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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtacttttaatttaacttatgtttctgttagggaatttgatttggtgacattggtgttcttgtttttattatttatttatttttttctatagCAACTTGCCACGCATGGGCTGTTTGACGTTTGTGTGAAAGCGACCGGTGACACACACATTGATGATCATCATACAAATGAAGATGTTGCACTTGCGCTCG

Basic information

species Vitis vinifera
transcript Vv05s0020g03430.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g03430.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G28420.2 (Glycine max), 3'ss of exon 2
gtcagtacttttaatttaacttatgtttctgttaggg-----aatttgatttggtgacattggtgttcttgtttttattattt--atttattttt--ttctatagCAACTTGCCACGCATGGGCTGTTTGACGTTTGTGTGAAAGCGACCGGTGACACACACATTGATGATCATCATACAAATGAAGATGTTGCACTTGCGCTCG
     |  |   || | ||| |      ||  || ||     || ||  |    ||| ||| | | |  || ||     |  |  | ||  || |  || |  ||||||||||  | ||||||||||| || ||   ||| || || || ||||||| ||| |||||||||||||| ||||||||||| ||||| |||||  | |
-----tcttgacaactaaacattaaaggctactaaggatgtaaaattattcacttgagatttgagataatggttgaggaaactgaacttggttgtgatttttcagCAACTTGCTTCACATGGGCTGTTAGATGTACATGTAAAGGCTACAGGTGACATACATATTGATGATCATCACACAAATGAAGACGTTGCCCTTGCTATTG

upper sequence: Vv05s0020g03430.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G39370.1 (Glycine max), 3'ss of exon 2
------------------------gtcagtacttttaat-ttaacttatgtttctgttagggaatttgatttggtgacattggtgttcttgtttttattattta-tttattttt--ttctatagCAACTTGCCACGCATGGGCTGTTTGACGTTTGTGTGAAAGCGACCGGTGACACACACATTGATGATCATCATACAAATGAAGATGTTGCACTTGCGCTCG
                        |  |  | ||  | | |||     || |  |      | || | |  |  |   |||    |  | ||| |    | | |  ||  || |  || |  ||||||||||  | || |||||||| || ||  |  | || || || ||||||| ||| |||||||||||||| || |||||||| ||||| |||||  | |
gtctagaaaagaatttatctccttggaaagatttgcattgttagaacctgatcataaataaggatgtaaaattattcaattaaaataatagttatggaaactaaacttggttgtgatttttcagCAACTTGCTTCACACGGGCTGTTCGATGTACGCATAAAGGCTACAGGTGACATACATATTGATGATCATCACACGAATGAAGACGTTGCCCTTGCTATTG

upper sequence: Vv05s0020g03430.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G14910.2 (Arabidopsis thaliana), 3'ss of exon 2
-----------------------------------------------------------gtcagtacttttaattt-------aacttatgtttctgttagggaatttgatttg-----gtgacattggtgttcttgtttttattatttatttatttttttctatagCAACTTGCCACGCATGGGCTGTTTGACGTTTGTGTGAAAGCGACCGGTGACACACACATTGATGATCATCATACAAATGAAGATGTTGCACTTGCGCTCG
                                                            | | || |||| |  |       | ||||      | | ||    ||   |||      ||   ||||   || |      | || ||| |  ||| ||||   |||||||||||  | |||||  |||| || ||    || | ||| || ||||| || |||||||||||||||||||| |||||||||||||| |||||  | |
gtaactaaacctttctccgtatcaatttgattttctgggagttgaaaatttcctcatgtttgattatttttgacattggaaagagcttaaacacttatgagtcggttcattttatatatgttgtattgaaattttatcaagtgttgtttgtg-attcttttgattagCAACTTGCTTCACATGGCTTGTTCGATGTACACGTAAGAGCTACTGGTGATACTCACATTGATGATCATCATACTAATGAAGATGTTGCTCTTGCCATTG

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|349810627|gb|FQ402870.1|FQ402870
EST:     GCGTTGCTCAAAATGATACTGGAATCCCCTTTCTCGATCATATGTTAGAT                         CAACTTGCCACGCATGGGCTGTTTGACGTTTGTGTGAAAGCGACCGGTGAC
genomic: GCGTTGCTCAAAATGATACTGGAATCCCCTTTCTCGATCATATGTTAGATgtcagtactt ... ttttctatagCAACTTGCCACGCATGGGCTGTTTGACGTTTGTGTGAAAGCGACCGGTGAC
EST: gi|349819838|gb|FQ404584.1|FQ404584
EST:     GCGTTGCTCAAAATGATACTGGAATCCCCTTTCTCGATCATATGTTAGAT                         CAACTTGCCACGCATGGGCTGTTTGACGTTTGTGTGAAAGCGACCGGTGAC
genomic: GCGTTGCTCAAAATGATACTGGAATCCCCTTTCTCGATCATATGTTAGATgtcagtactt ... ttttctatagCAACTTGCCACGCATGGGCTGTTTGACGTTTGTGTGAAAGCGACCGGTGAC
EST: gi|110373814|gb|EC938184.1|EC938184
EST:     GCGTTGCTCAAAATGATACTGGAATCCCCTTTCTCGATCATATGTTAGAT                         CAACTTGCCACGCATGGGCTGTTTGACGTTTGTGTGAAAGCGACCGGTGAC
genomic: GCGTTGCTCAAAATGATACTGGAATCCCCTTTCTCGATCATATGTTAGATgtcagtactt ... ttttctatagCAACTTGCCACGCATGGGCTGTTTGACGTTTGTGTGAAAGCGACCGGTGAC
EST: gi|32269286|gb|CD718445.1|CD718445
EST:     GCGTTGCTCAAAATGATACTGGAATCCCCTTTCTCGATCATATGTTAGAT                         CAACTTGCCACGCATGGGCTGTTTGACGTTTGTGTGAAAGCGACCGGTGAC
genomic: GCGTTGCTCAAAATGATACTGGAATCCCCTTTCTCGATCATATGTTAGATgtcagtactt ... ttttctatagCAACTTGCCACGCATGGGCTGTTTGACGTTTGTGTGAAAGCGACCGGTGAC
EST: gi|30303775|gb|CB980569.1|CB980569
EST:     GCGTTGCTCAAAATGATACTGGAATCCCCTTTCTCGATCATATGTTAGAT                         CAACTTGCCACGCATGGGCTGTTTGACGTTTGTGTGAAAGCGACCGGTGAC
genomic: GCGTTGCTCAAAATGATACTGGAATCCCCTTTCTCGATCATATGTTAGATgtcagtactt ... ttttctatagCAACTTGCCACGCATGGGCTGTTTGACGTTTGTGTGAAAGCGACCGGTGAC
EST: gi|161721145|gb|FC070387.1|FC070387
EST:     GCGTTGCTCAAAATGATACTGGAATCCCCTTTCTCGATCATATGTTAGAT                         CAACTTGCCACGCATGGGCTGTTTGACGTTTGTGTGAAAGCGACCGGTGAC
genomic: GCGTTGCTCAAAATGATACTGGAATCCCCTTTCTCGATCATATGTTAGATgtcagtactt ... ttttctatagCAACTTGCCACGCATGGGCTGTTTGACGTTTGTGTGAAAGCGACCGGTGAC
EST: gi|71859299|gb|DT008354.1|DT008354
EST:     GCGTTGCTCAAAATGATACTGGAATCCCCTTTCTCGATCATATGTTAGAT                         CAACTTGCCACGCATGGGCTGTTTGACGTTTGTGTGAAAGCGACCGGTGAC
genomic: GCGTTGCTCAAAATGATACTGGAATCCCCTTTCTCGATCATATGTTAGATgtcagtactt ... ttttctatagCAACTTGCCACGCATGGGCTGTTTGACGTTTGTGTGAAAGCGACCGGTGAC
EST: gi|349808885|gb|FQ406735.1|FQ406735
EST:     GCGTTGCTCAAAATGATACTGGAATCCCCTTTCTCGATCATATGTTAGAT                         CAACTTGCCACGCATGGGCTGTTTGACGTTTGTGTGAAAGCGACCGGTGAC
genomic: GCGTTGCTCAAAATGATACTGGAATCCCCTTTCTCGATCATATGTTAGATgtcagtactt ... ttttctatagCAACTTGCCACGCATGGGCTGTTTGACGTTTGTGTGAAAGCGACCGGTGAC
EST: gi|32272189|gb|CD721348.1|CD721348
EST:     GCGTTGCTCAAAATGATACTGGAATCCCCTTTCTCGATCATATGTTAGAT                         CAACTTGCCACGCATGGGCTGTTTGACGTTTGTGTGAAAGCGACCGGTGAC
genomic: GCGTTGCTCAAAATGATACTGGAATCCCCTTTCTCGATCATATGTTAGATgtcagtactt ... ttttctatagCAACTTGCCACGCATGGGCTGTTTGACGTTTGTGTGAAAGCGACCGGTGAC
EST: gi|110386630|gb|EC951244.1|EC951244
EST:     GCGTTGCTCAAAATGATACTGGAATCCCCTTTCTCGATCATATGTTAGAT                         CAACTTGCCACGCATGGGCTGTTTGACGTTTGTGTGAAAGCGACCGGTGAC
genomic: GCGTTGCTCAAAATGATACTGGAATCCCCTTTCTCGATCATATGTTAGATgtcagtactt ... ttttctatagCAACTTGCCACGCATGGGCTGTTTGACGTTTGTGTGAAAGCGACCGGTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatttggtgacattggtgttcttgtttttattatttatttatttttttctatagCAACTTGCCACGCATGGGCTGTTTGACGTTTGTGTGAAAGCGACCGGTGACACACACATTGATGATCATCATACAAATGAAGATGTTGCACTTGCGCTCG
 atttgat  putative branch site (score: 5)
                                  tttatttatttttttc  putative PPT
                 tgttcttgtttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtacttttaatttaacttatgtttctgttagggaatttgatttggtgacattggtgttcttgtttttattatttatttatttttttctatagCAACTTGCCACGCATGGGCTGTTTGACGTTTGTGTGAAAGCGACCGGTGACACACACATTGATGATCATCATACAAATGAAGATGTTGCACTTGCGCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG