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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcatcatgaatttagttcaataacctacattgaaaattaattttgttaattgggaaaatagcgtgctgacggtttaactatttcttttgaattatgcagGTACTGAACCATAATGCAGGGTCTGGATACAGTGCACCTGAGGTTGCCATGTCAGGTCAATATACTCTGAAGAGTGATGTTTACAGTTTTGGTGTAGTCA

Basic information

species Vitis vinifera
transcript Vv09s0002g00150.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g00150.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G004572_T01 (Zea mays), 3'ss of exon 13
tgcatcatgaatttagttcaataacctacattgaaaattaattttgttaattgggaaaatagcgtgctgacggttta-actatttcttttg------aattatgcagGTACTGAACCATAATGCAGGGTCTGGATACAGTGCACCTGAGGTTGCCATGTCAGGTCAATATACTCTGAAGAGTGATGTTTACAGTTTTGGTGTAGTCA------
          ||||     ||| ||  |   || || |    |    | |||   |  | | |   |||||   ||| | | ||  |||||      |||    ||  | | |       ||   |||||||| || ||||| |||||||| |  ||||| ||||| ||||| || ||||||||||| ||||| ||||| || ||||      
----------atttga---aatgacggaatatgtaattgctctcaaatgatttataccacatcccactgacaagttatattcttcattttgcttcaaaatggaacatctgcagGCTTCAGATCAGGGGTCTGGGTATAGTGCCCCTGAGGTCGAGATGTCCGGTCAGTATACCCTCAAGAGTGATGTCTACAGCTTTGGGGTCGTCATGCTGG

upper sequence: Vv09s0002g00150.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA03G42360.1 (Glycine max), 3'ss of exon 15
---tgcatcatgaatttagttcaataacctacattgaaaattaattttgttaattgggaaaatagcgtgctgacggtttaactatttcttttgaattatgcagGTACTGAACCATAATGCAGGGTCTGGATACAGTGCACCTGAGGTTGCCATGTCAGGTCAATATACTCTGAAGAGTGATGTTTACAGTTTTGGTGTAGTCA
      ||     || |  || |  ||   |  ||     || |    || | |        ||      |   | | ||||| ||  |     |||   ||| || ||||||||||||  || ||||||||   ||||||||| |||||| |||| ||||| |||||| |||| |||||||| ||||| ||||| || ||||
aggaatattgatcatgttcttaacaaatgcagcttttccttttacccagtgactctaagccctataaaattattgttctaactcttggtcgcacatt---cagATATTGAACCATAATGTTGGATCTGGATATGATGCACCTGAAGTTGCCTTGTCTGGTCAGTATACTTTGAAAAGTGATGTCTACAGCTTTGGAGTTGTCA

upper sequence: Vv09s0002g00150.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT1G53730.2 (Arabidopsis thaliana), 3'ss of exon 13
tgcatcatgaatttagttcaataacctacattgaaaattaattttgttaattgggaaaatagcgtgctgacggtttaactatttcttttgaattatgcagGTACTGAACCATAATGCAGGGTCTGGATACAGTGCACCTGAGGTTGCCATGTCAGGTCAATATACTCTGAAGAGTGATGTTTACAGTTTTGGTGTAGTCA---
            || | |  | || |     | |||| |   |||   | ||   ||  ||      ||   | |||  |  ||||   ||  | ||||| || | ||||| |  |  |     || || || |||||||| ||  | |||||||| |||||| || ||||||||||  ||||||||||||| ||||| |   
-----------gttggatatacaaacgtttctcaaaact--ctttaccatttctcaacttatt----tggttgcttagatcattct---gatatgtgcagTTATTAAACCAAACCGATGAA---GGGTATAGCGCACCTGAAGTATCAATGTCAGGCCAATATTCTTTGAAGAGTGACATTTACAGTTTTGGAGTAGTGATGC

upper sequence: Vv09s0002g00150.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT3G14350.3 (Arabidopsis thaliana), 3'ss of exon 14
-tgcatcatgaatttagttcaataacctacattgaaaattaattttgttaattgggaaaatagcgtgctgacggtttaactatttcttttgaattatgcagGTACTGAACCATAATGCAGGGTCTGGATACAGTGCACCTGAGGTTGCCATGTCAGGTCAATATACTCTGAAGAGTGATGTTTACAGTTTTGGTGTAGTCA---
 |  || ||    |    | ||   |  | | |   | |   | |   |   |          | ||      |||      | |   |   ||| ||||| |||| ||||| || |  |     |||||||| ||||| ||   | | |||||||| |||||  || ||||||| ||||||||||||||||| ||||| |   
gtatat-atagtatagactaaacttctcagaattctagtatctctctctctcttttgttcctccatggaacttgttcctaagtattcatgacattgtgcagCTACTAAACCAAAACGATGAA---GGATACAGCGCACCAGAAACTTCAATGTCAGGCCAATACTCTTTGAAGAGCGATGTTTACAGTTTTGGAGTAGTGATGC

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|110375773|gb|EC940790.1|EC940790
EST:     CACACCTTACAGACTGTGGGCTAGCAAGCTTCATCCCAAATGCTGATCAG                         GTACTGAACCATAATGCAGGGTCTGGATACAGTGCACCTGAGGTTGCCATG
genomic: CACACCTTACAGACTGTGGGCTAGCAAGCTTCATCCCAAATGCTGATCAGgtagattttg ... aattatgcagGTACTGAACCATAATGCAGGGTCTGGATACAGTGCACCTGAGGTTGCCATG
EST: gi|110701239|gb|EE078596.1|EE078596
EST:     CACACCTTACAGACTGTGGGCTAGCAAGCTTCATCCCAAATGCTGATCAN                         GTACTGAACCATAATGCAGGGTCTGGATACAGTGCACCTGAGGTTGCCATG
genomic: CACACCTTACAGACTGTGGGCTAGCAAGCTTCATCCCAAATGCTGATCAGgtagattttg ... aattatgcagGTACTGAACCATAATGCAGGGTCTGGATACAGTGCACCTGAGGTTGCCATG
EST: gi|349830454|gb|FQ416752.1|FQ416752
EST:     CACACCTTACAGACTGTGGGCTAGCAAGCTTCATCCCAAATGCTGATCAG                         GTACTGAACCATAATGCAGGGTCTGGATACAGTGCACCTGAGGTTGCCATG
genomic: CACACCTTACAGACTGTGGGCTAGCAAGCTTCATCCCAAATGCTGATCAGgtagattttg ... aattatgcagGTACTGAACCATAATGCAGGGTCTGGATACAGTGCACCTGAGGTTGCCATG
EST: gi|110391079|gb|EC956033.1|EC956033
EST:     CACACCTTACAGACTGTGGGCTAGCAAGCTTCATCCCAAATGCTGATCAG                         GTACTGAACCATAATGCAGGGTCTGGATACAGTGCACCTGAGGTTGCCATG
genomic: CACACCTTACAGACTGTGGGCTAGCAAGCTTCATCCCAAATGCTGATCAGgtagattttg ... aattatgcagGTACTGAACCATAATGCAGGGTCTGGATACAGTGCACCTGAGGTTGCCATG
EST: gi|110363514|gb|EC927108.1|EC927108
EST:     CACACCTTACAGACTGTGGGCTAGCAAGCTTCATCCCAAATGCTGATCAG                         GTACTGAACCATAATGCAGGGTCTGGATACAGTGCACCTGAGGTTGCCATG
genomic: CACACCTTACAGACTGTGGGCTAGCAAGCTTCATCCCAAATGCTGATCAGgtagattttg ... aattatgcagGTACTGAACCATAATGCAGGGTCTGGATACAGTGCACCTGAGGTTGCCATG
EST: gi|110360391|gb|EC923453.1|EC923453
EST:     CACACCTTACAGACTGTGGGCTAGCAAGCTTCATCCCAAATGCTGATCAG                         GTACTGAACCATAATGCAGGGTCTGGATACAGTGCACCTGAGGTTGCCATG
genomic: CACACCTTACAGACTGTGGGCTAGCAAGCTTCATCCCAAATGCTGATCAGgtagattttg ... aattatgcagGTACTGAACCATAATGCAGGGTCTGGATACAGTGCACCTGAGGTTGCCATG
EST: gi|110379506|gb|EC944705.1|EC944705
EST:     CACACCTTACAGACTGTGGGCTAGCAAGCTTCATCCCAAATGCTGATCAG                         GTACTGAACCATAATGCAGGGTCTGGATACAGTGCACCTGAGGTTGCCATG
genomic: CACACCTTACAGACTGTGGGCTAGCAAGCTTCATCCCAAATGCTGATCAGgtagattttg ... aattatgcagGTACTGAACCATAATGCAGGGTCTGGATACAGTGCACCTGAGGTTGCCATG
EST: gi|30321691|gb|CD004953.1|CD004953
EST:     CACACCTTACAGACTGTGGGCTAGCAAGCTTCATCCCAAATGCTGATCAG                         GTACTGAACCATAATGCAGGGTCTGGATACAGTGCACCTGAGGTTGCCATG
genomic: CACACCTTACAGACTGTGGGCTAGCAAGCTTCATCCCAAATGCTGATCAGgtagattttg ... aattatgcagGTACTGAACCATAATGCAGGGTCTGGATACAGTGCACCTGAGGTTGCCATG
EST: gi|27579137|gb|CB001832.1|CB001832
EST:     CACACCTTACAGACTGTGGGCTAGCAAGCTTCATCCCAAATGCTGATCAG                         GTACTGAACCATAATGCAGGGTCTGGATACAGTGCACCTGAGGTTGCCATG
genomic: CACACCTTACAGACTGTGGGCTAGCAAGCTTCATCCCAAATGCTGATCAGgtagattttg ... aattatgcagGTACTGAACCATAATGCAGGGTCTGGATACAGTGCACCTGAGGTTGCCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttaattgggaaaatagcgtgctgacggtttaactatttcttttgaattatgcagGTACTGAACCATAATGCAGGGTCTGGATACAGTGCACCTGAGGTTGCCATGTCAGGTCAATATACTCTGAAGAGTGATGTTTACAGTTTTGGTGTAGTCA
                            tttaactatttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcatcatgaatttagttcaataacctacattgaaaattaattttgttaattgggaaaatagcgtgctgacggtttaactatttcttttgaattatgcagGTACTGAACCATAATGCAGGGTCTGGATACAGTGCACCTGAGGTTGCCATGTCAGGTCAATATACTCTGAAGAGTGATGTTTACAGTTTTGGTGTAGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- catcatg
- - - - - - - - - -aataacc
- - - - - - - - - - - - - - - - - aaattaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -ggaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agcgtgc