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'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttattagaacctttttttgtggttgactttatatttatttgttcaaaaaattagcttctaatctggttcgaccaatcaaaatttttgtataatcttgcagGTTATGGGAAATCACGTGGCCATTACTGTAGGTGGATCAAACGGTCATTTTGAGCTGAATGTATTCAAGCCTCTGATTGCTAGTGGTCTCCTACGT

Basic information

species Vitis vinifera
transcript Vv07s0005g00880.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA10G02040.1 (Glycine max), 3'ss of exon 12
-----------------------------------------------ttattagaacctttttttgtggttgacttt----atatttatttgttcaaaaaattagcttctaatctggttcgaccaatcaaaatttttgt-ataatc------ttgcagGTTATGGGAAATCACGTGGCCATTACTGTAGGTGGATCAAACGGTCATTTTGAGCTGAATGTATTCAAGCCTCTGATTGCTAGTGGTCTCCTACGT
                                                |  | |||   |  || |        ||     |  | || |      | || ||   || ||   ||  | ||    ||  ||||  ||| || ||       || ||||| || ||||| || || ||  |||| || ||||||||||| |||||||||||||| ||||| ||||||||  ||||||| ||| ||||||| | |
gtagacatcaattcacctcattttattaaaatactttaatgttatgacttatggaatactgattggcaaacagtttctatgacttgtaataaaatcacaatttgaattttatggtgactggaaatttctgaattggtgtcatgattcatttatttcagGTCATTGGAAACCATGTTGCAGTTACAGTGGGTGGATCAAATGGTCATTTTGAGCTTAATGTGTTCAAGCCAATGATTGCCAGTTGTCTCCTGCAT

upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 12
------------------------------------------------ttattagaacctttttttgtggttgactttatatttatttgttcaaaaa--------attagcttctaatctggttcgaccaatcaaaatttttgtataatcttgcagGTTATGGGAAATCACGTGGCCATTACTGTAGGTGGATCAAACGGTCATTTTGAGCTGAATGTATTCAAGCCTCTGATTGCTAGTGGTCTCCTACGT
                                                |||| | |  ||  ||         | ||| |||  | ||||   ||||        |||   || ||   ||  | |     ||  ||||  |||      || ||||| || ||||| || || ||  |||| || ||||||||||| |||||||||||||| ||||| ||||||||  ||||||| ||| ||||||| | |
gtagacatcaattcacttcattttattaaaatactttaatgttatgacttatgaaatactgattggcaaacacagtttctatg-acttgtaataaaatcacacatattgaattttatggtgactgggaatttctgaattggtgtcatgaatttcagGTCATAGGAAACCATGTTGCAGTTACAGTGGGTGGATCAAATGGTCATTTTGAGCTTAATGTGTTCAAGCCAATGATTGCCAGTTGTCTCCTGCAT

upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA02G01930.1 (Glycine max), 3'ss of exon 12
----ttattagaacctttttttgtggttgact-ttatatttatt-tgttcaaaaaattagcttctaatctggt--tcgaccaatcaaaatttttgtata-atcttgcagGTTATGGGAAATCACGTGGCCATTACTGTAGGTGGATCAAACGGTCATTTTGAGCTGAATGTATTCAAGCCTCTGATTGCTAGTGGTCTCCTACGT
      || |   | |||| ||    |      ||||    ||| |  | |  |||     | |    | ||   |     |||     |  |  |  |    || ||||| |||||||| || || || || || || ||||||||||| |||||||||||||| ||||| ||||||||  ||||||| | | ||||||| | |
gtagacatcacttcattttattaaaatacttagttatgaccattgtagttagcaaacagtttccgtgacaggcaatttcttaattggtgtcatgattcacgaatttcagGTCATGGGAAACCATGTTGCAATCACAGTGGGTGGATCAAATGGTCATTTTGAGCTCAATGTGTTCAAGCCAATGATTGCCAATTGTCTCCTGCAT

upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT2G47510.1 (Arabidopsis thaliana), 3'ss of exon 13
-ttattagaacctttttttgtggt-tgactttatatttatttgttcaaaaaattagcttctaatctggttc---gaccaatcaaaat-ttttgtataatcttgcagGTTATGGGAAATCACGTGGCCATTACTGTAGGTGGATCAAACGGTCATTTTGAGCTGAATGTATTCAAGCCTCTGATTGCTAGTGGTCTCCTACGT
 | | |   | || |   |    | | | |  | |   ||   |  | |   | || || || | | ||||   |||   |     |       ||||  ||||||||||||||||| || || ||  | || || ||||| ||||| |||||||| ||  ||||||||||||||||  |||| || |||| |||  ||| |
gtaagtcccatctatcaatacattcttagtacagaccaatgaatctagatgctaaggttgtattattgttccttgactgtttgggttgcaaccaataacattgcagGTTATGGGAAACCATGTAGCTGTGACAGTTGGTGGGTCAAATGGTCATTTCGAATTGAATGTATTCAAGCCGGTGATCGCGAGTGCTCTTTTACAT

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|352794271|gb|FQ479513.1|FQ479513
EST:     GAAAGGTTAACCCTACTCAGTGTGAGGCTCTCACAATGGTCTGTGCTCAG                         GTTATGGGAAATCACGTGGCCATTACTGTAGGTGGATCAAACGGTCATTTT
genomic: GAAAGGTTAACCCTACTCAGTGTGAGGCTCTCACAATGGTCTGTGCTCAGgtaaagtttg ... aatcttgcagGTTATGGGAAATCACGTGGCCATTACTGTAGGTGGATCAAACGGTCATTTT
EST: gi|352781327|gb|FQ467773.1|FQ467773
EST:     GAAAGGTTACCCCTACTCAGTGTGAGGCTCTCACAATGGTCTGTGCTCAG                         GTTATGGGAAATCACGTGGCCATTACTGTAGGTGGATCAAACGGTCATTTT
genomic: GAAAGGTTAACCCTACTCAGTGTGAGGCTCTCACAATGGTCTGTGCTCAGgtaaagtttg ... aatcttgcagGTTATGGGAAATCACGTGGCCATTACTGTAGGTGGATCAAACGGTCATTTT
EST: gi|33402398|gb|CF208025.1|CF208025
EST:     GAAAGGTTACCCCTACTCAGTGTGAGGCTCTCACAATGGTCTGTGCTCAG                         GTTATGGGAAATCACGTGGCCATTACTGTAGGTGGATCAAACGGTCATTTT
genomic: GAAAGGTTAACCCTACTCAGTGTGAGGCTCTCACAATGGTCTGTGCTCAGgtaaagtttg ... aatcttgcagGTTATGGGAAATCACGTGGCCATTACTGTAGGTGGATCAAACGGTCATTTT
EST: gi|110363110|gb|EC926680.1|EC926680
EST:     GAAAGGTTAACCCTACTCAGTGTGAGGCTCTCACAATGGTCTGTGCTCAG                         GTTATGGGAAATCACGTGGCCATTACTGTAGGTGGATCAAACGGTCATTTT
genomic: GAAAGGTTAACCCTACTCAGTGTGAGGCTCTCACAATGGTCTGTGCTCAGgtaaagtttg ... aatcttgcagGTTATGGGAAATCACGTGGCCATTACTGTAGGTGGATCAAACGGTCATTTT
EST: gi|352773938|gb|FQ473070.1|FQ473070
EST:     CTCACAATGGTCTGTGCTCAG                         GTTATGGGAAATCACGTGGCCATTACTGTAGGTGGATCAAACGGTCATTTT
genomic: CTCACAATGGTCTGTGCTCAGgtaaagtttg ... aatcttgcagGTTATGGGAAATCACGTGGCCATTACTGTAGGTGGATCAAACGGTCATTTT
EST: gi|352782337|gb|FQ470240.1|FQ470240
EST:     TCTGTGTTCAG                         GTTATGGGAAATCACGTGGCCATTACTGTAGGTGGATCAAACGGTCATTTT
genomic: TCTGTGCTCAGgtaaagtttg ... aatcttgcagGTTATGGGAAATCACGTGGCCATTACTGTAGGTGGATCAAACGGTCATTTT
EST: gi|110407161|gb|EC972758.1|EC972758
EST:     GAAAGGTTAACCCTACTCAGTGTGAGGCTCTCACAATGGTCTGTGCTCAG                         GTTATGGGAAATCACGTGGCCATTACTGTAGGTGGATCAAACGGTCATTTT
genomic: GAAAGGTTAACCCTACTCAGTGTGAGGCTCTCACAATGGTCTGTGCTCAGgtaaagtttg ... aatcttgcagGTTATGGGAAATCACGTGGCCATTACTGTAGGTGGATCAAACGGTCATTTT
EST: gi|110361036|gb|EC924487.1|EC924487
EST:     GAAAGGTTAACCCTACTCAGTGTGAGGCTCTCACAATGGTCTGTGCTCAG                         GTTATGGGAAATCACGTGGCCATTACTGTAGGTGGATCAAACGGTCATTTT
genomic: GAAAGGTTAACCCTACTCAGTGTGAGGCTCTCACAATGGTCTGTGCTCAGgtaaagtttg ... aatcttgcagGTTATGGGAAATCACGTGGCCATTACTGTAGGTGGATCAAACGGTCATTTT
EST: gi|110698892|gb|EE076910.1|EE076910
EST:     GAAAGGTTAACCCTACTCAGTGTGAGGCTCTCACAATGGTCTGTGCTCAG                         GTTATGGGAAATCACGTGGCCATTACTGTAGGTGGATCAAACGGTCATTTT
genomic: GAAAGGTTAACCCTACTCAGTGTGAGGCTCTCACAATGGTCTGTGCTCAGgtaaagtttg ... aatcttgcagGTTATGGGAAATCACGTGGCCATTACTGTAGGTGGATCAAACGGTCATTTT
EST: gi|351045827|gb|FQ441012.1|FQ441012
EST:     GAAAGGTTAACCCTACTCAGTGTGAGGCTCTCACAATGGTCTGTGCTCAG                         GTTATGGGAAATCACGTGGCCATTACTGTAGGTGGATCAAACGGTCATTTT
genomic: GAAAGGTTAACCCTACTCAGTGTGAGGCTCTCACAATGGTCTGTGCTCAGgtaaagtttg ... aatcttgcagGTTATGGGAAATCACGTGGCCATTACTGTAGGTGGATCAAACGGTCATTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaattagcttctaatctggttcgaccaatcaaaatttttgtataatcttgcagGTTATGGGAAATCACGTGGCCATTACTGTAGGTGGATCAAACGGTCATTTTGAGCTGAATGTATTCAAGCCTCTGATTGCTAGTGGTCTCCTACGT
          ttctaat  putative branch site (score: 2)
                            aatcaaaatttttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttattagaacctttttttgtggttgactttatatttatttgttcaaaaaattagcttctaatctggttcgaccaatcaaaatttttgtataatcttgcagGTTATGGGAAATCACGTGGCCATTACTGTAGGTGGATCAAACGGTCATTTTGAGCTGAATGTATTCAAGCCTCTGATTGCTAGTGGTCTCCTACGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - gtggttg
- - - - - - - - - - - - - - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctggttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaatca