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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttcaactagtctttgcatctctcattactttatatttgcttttgttaatgtttaatatttaaagacattctaacccatcatgcgatatctatctgcagGCACTGCCAGTTTTTACATTTGCAAATCAGGCAGGGCTTGACATGCTTGAGACAACCTTAGTAGCCCTTCAGGATATAACTCTGGAGAAGACCTTTGATG

Basic information

species Vitis vinifera
transcript Vv04s0008g03250.t01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g03250.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA04G09000.1 (Glycine max), 3'ss of exon 13
--acttcaacta--gtctttgcatctctcattactttatatttgcttttgttaatgtttaatatttaaagacattctaacccatcatgcgatatctatctgcagGCACTGCCAGTTTTTACATTTGCAAATCAGGCAGGGCTTGACATGCTTGAGACAACCTTAGTAGCCCTTCAGGATATAACTCTGGAGAAGACCTTTGATG
   | | |  ||  ||||||  |  | |  || | | || |||  | || |  |    ||||||| || || | | |||      ||  ||| | | |   |||||| | || ||||| || ||||||||||| || || |||||||||||||||||||| || || || ||||| || || |||||||| ||||  |||||||
tatccttatttaccgtcttttaagttttatttccatcatttttcttattctacaatgataatatt-aaggaaagtataaata--tatatgatttttttgc-cagGCATTACCCGTTTTCACGTTTGCAAATCAAGCTGGACTTGACATGCTTGAGACAACATTGGTTGCACTTCAAGACATCACTCTGGAAAAGATTTTTGATG

upper sequence: Vv04s0008g03250.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA06G09100.2 (Glycine max), 3'ss of exon 7
---acttcaactagtctttgcatctctcattactttatatttgcttttgttaatgtttaatatttaaagacattctaacccatcatgcgatatctatctgcagGCACTGCCAGTTTTTACATTTGCAAATCAGGCAGGGCTTGACATGCTTGAGACAACCTTAGTAGCCCTTCAGGATATAACTCTGGAGAAGACCTTTGATG
    | | |  || | | |  |  | |  || | | || |||  | || |  |    || |||| || || ||| ||||  |  ||     || | ||  |||||| | || ||||| || ||||||||||| || || |||||||||||||||||||| || || || ||||| || || |||||||| ||||  |||||||
ttatccttatttactatcttgagttttatttccatcatttttcttattctacaatgatagtatt-aaggaaattataacttaatatatatgatttttc--cagGCATTACCCGTTTTCACGTTTGCAAATCAAGCTGGACTTGACATGCTTGAGACAACTTTGGTTGCACTTCAAGACATCACTCTGGAAAAGATTTTTGATG
















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|30252239|gb|CB969790.1|CB969790
EST:     TCAAAACTCTCTGGCATCACTCTGATGCTGTCATGTGCTGCTCGTTAAAG                         GCACTGCCAGTTTTTACATTTGCAAATCAGGCAGGGCTTGACATGCTTGAG
genomic: TCAAAACTCTCTGGCATCACTCTGATGCTGTCATGTGCTGCTCGTTAAAGgtaattgctt ... ctatctgcagGCACTGCCAGTTTTTACATTTGCAAATCAGGCAGGGCTTGACATGCTTGAG
EST: gi|30252269|gb|CB969820.1|CB969820
EST:     TCAAAACTCTCTGGCATCACTCTGATGCTGTCATGTGCTGCTCGTTAAAG                         GCACTGCCAGTTTTTACATTTGCAAATCAGGCAGGGCTTGACATGCTTGAG
genomic: TCAAAACTCTCTGGCATCACTCTGATGCTGTCATGTGCTGCTCGTTAAAGgtaattgctt ... ctatctgcagGCACTGCCAGTTTTTACATTTGCAAATCAGGCAGGGCTTGACATGCTTGAG
EST: gi|30252245|gb|CB969796.1|CB969796
EST:     TCAAAACTCTCTGGCATCACTCTGATGCTGTCATGTGCTGCTCGTTAAAG                         GCACTGCCAGTTTTTACATTTGCAAATCAGGCAGGGCTTGACATGCTTGAG
genomic: TCAAAACTCTCTGGCATCACTCTGATGCTGTCATGTGCTGCTCGTTAAAGgtaattgctt ... ctatctgcagGCACTGCCAGTTTTTACATTTGCAAATCAGGCAGGGCTTGACATGCTTGAG
EST: gi|30252272|gb|CB969823.1|CB969823
EST:     TCAAAACTCTCTGGCATCACTCTGATGCTGTCATGTGCTGCTCGTTAAAG                         GCACTGCCAGTTTTTACATTTGCAAATCAGGCAGGGCTTGACATGCTTGAG
genomic: TCAAAACTCTCTGGCATCACTCTGATGCTGTCATGTGCTGCTCGTTAAAGgtaattgctt ... ctatctgcagGCACTGCCAGTTTTTACATTTGCAAATCAGGCAGGGCTTGACATGCTTGAG
EST: gi|71872227|gb|DT021282.1|DT021282
EST:     TCAAAACTCTCTGGCATCACTCTGATGCTGTCATGTGCTGCTCGTTAAAG                         GCACTGCCAGTTTTTACATCTGCAAATCAGGCAGGGCTTGACATGCTTGAG
genomic: TCAAAACTCTCTGGCATCACTCTGATGCTGTCATGTGCTGCTCGTTAAAGgtaattgctt ... ctatctgcagGCACTGCCAGTTTTTACATTTGCAAATCAGGCAGGGCTTGACATGCTTGAG
EST: gi|77581121|gb|DV219486.1|DV219486
EST:     TCAAAACTCTCTGGCATCACTCTGATGCTGTCATGTGCTGCTCGTTAAAG                         GCACTGCCAGTTTTTACATTTGCAAATCAGGCAGGGCTTGACATGCTTGAG
genomic: TCAAAACTCTCTGGCATCACTCTGATGCTGTCATGTGCTGCTCGTTAAAGgtaattgctt ... ctatctgcagGCACTGCCAGTTTTTACATTTGCAAATCAGGCAGGGCTTGACATGCTTGAG
EST: gi|110364307|gb|EC923836.1|EC923836
EST:     TCAAAACTCTCTGGCATCACTCTGATGCTGTCATGTGCTGCTCGTTAAAG                         GCACTGCCAGTTTTTACATTTGCAAATCAGGCAGGGCTTGACATGCTTGAG
genomic: TCAAAACTCTCTGGCATCACTCTGATGCTGTCATGTGCTGCTCGTTAAAGgtaattgctt ... ctatctgcagGCACTGCCAGTTTTTACATTTGCAAATCAGGCAGGGCTTGACATGCTTGAG
EST: gi|22012604|gb|BQ797638.1|BQ797638
EST:     TCAAAACTCTCTGGCATCACTCTGATGCTGTCATGTGCTGCTCGTTAAAG                         GCACTGCCAGTTTTTACATTTGCAAATCAGGCAGGGCTTGACATGCTTGAG
genomic: TCAAAACTCTCTGGCATCACTCTGATGCTGTCATGTGCTGCTCGTTAAAGgtaattgctt ... ctatctgcagGCACTGCCAGTTTTTACATTTGCAAATCAGGCAGGGCTTGACATGCTTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttaatgtttaatatttaaagacattctaacccatcatgcgatatctatctgcagGCACTGCCAGTTTTTACATTTGCAAATCAGGCAGGGCTTGACATGCTTGAGACAACCTTAGTAGCCCTTCAGGATATAACTCTGGAGAAGACCTTTGATG
                        ttctaac  putative branch site (score: 1)
                                            tctatct  putative PPT
       tttaatatttaaagac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttcaactagtctttgcatctctcattactttatatttgcttttgttaatgtttaatatttaaagacattctaacccatcatgcgatatctatctgcagGCACTGCCAGTTTTTACATTTGCAAATCAGGCAGGGCTTGACATGCTTGAGACAACCTTAGTAGCCCTTCAGGATATAACTCTGGAGAAGACCTTTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
-cttcaac
- - - - - - ctttgca
- - - - - - - - - - ctctcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaagaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taaccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgcga