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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGGAGGATGCAGGCTACGCTGTTGGGGCCCGAGTTCTAGAACTCCTTTGCCATAGGGATAAGgtgtgatgctttctcattagacatctttaacatgtgcatattatcatttgttgacaatgaatggtttattatttatgtgaattatattaattaatccaaa...

Basic information

species Vitis vinifera
transcript Vv11s0037g00110.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0037g00110.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA11G34840.1 (Glycine max), 5'ss of exon 4
ACTGGAGGATGCAGGCTACGCTGTTGGGGCCCGAGTTCTAGAACTCCTTTGCCATAGGGATAAGgtgtgatgctttctcattagacatctttaacatgtgcatattatcatttgttgacaatgaa-tggtttattatttatgtgaattatattaattaatccaaa---------
|||||||||||| || || || |||||||| |||||||| || || |||||||| || |||||||| || |  | | ||| |||   || | ||         |  || | ||||| |  || |  ||| |||    |   |  ||| | ||||   || |             
ACTGGAGGATGCTGGATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGgtatggt-ttctgtcactagttctcgtaaa---------agaattagttgtttatcataacctggattaaatatcgaggaaatcaaattaggcaacctcggaccctgatt

upper sequence: Vv11s0037g00110.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA18G03480.1 (Glycine max), 5'ss of exon 4
ACTGGAGGATGCAGGCTACGCTGTTGGGGCCCGAGTTCTAGAACTCCTTTGCCATAGGGATAAGgtgtgatgctttctcattagacatctttaacatgtgcatattatcatttgttgacaatgaatggtttattatttatgtgaattatattaattaatccaaa----
 ||||||||||| || || || |||||||| |||||||| || || |||||||| || |||||||| ||  |  |  ||| |||   |  | ||  | | |||  | |    |  | |  || ||   |  |  |   ||   | |   ||     |||||       
-CTGGAGGATGCTGGATATGCGGTTGGGGCTCGAGTTCTTGAGCTGCTTTGCCACAGAGATAAGGtatgccggctg-tcactagttcttgtaaaatttttcattgttttgcataatcaagattaaatatcaaggaa--atcaaattcgaatctggcaatcctggaccc
















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|110415074|gb|EC980946.1|EC980946
EST:     GCTACGCTGTTGGGGCCCGAGTTCTAGAACTCCTTTGCCATAGGGATAAG                         GGAAACAGAAGGGAGACACGACTATTGGGTATTCTTTCTTTTGTACACAGT
genomic: GCTACGCTGTTGGGGCCCGAGTTCTAGAACTCCTTTGCCATAGGGATAAGgtgtgatgct ... gatgccacagGGAAACAGAAGGGAGACACGACTATTGGGTATTCTTTCTTTTGTACACAGT
EST: gi|34543363|gb|CF511595.1|CF511595
EST:     TACGCTGTTGGGGCCCGAGTTCTAGGACTCCTTTGCCATAGGGATAAG                         GGAAACAGAAGGGAGACACGCCTATTGGGTATTCTTTCTTTTGTACACAGT
genomic: TACGCTGTTGGGGCCCGAGTTCTAGAACTCCTTTGCCATAGGGATAAGgtgtgatgct ... gatgccacagGGAAACAGAAGGGAGACACGACTATTGGGTATTCTTTCTTTTGTACACAGT
EST: gi|34543277|gb|CF511509.1|CF511509
EST:     GCTACGCTGTTGGGGCCCGAGTTCTAGGACTCCTTTGCCATAGGGATAAG                         GGAAACAGAAGGGAGACACGACTATTGGGTATTCTTTCTTTTGTACACAGT
genomic: GCTACGCTGTTGGGGCCCGAGTTCTAGAACTCCTTTGCCATAGGGATAAGgtgtgatgct ... gatgccacagGGAAACAGAAGGGAGACACGACTATTGGGTATTCTTTCTTTTGTACACAGT
EST: gi|349827547|gb|FQ422415.1|FQ422415
EST:     GCTACGCTGTTGGGGCCCGAGTTCTAGAACTCCTTTGCCATAGGGATAAG                         GGAAACAGAAGGGAGACACGACTATTGGGTATTCTTTCTTTTGTACACAGT
genomic: GCTACGCTGTTGGGGCCCGAGTTCTAGAACTCCTTTGCCATAGGGATAAGgtgtgatgct ... gatgccacagGGAAACAGAAGGGAGACACGACTATTGGGTATTCTTTCTTTTGTACACAGT
EST: gi|351018852|gb|FQ425754.1|FQ425754
EST:     GCTACGCTGTTGGGGCCCGAGTTCTAGAACTCCTTTGCCATAGGGATAAG                         GGAAACAGAAGGGAGACACGACTATTGGGTATTCTTTCTTTTGTACACAGT
genomic: GCTACGCTGTTGGGGCCCGAGTTCTAGAACTCCTTTGCCATAGGGATAAGgtgtgatgct ... gatgccacagGGAAACAGAAGGGAGACACGACTATTGGGTATTCTTTCTTTTGTACACAGT
EST: gi|33408903|gb|CF214530.1|CF214530
EST:     GCTACGCTGTTGGGGCCCGAGTTCTAGAACTCCTTTGCCATAGGGATAAG                         GGAAACAGAAGGGAGACACGACTATTGGGTATTCTTTCTTTTGTACACAGT
genomic: GCTACGCTGTTGGGGCCCGAGTTCTAGAACTCCTTTGCCATAGGGATAAGgtgtgatgct ... gatgccacagGGAAACAGAAGGGAGACACGACTATTGGGTATTCTTTCTTTTGTACACAGT
EST: gi|110406906|gb|EC972493.1|EC972493
EST:     GCTACGCTGTTGGGGCCCGAGTTCTAGAACTCCTTTGCCATAGGGATAAG                         GGAAACAGAAGGGAGACACGACTATTGGGTATTCTTTCTTTTGTACACAGT
genomic: GCTACGCTGTTGGGGCCCGAGTTCTAGAACTCCTTTGCCATAGGGATAAGgtgtgatgct ... gatgccacagGGAAACAGAAGGGAGACACGACTATTGGGTATTCTTTCTTTTGTACACAGT
EST: gi|351041121|gb|FQ444098.1|FQ444098
EST:     GCTACGCTGTTGGGGCCCGAGTTCTAGAACTCCTTTGCCGTAGGGATAAG                         GGAAACAGAAGGGAGACACGACTATTGGGTATTCTTTCTTTTGTACACAGT
genomic: GCTACGCTGTTGGGGCCCGAGTTCTAGAACTCCTTTGCCATAGGGATAAGgtgtgatgct ... gatgccacagGGAAACAGAAGGGAGACACGACTATTGGGTATTCTTTCTTTTGTACACAGT
EST: gi|33408990|gb|CF214617.1|CF214617
EST:     GCTACGCTGTTGGGGCCCGAGTTCTAGAACTCCTTTGCCATAGGGATAAG                         GGAAACAGAAGGGAGACACGACTATTGGGTATTCTTTCTTTTGTACACAGT
genomic: GCTACGCTGTTGGGGCCCGAGTTCTAGAACTCCTTTGCCATAGGGATAAGgtgtgatgct ... gatgccacagGGAAACAGAAGGGAGACACGACTATTGGGTATTCTTTCTTTTGTACACAGT
EST: gi|349827476|gb|FQ422344.1|FQ422344
EST:     GCTACGCTGTTGGGGCCCGAGTTCTAGAACTCCTTTGCCATAGGGATAAG                         GGAAACAGAAGGGAGACACGACTATTGGGTATTCTTTCTTTTGTACACAGT
genomic: GCTACGCTGTTGGGGCCCGAGTTCTAGAACTCCTTTGCCATAGGGATAAGgtgtgatgct ... gatgccacagGGAAACAGAAGGGAGACACGACTATTGGGTATTCTTTCTTTTGTACACAGT
EST: gi|110362846|gb|EC926403.1|EC926403
EST:     GCTACGCTGTTGGGGCCCGAGTTCTAGAACTCCTTTGCCATAGGGATAAG                         GGAAACAGAAGGGAGACACGACTATTGGGTATTCTTTCTTTTGTACACAGT
genomic: GCTACGCTGTTGGGGCCCGAGTTCTAGAACTCCTTTGCCATAGGGATAAGgtgtgatgct ... gatgccacagGGAAACAGAAGGGAGACACGACTATTGGGTATTCTTTCTTTTGTACACAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTGGAGGATGCAGGCTACGCTGTTGGGGCCCGAGTTCTAGAACTCCTTTGCCATAGGGATAAGgtgtgatgctttctcattagacatctttaacatgtgcatattatcatttgttgacaatgaatggtttattatttatgtgaattatattaattaatccaaa

- - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaatgaa