagaaaaaaaa-
|||| ||| | ||||||||||| |||||||| ||||| ||||| || | ||||||| |||| ||||| ||||| || || |||||||||||||||||||||| | ||||  | | |||     | | | |||||  |||   | | | || || |    ||||  ||  ||||  |    ||       |  |   ||   | 
TTCTGACCCTTCATGAAATGCTTCCATTGGCTTTTGATTATGCGGGACAGAAGCAATCTGTGAAGGCTGTCTTTTTGGGGATGGCTTTCATGTCTGCAAGgtcagaatctcatttctaatcaaatagtttttcaagagctgatgatatagcttttt---atttttatttttttattgctactttggtaagatatttaatgcat

upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA11G14090.1 (Glycine max), 5'ss of exon 9
TTCTTACCTTGCATGAAATGCTGCCATTGGCATTTGACTATGCTGGGCCGAAGCAAGCTGTCAAGGCAGTCTTCTTTGGAATGGCTTTCATGTCTGCAAGgtaa-aatcaactcctagcag--gacactctttcaga-agccatttaaaaagtttctggtaatttcaatgattttggtagccctacaacctggaagaaaaaaaa----------------------------------
|||| ||| | ||||| ||||||||| | || ||||| ||||| || |  || ||| |||| ||||| ||||| | |||||||||||||||||||||||||||| ||| ||  |||    |   | |      || | |   | ||| ||    | || |  ||    | | ||||||| |  |  ||    | | ||    |                                   
TTCTAACCCTTCATGAGATGCTGCCACTTGCTTTTGAGTATGCGGGACAAAAACAATCTGTTAAGGCCGTCTTTTGTGGAATGGCTTTCATGTCTGCAAGgtaataataaaagcctcattgccaatataaaaacaaataaaaacttagaaccaatttgctttttgttgttactttggtaactatttaatgcagtacaactgtacaaggtgttaacatttagtattggtggatgtgcag

upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: AT3G20870.1 (Arabidopsis thaliana), 5'ss of exon 11
TTCTTACCTTGCATGAAATGCTGCCATTGGCATTTGACTATGCTGGGCCGAAGCAAGCTGTCAAGGCAGTCTTCTTTGGAATGGCTTTCATGTCTGCAAGgtaaaatcaactcctagcaggacactctttcagaagccatttaaaaagtttctggta-atttcaatgattttggtagc-cctacaacctggaagaaaaaaaa--
| || || ||||| |||||||| || ||||||||||| ||||| || | ||| |||||||| || || || || ||||| ||||| |  |||||||| ||||||||       |  | || || |   |||| ||   || ||     | |     | | || |    ||    |||  | | || ||| | |   ||   |  
TCCTAACATTGCACGAAATGCTTCCTTTGGCATTTGATTATGCGGGACAGAAACAAGCTGTGAAAGCTGTGTTTTTTGGCATGGCATGTATGTCTGCGAGgtaaaaatgcaaacctg-agaacccatattcataa---atctacttgctgtaaaacataattgaggccttgaaatagtacttgcatcctaggattcaacctagt

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|30251805|gb|CB969538.1|CB969538
EST:     AAGCAAGCTGTCAAGGCAGTCTTCTTTGGAATGGCTTTCATGTCTGCAAG                         CCTTTATTTTCTTGAAATCAGCTTACCCAAAGACATGAGCTTGTAGCTATT
genomic: AAGCAAGCTGTCAAGGCAGTCTTCTTTGGAATGGCTTTCATGTCTGCAAGgtaaaatcaa ... ggttttgcagCCTTTATTTTCTTGAAATCAGCTTACCCAAAGACATGAGCTTGTAGCTATT
EST: gi|110693658|gb|EE070084.1|EE070084
EST:     AAGCAAGCTGTCAAGGCAGTCTTCTTTGGAATGGCTTTCATGTCTGCAAG                         CCTTTATTTTCTTGAAATCAGCTTACCCAAAGACATGAGCTTGTAGCTATT
genomic: AAGCAAGCTGTCAAGGCAGTCTTCTTTGGAATGGCTTTCATGTCTGCAAGgtaaaatcaa ... ggttttgcagCCTTTATTTTCTTGAAATCAGCTTACCCAAAGACATGAGCTTGTAGCTATT
EST: gi|30251808|gb|CB969541.1|CB969541
EST:     AAGCAAGCTGTCAAGGCAGTCTTCTTTGGAATGGCTTTCATGTCTGCAAG                         CCTTTATTTTCTTGAAATCAGCTTACCCAAAGACATGAGCTTGTAGCTATT
genomic: AAGCAAGCTGTCAAGGCAGTCTTCTTTGGAATGGCTTTCATGTCTGCAAGgtaaaatcaa ... ggttttgcagCCTTTATTTTCTTGAAATCAGCTTACCCAAAGACATGAGCTTGTAGCTATT
EST: gi|110382518|gb|EC946816.1|EC946816
EST:     AAGCAAGCTGTCAAGGCAGTCTTCTTTGGAATGGCTTTCATGTCTGCAAG                         CCTTTATTTTCTTGAAATCAGCTTACCCAAAGACATGAGCTTGTAGCTATT
genomic: AAGCAAGCTGTCAAGGCAGTCTTCTTTGGAATGGCTTTCATGTCTGCAAGgtaaaatcaa ... ggttttgcagCCTTTATTTTCTTGAAATCAGCTTACCCAAAGACATGAGCTTGTAGCTATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCTTACCTTGCATGAAATGCTGCCATTGGCATTTGACTATGCTGGGCCGAAGCAAGCTGTCAAGGCAGTCTTCTTTGGAATGGCTTTCATGTCTGCAAGgtaaaatcaactcctagcaggacactctttcagaagccatttaaaaagtttctggtaatttcaatgattttggtagccctacaacctggaagaaaaaaaa

- - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caggaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa