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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattcttgatcactatttttaccatgtatcataacaataaattgaagttattgaccatgctgcttatcttagtgttgcccatgtttatatgtataaacagGCTCAACAGGCTTACCTTATTGGCAATAAGGCACTAGCTAAGGAACTGAGCCTTAAAGGGAAGCTGCACAGCATTCATATGAAGGCAGCTCATGGAAAAG

Basic information

species Vitis vinifera
transcript Vv04s0008g02100.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g02100.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G33510.1 (Glycine max), 3'ss of exon 4
cattcttgatcactatttttaccatgtatcataacaataaattgaagtt-attgaccatgctgctt----atcttagtgttgcccatgtttatatgtataaacagGCTCAACAGGCTTACCTTATTGGCAATAAGGCACTAGCTAAGGAACTGAGCCTTAAAGGGAAGCTGCACAGCATTCATATGAAGGCAGCTCATGGAAAAG
    |   | |   | |||  || |||| |    ||| |  |  ||||  |   | | |  |  ||       | ||| |    | |  | ||||  |||||||||| | ||| || |||||||||||||| ||||| || || ||||| || ||  |||| ||| | ||||||| ||| |||||||| ||||||||||||||||
----caacaactgcactttatccctgtagctgggcaagaggtgtaagtccacccatcctaatattttgtagcttgagtttaattcttcataatata-ataaacagGCACGACAAGCCTACCTTATTGGCAACAAGGCCCTTGCAAAGGAGCTAAGTGTTAAGGGGCAACTGCACAACATGCATATGAAAGCAGCTCATGGAAAAG

upper sequence: Vv04s0008g02100.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G06030.2 (Glycine max), 3'ss of exon 4
cattcttgatcactatttttaccatgtatcataacaa-taaattgaagtt--attgaccatgctgcttatcttagtgttgcccatgtttatatgtataaacagGCTCAACAGGCTTACCTTATTGGCAATAAGGCACTAGCTAAGGAACTGAGCCTTAAAGGGAAGCTGCACAGCATTCATATGAAGGCAGCTCATGGAAAAG
  |  || |  | ||     || | || || || | | | | |||   ||  ||  |     ||  || | |||   ||       |||  || |  |||||||| || || || || |||||||| ||||| || ||||| |||||||| ||   ||||||| | ||||||| ||| ||||||||||  |||||||||||||
--tagttcaagaataaaca-acaaagtctcttatcgagtcatttgttcttgaatctatttgactttttgttttaagtttaatttctttttcatttgaaaacagGCACAGCAAGCCTATCTTATTGGTAATAAAGCCCTAGCAAAGGAACTAAGTGCTAAAGGGCAACTGCACAACATGCATATGAAGGTTGCTCATGGAAAAG

upper sequence: Vv04s0008g02100.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G06010.1 (Glycine max), 3'ss of exon 4
cattcttga-tcactatttttaccatgtatcataacaataaattgaagttattgaccatgctgcttatcttagtgtt-gcccatgtttatatgtataaacagGCTCAACAGGCTTACCTTATTGGCAATAAGGCACTAGCTAAGGAACTGAGCCTTAAAGGGAAGCTGCACAGCATTCATATGAAGGCAGCTCATGGAAAAG
  |||  || | |  |       |   |||     || |   ||      ||  |     ||  || | |||  |||        |||  || |  |||||||| || || || || || |||||  |||| || ||||| |||||||| ||   ||||||| | ||||||| ||| ||||||||||| |||||||||||||
agttcaagaataaacaacaaagtctcttattgagtcatttgtttttga--atctatttgacttttttttttaaagtttaattggattttaatttgaaaacagGCACAGCAAGCCTATCTAATTGGTGATAAAGCCCTAGCAAAGGAACTAAGTGCTAAAGGGCAACTGCACAACATGCATATGAAGGCTGCTCATGGAAAAG

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|110382278|gb|EC939049.1|EC939049
EST:     GGGAAGAAGCTCGTGACCATGCACGCCTACGTAATGCATATTTTGAACAG                         GCTCAACAGGCTTACCTTATTGGCAATAAGGCACTAGCTAAGGAACTGAGC
genomic: GGGAAGAAGCTCGTGACCATGCACGCCTACGTAATGCATATTTTGAACAGgtatatctta ... gtataaacagGCTCAACAGGCTTACCTTATTGGCAATAAGGCACTAGCTAAGGAACTGAGC
EST: gi|34543212|gb|CF511444.1|CF511444
EST:     GGGAAGAAGCTCGTGACCATGCACGCCTACGTAATGCATATTTTGAACAG                         GCTCAACAGGCTTACCTTATTGGCAATAAGGCACTAGCTAAGGAACTGAGC
genomic: GGGAAGAAGCTCGTGACCATGCACGCCTACGTAATGCATATTTTGAACAGgtatatctta ... gtataaacagGCTCAACAGGCTTACCTTATTGGCAATAAGGCACTAGCTAAGGAACTGAGC
EST: gi|161711452|gb|FC061217.1|FC061217
EST:     GGGAAGAAGCTCGTGACCATGCACGCCTACGTAATGCATATTTTGAACAG                         GCTCAACAGGCTTACCTTATTGGCAATAAGGCACTAGCTAAGGAACTGAGC
genomic: GGGAAGAAGCTCGTGACCATGCACGCCTACGTAATGCATATTTTGAACAGgtatatctta ... gtataaacagGCTCAACAGGCTTACCTTATTGGCAATAAGGCACTAGCTAAGGAACTGAGC
EST: gi|33403975|gb|CF209602.1|CF209602
EST:     GGGAAGAAGCTCGTGACCATGCACGCCTACGTAATGCATATTTTGAACAG                         GCTCAACAGGCTTACCTTATTGGCAATAAGGCACTAGCTAAGGAACTGAGC
genomic: GGGAAGAAGCTCGTGACCATGCACGCCTACGTAATGCATATTTTGAACAGgtatatctta ... gtataaacagGCTCAACAGGCTTACCTTATTGGCAATAAGGCACTAGCTAAGGAACTGAGC
EST: gi|34543102|gb|CF511334.1|CF511334
EST:     GGGAAGAAGCTCGTGACCATGCACGCCTACGTAATGCATATTTTGAACAG                         GCTCAACAGGCTTACCTTATTGGCAATAAGGCACTAGCTAAGGAACTGAGC
genomic: GGGAAGAAGCTCGTGACCATGCACGCCTACGTAATGCATATTTTGAACAGgtatatctta ... gtataaacagGCTCAACAGGCTTACCTTATTGGCAATAAGGCACTAGCTAAGGAACTGAGC
EST: gi|34543129|gb|CF511361.1|CF511361
EST:     GGGAAGAAGCTCGTGACCATGCACGCCTACGTAATGCATATTTTGAACAG                         GCTCAACAGGCTTACCTTATTGGCAATAAGGCACTAGCTAAGGAACTGAGC
genomic: GGGAAGAAGCTCGTGACCATGCACGCCTACGTAATGCATATTTTGAACAGgtatatctta ... gtataaacagGCTCAACAGGCTTACCTTATTGGCAATAAGGCACTAGCTAAGGAACTGAGC
EST: gi|34542306|gb|CF510538.1|CF510538
EST:     GGGAAGAAGCTCGTGACCATGCACGCCTACGTAATGCATATTTTGAACAG                         GCTCAACAGGCTTACCTTATTGGCAATAAGGCACTAGCTAAGGAACTGAGC
genomic: GGGAAGAAGCTCGTGACCATGCACGCCTACGTAATGCATATTTTGAACAGgtatatctta ... gtataaacagGCTCAACAGGCTTACCTTATTGGCAATAAGGCACTAGCTAAGGAACTGAGC
EST: gi|34542224|gb|CF510456.1|CF510456
EST:     GGGAAGAAGCTCGTGACCATGCACGCCTACGTAATGCATATTTTGAACAG                         GCTCAACAGGCTTACCTTATTGGCAATAAGGCACTAGCTAAGGAACTGAGC
genomic: GGGAAGAAGCTCGTGACCATGCACGCCTACGTAATGCATATTTTGAACAGgtatatctta ... gtataaacagGCTCAACAGGCTTACCTTATTGGCAATAAGGCACTAGCTAAGGAACTGAGC
EST: gi|33404062|gb|CF209689.1|CF209689
EST:     GGGAAGAAGCTCGTGACCATGCACGCCTACGTAATGCATATTTTGAACAG                         GCTCAACAGGCTTACCTTATTGGCAATAAGGCACTAGCTAAGGAACTGAGC
genomic: GGGAAGAAGCTCGTGACCATGCACGCCTACGTAATGCATATTTTGAACAGgtatatctta ... gtataaacagGCTCAACAGGCTTACCTTATTGGCAATAAGGCACTAGCTAAGGAACTGAGC
EST: gi|34543186|gb|CF511418.1|CF511418
EST:     GGGAAGAAGCTCGTGACCATGCACGCCTACGTAATGCATATTTTGAACAG                         GCTCAACAGGCTTACCTTATTGGCAATAAGGCACTAGCTAAGGAACTGAGC
genomic: GGGAAGAAGCTCGTGACCATGCACGCCTACGTAATGCATATTTTGAACAGgtatatctta ... gtataaacagGCTCAACAGGCTTACCTTATTGGCAATAAGGCACTAGCTAAGGAACTGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttattgaccatgctgcttatcttagtgttgcccatgtttatatgtataaacagGCTCAACAGGCTTACCTTATTGGCAATAAGGCACTAGCTAAGGAACTGAGCCTTAAAGGGAAGCTGCACAGCATTCATATGAAGGCAGCTCATGGAAAAG
   tattgac  putative branch site (score: 2)
                                   atgtttatatgtataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattcttgatcactatttttaccatgtatcataacaataaattgaagttattgaccatgctgcttatcttagtgttgcccatgtttatatgtataaacagGCTCAACAGGCTTACCTTATTGGCAATAAGGCACTAGCTAAGGAACTGAGCCTTAAAGGGAAGCTGCACAGCATTCATATGAAGGCAGCTCATGGAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - -ccatgta
- - - - - - - - - - - - - - - - - -aataaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - ccatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccatgt