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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGGTCCTTCTTGCAGGGGGTGCTTTGTTAAGTACGCTATCCATTCGTCTTGGCTACAAGCTGAAGCAGGCTCTGGACACAAAGCAACAGGAGAATGCAAgtaatggtttgaaaggttttttcataagtaaagcattggcaagttttcttagtttacctgcttctaacattcagagttacttaaaaattcag

Basic information

species Vitis vinifera
transcript Vv16s0039g01400.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0039g01400.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA12G01670.1 (Glycine max), 5'ss of exon 2
TGGGTCCTTCTTGCAGGGGGTGCTTTGTTAAGTACGCTATCCATTCGTCTTGGCTACAAGCTGAAGCAGGCTCTGGACACAAAGCAACAGGAGAATGCAAgtaatggtttgaaaggttttttcata--------agtaaagcattggcaagttttcttagtttacctgctt--ctaacattcagagttacttaaaaattcag--------------------------------------------------------------------------
               |  ||||||||||| ||||| ||||||||||| ||||| |||||| |||||||||| || ||| | ||||   || | ||||||| || ||||  |||||||  ||   ||         | | | ||||  |    ||   |  ||  ||| | |   ||  |||     |||    ||     |                                                                           
---------------GCTGGTGCTTTGTTGAGTACTCTATCCATTCGCCTTGGTTACAAGTTGAAGCAGGCACTTGACTCGAAGCCGAAGCAAAATGCAACTACTGGTCAGAAAGgtccttatgtacttttggggggacaccattctcccccttctgtgtttcccctcccttgttattatttttttttatcctaagtgggaaaataaacttaacttaaaaaggtatagtgccttggtctatagtggattcttacttcatattgtttgttactacag

upper sequence: Vv16s0039g01400.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA09G35690.1 (Glycine max), 5'ss of exon 2
TGGGTCCTTCTTGCAGGGGGTGCTTTGTTAAGTACGCTATCCATTCGTCTTGGCTACAAGCTGAAGCAGGCTCTGGACACAAAGCAACAGGAGAATGCAAgtaatggtttgaaaggttttttcataa-gtaaagcattggcaagttttcttagtttac--ctgcttctaacattcagagttacttaa-aaattcag----------------------------------------------------------------------
               |  ||||||||||| ||||| ||||||||||| || || |||||| | ||||||||  | ||| | ||||   || | ||||||| || ||||  |||||||  ||   ||  ||   |      | | | | |    | | |   |  || |   || |  |||     || ||| |||                                                                       
---------------GCTGGTGCTTTGTTGAGTACCCTATCCATTCGCCTCGGTTACAAGTTAAAGCAGGCAGTCGACTCCAAGCCGAAGCAAAATGCAACTACTGGTCAGAAAGgtccttatgtactgtttgggggacaccattctcccccttctgcgtttaatttttttatcctaagtgggaaaataaactcaacttaatagtcaaaatggtttagtgcctttgtctattgtggattcttacttcatattatttgttactacag

upper sequence: Vv16s0039g01400.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA09G35690.2 (Glycine max), 5'ss of exon 2
TGGGTCCTTCTTGCAGGGGGTGCTTTGTTAAGTACGCTATCCATTCGTCTTGGCTACAAGCTGAAGCAGGCTCTGGACACAAAGCAACAGGAGAATGCAAgtaatggtttgaaaggttttttcataa-gtaaagcattggcaagttttcttagtttac--ctgcttctaacattcagagttacttaa-aaattcag----------------------------------------------------------------------
       || |||| |  ||||||||||| ||||| ||||||||||| || || |||||| | ||||||||  | ||| | ||||   || | ||||||| || ||||  |||||||  ||   ||  ||   |      | | | | |    | | |   |  || |   || |  |||     || ||| |||                                                                       
------ATTTTTGCTGCTGGTGCTTTGTTGAGTACCCTATCCATTCGCCTCGGTTACAAGTTAAAGCAGGCAGTCGACTCCAAGCCGAAGCAAAATGCAACTACTGgtcagaaaggtccttatgtactgtttgggggacaccattctcccccttctgcgtttaatttttttatcctaagtgggaaaataaactcaacttaatagtcaaaatggtttagtgcctttgtctattgtggattcttacttcatattatttgttactacag

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|352786584|gb|FQ479791.1|FQ479791
EST:     TGGCTACAAGCTGAAGCAGGCTCTGGACACAAAGCAACAGGAGAATGCAA                         GTAGTGGGAAATCTGCTGACAGAAATAAGTCGGGAGCTTGTCGTTTGCATT
genomic: TGGCTACAAGCTGAAGCAGGCTCTGGACACAAAGCAACAGGAGAATGCAAgtaatggttt ... aaaaattcagGTAGTGGGAAATCTGCTGACAGAAATAAGTCGGGAGCTTGTCGTTTGCATT
EST: gi|110703635|gb|EE080653.1|EE080653
EST:     AGCAAGCTCTGGACACAAAGCAACAGGAGAATGCAA                         GTAGTGGGAAATCTGCTGACAGAAATAAGTCGGGAGCTTGTCGTTTGCATT
genomic: AGCAGGCTCTGGACACAAAGCAACAGGAGAATGCAAgtaatggttt ... aaaaattcagGTAGTGGGAAATCTGCTGACAGAAATAAGTCGGGAGCTTGTCGTTTGCATT
EST: gi|161716410|gb|FC064917.1|FC064917
EST:     TGGCTACAAGCTGAAGCAGGCTCTGGACACAAAGCAACAGGAGAATGCAA                         GTAGTGGGAAATCTGCTGACAGAAATAAGTCGGGAGCTTGTCGTTTGCATT
genomic: TGGCTACAAGCTGAAGCAGGCTCTGGACACAAAGCAACAGGAGAATGCAAgtaatggttt ... aaaaattcagGTAGTGGGAAATCTGCTGACAGAAATAAGTCGGGAGCTTGTCGTTTGCATT
EST: gi|351052473|gb|FQ452506.1|FQ452506
EST:     TGGCTACAAGCTGAAGCAGGCTCTGGACACAAAGCAACAGGAGAATGCAA                         GTAGTGGGAAATCTGCTGACAGAAATAAGTCGGGAGCTTGTCGTTTGCATT
genomic: TGGCTACAAGCTGAAGCAGGCTCTGGACACAAAGCAACAGGAGAATGCAAgtaatggttt ... aaaaattcagGTAGTGGGAAATCTGCTGACAGAAATAAGTCGGGAGCTTGTCGTTTGCATT
EST: gi|351034202|gb|FQ463136.1|FQ463136
EST:     TGGCTACAAGCTGAAGCAGGCTCTGGACACAAAGCAACAGGAGAATGCAA                         GTAGTGGGAAATCTGCTGACAGAAATAAGTCGGGAGCTTGTCGTTTGCATT
genomic: TGGCTACAAGCTGAAGCAGGCTCTGGACACAAAGCAACAGGAGAATGCAAgtaatggttt ... aaaaattcagGTAGTGGGAAATCTGCTGACAGAAATAAGTCGGGAGCTTGTCGTTTGCATT
EST: gi|351045451|gb|FQ440636.1|FQ440636
EST:     TGGCTACAAGCTGAAGCAGGCTCTGGACACAAAGCAACAGGAGAATGCAA                         GTAGTGGGAAATCTGCTGACAGAAATAAGTCGGGAGCTTGTCGTTTGCATT
genomic: TGGCTACAAGCTGAAGCAGGCTCTGGACACAAAGCAACAGGAGAATGCAAgtaatggttt ... aaaaattcagGTAGTGGGAAATCTGCTGACAGAAATAAGTCGGGAGCTTGTCGTTTGCATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGGTCCTTCTTGCAGGGGGTGCTTTGTTAAGTACGCTATCCATTCGTCTTGGCTACAAGCTGAAGCAGGCTCTGGACACAAAGCAACAGGAGAATGCAAgtaatggtttgaaaggttttttcataagtaaagcattggcaagttttcttagtttacctgcttctaacattcagagttacttaaaaattcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA