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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcactcttagttcatacttgatacttctacagattatcatacagagcagcttttgatctgcaattatttatcatgtttttcttccctttattaaatagGAAGAAGGGGTGGAGATAACTGCTAATTCACTTCATCCTGGAGCAATTGCCACCAATCTTCTGCGGTACCACAGCTTTCTGGATG

Basic information

species Vitis vinifera
transcript Vv02s0025g03380.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g03380.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G01870.1 (Glycine max), 3'ss of exon 4
-------------------------------------------------------------------------------------tttcact--cttagttca-tacttgatacttctacagattatcataca------gagcagctt-ttgatctgcaattatttatcatgtttttct-tccctttattaaatagGAAGAAGGGGTGGAGATAACTGCTAATTCACTTCATCCTGGAGCAATTGCCACCAATCTTCTGCGGTACCACAGCTTTCTGGATG
                                                                                     | | | |  | |  |||| || | |||  | |    |  | |  |  |      || || ||| ||| ||     | || ||  ||  ||   | | || || ||  | |||||||||| ||||| |||||||  || || |||||||||||| ||||||  || ||| ||||||| |||||   || | |  |||
gtattatattcatgaaaagtcatctctaatttatggaatttcattgattccactttatttactgcaatatttagagtctcatgtctgtaaatagcctgcttcagtaatagattttcccgttgtcttttgtctaattattgaacaacttattggtcaagtttgatgtagaatccttgcatattcccttttttgacagGAAGAAGGAGTGGAAATAACTGTCAACTCCCTTCATCCTGGATCAATTGTTACAAATATTCTGCGATACCATGACTATATTAATG

upper sequence: Vv02s0025g03380.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT4G11410.1 (Arabidopsis thaliana), 3'ss of exon 5
tttcactcttagttcatacttgatacttctacagattatcatacagagcagcttttgatctgcaattatttatcatg-tttttcttccctttatt--aaatagGAAGAAGGGGTGGAGATAACTGCTAATTCACTTCATCCTGGAGCAATTGCCACCAATCTTCTGCGGTACCACAGCTTTCTGGATG
 |    |  || |||  | ||||| | |    ||   ||   | ||  ||       | ||  |    ||     || ||  ||||   |||  |  ||| ||||| |||| ||| | || |||||||||||||||||||||||| | |||   ||||||||| | || |||||||||||  |  || 
gtaagatagtatttcgcagttgattcgt----agtcaattccaaaggtcaaagagaaagctagaggagttaggtttggttcatctttgttttgcttaaaacagGAACAAGGTGTGAATATCACTGCTAATTCACTTCATCCTGGATCCATTATGACCAATCTTTTACGCTACCACAGCTTCATAAATA
















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|110362262|gb|EC925782.1|EC925782
EST:     CAAAGCTTGCTAACATATTGCACGCTAATGAGCTTGCAAAGCGCCTGCAG                         GAAGAAGGGGTGGAGATAACTGCTAATTCACTTCATCCTGGAGCAATTGCC
genomic: CAAAGCTTGCTAACATATTGCACGCTAATGAGCTTGCAAAGCGCCTGCAGgtactctata ... tattaaatagGAAGAAGGGGTGGAGATAACTGCTAATTCACTTCATCCTGGAGCAATTGCC
EST: gi|110369965|gb|EC934139.1|EC934139
EST:     CAAAGCTTGCTAACATATTGCACGCTAATGAGCTTGCAAAGCGCCTGCAG                         GAAGAAGGGGTGGAGATAACTGCTAATTCACTTCATCCTGGAGCAATTGCC
genomic: CAAAGCTTGCTAACATATTGCACGCTAATGAGCTTGCAAAGCGCCTGCAGgtactctata ... tattaaatagGAAGAAGGGGTGGAGATAACTGCTAATTCACTTCATCCTGGAGCAATTGCC
EST: gi|34543255|gb|CF511487.1|CF511487
EST:     CAAAGCTTGCTAACATATTGCACGCTAATGAGCTTGCAGAGCGCCTGCAG                         GAAGAAGGGGTGGAGATAACTGCTAATTCACTTCATCCTGGAGCAATTGCC
genomic: CAAAGCTTGCTAACATATTGCACGCTAATGAGCTTGCAAAGCGCCTGCAGgtactctata ... tattaaatagGAAGAAGGGGTGGAGATAACTGCTAATTCACTTCATCCTGGAGCAATTGCC
EST: gi|110394584|gb|EC959749.1|EC959749
EST:     CAAAGCTTGCTAACATATTGCACGCTAATGAGCTTGCAAAGCGCCTGCAG                         GAAGAAGGGGTGGAGATAACTGCTAATTCACTTCATCCTGGAGCAATTGCC
genomic: CAAAGCTTGCTAACATATTGCACGCTAATGAGCTTGCAAAGCGCCTGCAGgtactctata ... tattaaatagGAAGAAGGGGTGGAGATAACTGCTAATTCACTTCATCCTGGAGCAATTGCC
EST: gi|71868300|gb|DT017355.1|DT017355
EST:     CAAAGCTTGCTAACATATTGCACGCTAATGAGCTTGCAAAGCGCCTGCAG                         GAAGAAAAGGTGGAGATAACTGCTAATTCACTTCATCCTGGAGCAATTGCC
genomic: CAAAGCTTGCTAACATATTGCACGCTAATGAGCTTGCAAAGCGCCTGCAGgtactctata ... tattaaatagGAAGAAGGGGTGGAGATAACTGCTAATTCACTTCATCCTGGAGCAATTGCC
EST: gi|110361021|gb|EC924471.1|EC924471
EST:     CAAAGCTTGCTAACATATTGCACGCTAATGAGCTTGCAAAGCGCCTGCAG                         GAAGAAGGGGTGGAGATAACTGCTAATTCACTTCATCCTGGAGCAATTGCC
genomic: CAAAGCTTGCTAACATATTGCACGCTAATGAGCTTGCAAAGCGCCTGCAGgtactctata ... tattaaatagGAAGAAGGGGTGGAGATAACTGCTAATTCACTTCATCCTGGAGCAATTGCC
EST: gi|22007077|gb|BQ792111.1|BQ792111
EST:     CAAAGCTTGCTAACATATTGCACGCTAATGAGCATGCAAAGCGCCTGCAG                         GAAGAAGGGGTGGAGATAACTGCTAATTCACTTCATCCTGGAGCAATTGCC
genomic: CAAAGCTTGCTAACATATTGCACGCTAATGAGCTTGCAAAGCGCCTGCAGgtactctata ... tattaaatagGAAGAAGGGGTGGAGATAACTGCTAATTCACTTCATCCTGGAGCAATTGCC
EST: gi|110417605|gb|EC983675.1|EC983675
EST:     CAAAGCTTGCTAACATATTGCACGCTAATGAGCTTGCAAAGCGCCTGCAG                         GAAGAAGGCGTGGAGATAACTGCTAATTCACTTCATCCTGGAGCAATTGCC
genomic: CAAAGCTTGCTAACATATTGCACGCTAATGAGCTTGCAAAGCGCCTGCAGgtactctata ... tattaaatagGAAGAAGGGGTGGAGATAACTGCTAATTCACTTCATCCTGGAGCAATTGCC
EST: gi|34543342|gb|CF511574.1|CF511574
EST:     CAAAGCTTGCTAACATATTGCACGCTAATGAGCTTGCAGAGCGCCTGCAG                         GAAGAAGGGGTGGAGATAACTGCTAATTCACTTCATCCTGGAGCAATTGCC
genomic: CAAAGCTTGCTAACATATTGCACGCTAATGAGCTTGCAAAGCGCCTGCAGgtactctata ... tattaaatagGAAGAAGGGGTGGAGATAACTGCTAATTCACTTCATCCTGGAGCAATTGCC
EST: gi|110712661|gb|EE087900.1|EE087900
EST:     CAAAGCTTGCTAACATATTGCACGCTAATGAGCTTGCAAAGCGCCTGCAN                         GAAGAAGGCGTGGAGATAACTGCTAATTCACTTCATCCTGGAGCAATTGCC
genomic: CAAAGCTTGCTAACATATTGCACGCTAATGAGCTTGCAAAGCGCCTGCAGgtactctata ... tattaaatagGAAGAAGGGGTGGAGATAACTGCTAATTCACTTCATCCTGGAGCAATTGCC
EST: gi|34415314|gb|CF414068.1|CF414068
EST:     CAAAGCTTGCTAACATATTGCACGCTAATGAGCTTGCAAAGCGCCTGCAG                         GAAGAAGGGGTGGAGATAACTGCTAATTCACTTCATCCTGGAGCAATTGCC
genomic: CAAAGCTTGCTAACATATTGCACGCTAATGAGCTTGCAAAGCGCCTGCAGgtactctata ... tattaaatagGAAGAAGGGGTGGAGATAACTGCTAATTCACTTCATCCTGGAGCAATTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagcagcttttgatctgcaattatttatcatgtttttcttccctttattaaatagGAAGAAGGGGTGGAGATAACTGCTAATTCACTTCATCCTGGAGCAATTGCCACCAATCTTCTGCGGTACCACAGCTTTCTGGATG
       ttttgat  putative branch site (score: 4)
                       tttatcatgtttttct  putative PPT
                  aattatttatcatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcactcttagttcatacttgatacttctacagattatcatacagagcagcttttgatctgcaattatttatcatgtttttcttccctttattaaatagGAAGAAGGGGTGGAGATAACTGCTAATTCACTTCATCCTGGAGCAATTGCCACCAATCTTCTGCGGTACCACAGCTTTCTGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - -cttctac
- - - - - - - - - - - - - - - - - - - - atacaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgcaat