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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCTCTTGGTGCTGGTCCTGTCCCTGCTCTTCTTCTTCCAGAAATATTTGCCTCTAGAATCAGGGCAAAAGCAGTTGCTTTATCATTAGGCATGCATTGGgtaagtgaagaagaaatgatcctgttactactgatttttttcttatcaaagatgcactttgaaagattcagtattgcctgtagtttttgctttctctctg...

Basic information

species Vitis vinifera
transcript Vv14s0006g02720.t01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0006g02720.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: LOC_Os01g04190.1 (Oryza sativa), 5'ss of exon 13
CTCTCTTGGTGCTGGTCCTGTCCCTGCTCTTCTTCTTCCAGAAATATTTGCCTCTAGAATCAGGGCAAAAGCAGTTGCTTTATCATTAGGCATGCATTGGgtaagtgaagaagaaatgatcctgttactactgatttttttcttat-caaagatgcactttgaaagattcagta-ttgcctgtagtttttgctttctctctg
  ||||||| ||||| || || || ||  | || ||||| |||||||||||||| ||||| ||||| ||||| ||||| |||||  | |||||||| ||||||||| | |         |    | |    |||    ||| | ||      |   |   |   || || | |  ||  || ||   ||     | | |   
TGCTCTTGGAGCTGGCCCAGTTCCAGCATTGCTCCTTCCTGAAATATTTGCCTCCAGAATAAGGGCTAAAGCTGTTGCATTATCTCTGGGCATGCACTGGgtaagttatgcttggtgtgttggatgaagtttgacagatttgtgatgtggttagctataatattagtttaactgcttttctatataattgaaaatatttt--

upper sequence: Vv14s0006g02720.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GRMZM2G098011_T01 (Zea mays), 5'ss of exon 13
CTCTCTTGGTGCTGGTCCTGTCCCTGCTCTTCTTCTTCCAGAAATATTTGCCTCTAGAATCAGGGCAAAAGCAGTTGCTTTATCATTAGGCATGCATTGGgtaagtgaagaagaa--atgatcctgttactactgatt--tttttcttatcaaagatgcactttgaaag-attcagtattgcctgtagtttttgctttctctctg
  |||| || ||||||||||| ||||| || |||||||| |||||||||||||| ||||| ||||| || || ||||| |||||  |||||||||| ||||| ||| |  |      ||      | || |||  | |   | |  || ||  |  | | |  | | |  ||    ||||   ||| || | |  |  ||     
TGCTCTAGGAGCTGGTCCTGTTCCTGCCCTGCTTCTTCCTGAAATATTTGCCTCCAGAATAAGGGCCAAGGCTGTTGCATTATCTCTAGGCATGCACTGGgtgagtcacaactgttcatacatacgctaataccaaatgcatataattgtcctaagtccccaatcacattatgttttattcattgtggtatatcttgcct-----

upper sequence: Vv14s0006g02720.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GRMZM2G153704_T02 (Zea mays), 5'ss of exon 13
CTCTCTTGGTGCTGGTCCTGTCCCTGCTCTTCTTCTTCCAGAAATATTTGCCTCTAGAATCAGGGCAAAAGCAGTTGCTTTATCATTAGGCATGCATTGGgtaagtgaaga------agaaatgatcctgt-tactactgatttttttcttatcaaagatgcactttgaaagattcagtattgcctgtagtttttgctttctctctg
  |||| || || || ||||| || || || |||||||| |||||||||||||| ||||| ||||| || || || || |||||  |||||||||| ||||| ||| | ||      | | ||   |   | ||| |   || | |   |   | |||   || |||   | |||| || ||     | || ||   |         
TGCTCTAGGAGCGGGCCCTGTTCCAGCGCTACTTCTTCCTGAAATATTTGCCTCGAGAATAAGGGCCAAGGCTGTCGCATTATCTCTAGGCATGCACTGGgtgagtcatgattgttcacacatacgctaatataccaaacatatataattgtcctaagtcccaatttatcacattctgttttattcattgtgttatatcg-------

upper sequence: Vv14s0006g02720.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA13G07780.2 (Glycine max), 5'ss of exon 13
CTCTCTTGGTGCTGGTCCTGTCCCTGCTCTTCTTCTTCCAGAAATATTTGCCTCTAGAATCAGGGCAAAAGCAGTTGCTTTATCATTAGGCATGCATTGGgtaagtgaa------gaagaaatgatcctgttactactgatttttttcttatcaaagatgcactttgaaagattcagtattgcctgtagtttttgctttctctctg
||||||||||||||||||||| ||||| |||||||| || || |||||||| |||||||| || |||||||||||| |||| ||||||||||  |||||||| |||||       |  |||   |   | ||||   || ||     |||      |    |  ||  ||  |    || | | |  |   |        |     
CTCTCTTGGTGCTGGTCCTGTGCCTGCCCTTCTTCTACCGGAGATATTTGCTTCTAGAATTAGAGCAAAAGCAGTTTCTTTGTCATTAGGCACACATTGGgtgagtgacttcactgtggaacctaatattttacctgtggttgaggcctttatcttgccatatatttgaaatt---atacttcttaaaagctaaaaaaattaa---

upper sequence: Vv14s0006g02720.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: AT5G16150.1 (Arabidopsis thaliana), 5'ss of exon 13
CTCTCTTGGTGCTGGTCCTGTCCCTGCTCTTCTTCTTCCAGAAATATTTGCCTCTAGAATCAGGGCAAAAGCAGTTGCTTTATCATTAGGCATGCATTGGgtaagtgaagaagaaatgatcctgttactactgatttttttcttatcaaagatgcactttgaaagattcagtattgcctgtagtttttgctttctctctg
||| ||||||||||| || || || ||||||||||||||||| |||||||| ||  ||||||| |||||||| || ||| | ||  | |||||||| ||||||  |       | ||    || |   |  |   |   |||  | || || | |   |       |  | | ||   | |   ||||||  |  |    
CTCACTTGGTGCTGGCCCGGTACCGGCTCTTCTTCTTCCAGAGATATTTGCATCCCGAATCAGAGCAAAAGCCGTCGCTCTTTCTCTCGGCATGCACTGGgtatat-------acatatatctataggtttta--tgggttcagaacagagtttcttctctctgtttctaatgttttgtttctcttttgccctaacag--

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|110396221|gb|EC961902.1|EC961902
EST:     CCTCTAGAATAAGGGCAAAAGCAGTTGCTTTATCATTAGGCATGCATTGG                         ATCTCAAACTTCGTGATTGGGCTTTACTTCTTGAGCGTTGTAAACAAGTTC
genomic: CCTCTAGAATCAGGGCAAAAGCAGTTGCTTTATCATTAGGCATGCATTGGgtaagtgaag ... attgtatcagATCTCAAACTTTGTGATTGGGCTTTACTTCTTGAGCGTTGTAAACAAGTTC
EST: gi|110403571|gb|EC969185.1|EC969185
EST:     CCTCTAGAATAAGGGCAAAAGCAGTTGCTTTATCATTAGGCATGCATTGG                         ATCTCAAACTTCGTGATTGGGCTTTACTTCTTGAGCGT
genomic: CCTCTAGAATCAGGGCAAAAGCAGTTGCTTTATCATTAGGCATGCATTGGgtaagtgaag ... attgtatcagATCTCAAACTTTGTGATTGGGCTTTACTTCTTGAGCGT
EST: gi|110425042|gb|EC991417.1|EC991417
EST:     CCTCTAGAATAAGGGCAAAAGCAGTTGCTTTATCATTAGGCATGCATTGG                         ATCTCAAACTTCGTGATTGGGCTTTACTTCTTGAGCGTTGTAAACAAGTTC
genomic: CCTCTAGAATCAGGGCAAAAGCAGTTGCTTTATCATTAGGCATGCATTGGgtaagtgaag ... attgtatcagATCTCAAACTTTGTGATTGGGCTTTACTTCTTGAGCGTTGTAAACAAGTTC
EST: gi|30252112|gb|CB968751.1|CB968751
EST:     CCTCTAGAATAAGGGCAAAAGCAGTTGCTTTATCATTAGGCATGCATTGG                         ATCCCAAACTTCGTGATTGGGCTTTACTTCTTGAGCGTTGTAAACAAGTTC
genomic: CCTCTAGAATCAGGGCAAAAGCAGTTGCTTTATCATTAGGCATGCATTGGgtaagtgaag ... attgtatcagATCTCAAACTTTGTGATTGGGCTTTACTTCTTGAGCGTTGTAAACAAGTTC
EST: gi|110370956|gb|EC934605.1|EC934605
EST:     CCTCTAGAATAAGGGCAAAAGCAGTTGCTTTATCATTAGGCATGCATTGG                         ATCTCAAACTT
genomic: CCTCTAGAATCAGGGCAAAAGCAGTTGCTTTATCATTAGGCATGCATTGGgtaagtgaag ... attgtatcagATCTCAAACTT
EST: gi|110376760|gb|EC941834.1|EC941834
EST:     CCTCTAGAATAAGGGCAAAAGCAGTTGCTTTATCATTAGGCATGCATTGG                         ATCTCAAACTTCGTGATTGGGCTTTACTTCTTGAGCGTTGTAAACAAGTTC
genomic: CCTCTAGAATCAGGGCAAAAGCAGTTGCTTTATCATTAGGCATGCATTGGgtaagtgaag ... attgtatcagATCTCAAACTTTGTGATTGGGCTTTACTTCTTGAGCGTTGTAAACAAGTTC
EST: gi|30252199|gb|CB969750.1|CB969750
EST:     CCTTTAGAATAAGGGCAAAAGCAGTTGCTTTATCATTAGGCATGCATTGG                         ATCCCAAACTTCGTGATTGGGCTTTACTTCTTGAGCGTTGTAAACAAGTTC
genomic: CCTCTAGAATCAGGGCAAAAGCAGTTGCTTTATCATTAGGCATGCATTGGgtaagtgaag ... attgtatcagATCTCAAACTTTGTGATTGGGCTTTACTTCTTGAGCGTTGTAAACAAGTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCTCTTGGTGCTGGTCCTGTCCCTGCTCTTCTTCTTCCAGAAATATTTGCCTCTAGAATCAGGGCAAAAGCAGTTGCTTTATCATTAGGCATGCATTGGgtaagtgaagaagaaatgatcctgttactactgatttttttcttatcaaagatgcactttgaaagattcagtattgcctgtagtttttgctttctctctg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atcaaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaagat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttctctc