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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttattttttatttcaattttatagattatcttcatttgttattgtgagtttgagtttgatgctattaatcttataagagggttggtattcttttgagcagGTCCCAGCAGAAAACCATCATAAATGCTATGGCTGTCAATGAAGAAGGTGTGATGGCTACAGCAG

Basic information

species Vitis vinifera
transcript Vv05s0077g02310.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0077g02310.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: LOC_Os03g21990.1 (Oryza sativa), 3'ss of exon 15
ttattttttatttcaa---ttttatagattatcttcatttgttattgtgagtttg--agtttgatgcta-ttaatcttataagagggttggtattcttttgagcagGTCCCAGCAGAAAACCATCATAAATGCTATGGCTGTCAATGAAGAAGGTGTGATGGCTACAGCAG
     | | |||||||    |||    | | |  | | |||| |  |     | |  ||  | ||   | |||| ||| | |  |  |||  |   ||     |||||||||||||||||||||||||||  | |||||||| |||||||| |||||  |||| || | ||
agcaatgtgatttcaagggctttgcttactgttgtaacttgtaaacgaacaatagctaggatcatataacttaaacttgtcaccga-ttgtcaccttt-----cagGTCCCAGCAGAAAACCATCATAAACTCAATGGCTGTAAATGAAGATGGTGTCTTGGCAACTGGAG
















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|110416775|gb|EC982779.1|EC982779
EST:     AACATAAAGAAATTTAATCTTCCGAAAGGGGAATTTTTGCACAACATGCT                         GTCCCAGCAGAAAACCATCATAAATGCTATGGCTGTCAATGAAGAAGGTGT
genomic: AACATAAAGAAATTTAATCTTCCGAAAGGGGAATTTTTGCACAACATGCTgtgagttttc ... ttttgagcagGTCCCAGCAGAAAACCATCATAAATGCTATGGCTGTCAATGAAGAAGGTGT
EST: gi|83275899|gb|DV939907.1|DV939907
EST:     ACATAAAGAAATTTAA-CTTCCGAAAGGAGAATTTTTGCACAACATGCT                         GTCCCAGCAGAAAACCATCATAAATGCTATGGCTGTCAATGAAGAAGGTGT
genomic: ACATAAAGAAATTTAATCTTCCGAAAGGGGAATTTTTGCACAACATGCTgtgagttttc ... ttttgagcagGTCCCAGCAGAAAACCATCATAAATGCTATGGCTGTCAATGAAGAAGGTGT
EST: gi|254917683|gb|GR903335.1|GR903335
EST:     AACATAAAGAAATTTAATCTTCCGAAAGGGGAATTTTTGCACAACATGCT                         GTCCCAGCAGAAAACCATCATAAATGCTATGGCTGTCAATGAAGAAGGTGT
genomic: AACATAAAGAAATTTAATCTTCCGAAAGGGGAATTTTTGCACAACATGCTgtgagttttc ... ttttgagcagGTCCCAGCAGAAAACCATCATAAATGCTATGGCTGTCAATGAAGAAGGTGT
EST: gi|349818063|gb|FQ408838.1|FQ408838
EST:     AACATAAAGAAATTTAATCTTCCGAAAGGGGAATTTTTGCACAACATGCT                         GTCCCAGCAGAAAACCATCATAAATGCTATGGCTGTCAATGAAGAAGGTGT
genomic: AACATAAAGAAATTTAATCTTCCGAAAGGGGAATTTTTGCACAACATGCTgtgagttttc ... ttttgagcagGTCCCAGCAGAAAACCATCATAAATGCTATGGCTGTCAATGAAGAAGGTGT
EST: gi|351038798|gb|FQ464664.1|FQ464664
EST:     AACATAAAGAAATTTAATCTTCCGAAAGGGGAATTTTTGCACAACATGCT                         GTCCCAGCAGAAAACCATCATAAATGCTATGGCTGTCAATGAAGAAGGTGT
genomic: AACATAAAGAAATTTAATCTTCCGAAAGGGGAATTTTTGCACAACATGCTgtgagttttc ... ttttgagcagGTCCCAGCAGAAAACCATCATAAATGCTATGGCTGTCAATGAAGAAGGTGT
EST: gi|110384526|gb|EC948969.1|EC948969
EST:     AACATAAAGAAATTTAATCTTCCGAAAGGAGAATTTTTGCACAACATGCT                         GTCCCAGCAGAAAACCATCATAAATGCTATGGCTGTCAATGAAGAAGGTGT
genomic: AACATAAAGAAATTTAATCTTCCGAAAGGGGAATTTTTGCACAACATGCTgtgagttttc ... ttttgagcagGTCCCAGCAGAAAACCATCATAAATGCTATGGCTGTCAATGAAGAAGGTGT
EST: gi|110724126|gb|EE099691.1|EE099691
EST:     AACATAAAGAAATTTAATCTTCCGAAAGGGGAATTTTTGCACAACATGCT                         GTCCCAGCAGAAAACCATCATAAATGCTATGGCTGTCAATGAAGAAGGTGT
genomic: AACATAAAGAAATTTAATCTTCCGAAAGGGGAATTTTTGCACAACATGCTgtgagttttc ... ttttgagcagGTCCCAGCAGAAAACCATCATAAATGCTATGGCTGTCAATGAAGAAGGTGT
EST: gi|110418369|gb|EC984516.1|EC984516
EST:     AACATAAAGAAATTTAATCTTCCGAAAGGAGAATTTTTGCACAACATGCT                         GTCCCAGCAGAAAACCATCATAAATGCTATGGCTGTCAATGAAGAAGGTGT
genomic: AACATAAAGAAATTTAATCTTCCGAAAGGGGAATTTTTGCACAACATGCTgtgagttttc ... ttttgagcagGTCCCAGCAGAAAACCATCATAAATGCTATGGCTGTCAATGAAGAAGGTGT
EST: gi|110418288|gb|EC984425.1|EC984425
EST:     AACATAAAGAAATTTAATCTTCCGAAAGGAGAATTTTTGCACAACATGCT                         GTCCCAGCAGAAAACCATCATAAATGCTATGGCTGTCAATGAAGAAGGTGT
genomic: AACATAAAGAAATTTAATCTTCCGAAAGGGGAATTTTTGCACAACATGCTgtgagttttc ... ttttgagcagGTCCCAGCAGAAAACCATCATAAATGCTATGGCTGTCAATGAAGAAGGTGT
EST: gi|77581807|gb|DV219858.1|DV219858
EST:     AACATAAAGAAATTTAATCTTCCGAAAGGGGAATTTTTGCACAACATGCT                         GTCCCAGCAGAAAACCATCATAAATGCTATGGCTGTCAATGAAGAAGGTGT
genomic: AACATAAAGAAATTTAATCTTCCGAAAGGGGAATTTTTGCACAACATGCTgtgagttttc ... ttttgagcagGTCCCAGCAGAAAACCATCATAAATGCTATGGCTGTCAATGAAGAAGGTGT
EST: gi|110699826|gb|EE077177.1|EE077177
EST:     AATTTTTGCACAACATGCT                         GTCCCAGCAGAAAACCATCATAAATGCTATGGCTGTCAATGAAGAAGGTGT
genomic: AATTTTTGCACAACATGCTgtgagttttc ... ttttgagcagGTCCCAGCAGAAAACCATCATAAATGCTATGGCTGTCAATGAAGAAGGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtttgagtttgatgctattaatcttataagagggttggtattcttttgagcagGTCCCAGCAGAAAACCATCATAAATGCTATGGCTGTCAATGAAGAAGGTGTGATGGCTACAGCAG
                 tattaat  putative branch site (score: 2)
                                        tattctttt  putative PPT
                 tattaatcttataaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttattttttatttcaattttatagattatcttcatttgttattgtgagtttgagtttgatgctattaatcttataagagggttggtattcttttgagcagGTCCCAGCAGAAAACCATCATAAATGCTATGGCTGTCAATGAAGAAGGTGTGATGGCTACAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggttgg