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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccttctgaaccatatatcctgattgaggacaccttctaaaactggttagtgtaatatattttatgtttctattgaacttgttctgattattatgtcacagGTCATTACAGGTTTTGAACCAAAAGAACGCTGTATGCTTCTTAAATTTGTGACAAGTTGTTCTCGAGCTCCATTACTTGGATTTAAACACCTGCAGCCAA

Basic information

species Vitis vinifera
transcript Vv08s0007g04290.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g04290.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os03g47949.1 (Oryza sativa), 3'ss of exon 7
ccttctgaaccatatatcctgattgaggacaccttctaaaa---ctggttagtgtaatatattttatgtttctattgaacttgttctgattattatgtcacagGTCATTACAGGTTTTGAACCAAAAGAACGCTGTATGCTTCTTAAATTTGTGACAAGTTGTTCTCGAGCTCCATTACTTGGATTTAAACACCTGCAGCCAA
       | | || | | ||||||||  | |      | ||    |||| |  |    |  |   ||| |  || | ||  | |  |  ||   ||||  ||||| || | ||| ||| | |||| |||||| || ||||| || || ||||||||||| ||||| |||||||||||||||||||| ||  |  |||||||  
-agatgaagctatttttactgattgacaataaacaaaagaaattttggtgaaggctgaa-gtggaatgatcataataaaaatatggtttttggaatgt-gcagGTTATCAAAGGATTTAAGCCAACAGAACGTTGCATGCTACTGAAGTTTGTGACAAGCTGTTCCCGAGCTCCATTACTTGGATTCAAGTATTTGCAGCCTT

upper sequence: Vv08s0007g04290.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA03G34650.1 (Glycine max), 3'ss of exon 12
ccttctgaaccatatatcctga--ttgaggacacc--ttctaaaactggttagtgtaatatattttatgtttctattgaacttgttctgattattatgtcacagGTCATTACAGGTTTTGAACCAAAAGAACGCTGTATGCTTCTTAAATTTGTGACAAGTTGTTCTCGAGCTCCATTACTTGGATTTAAACACCTGCAGCCAA
|||  ||||  |||| |   ||  ||  | |  |   || |  |  ||   | | ||| |||| |    |||  |||       ||||    | | ||| |||||| |||| ||| |||||||| ||||| ||||||||||||||||||||||| || ||||||||||| |||||||||||||| || ||| || |||||||| 
cctggtgaattatatttgaagagtttatgcatgctatttgtgcagatgccaattttaagatatct---attttcattttctgctttcttccaactgtgt-acagGTAATTAAAGGCTTTGAACCTAAAGAGCGCTGTATGCTTCTTAAATTTGTCACCAGTTGTTCTCGTGCTCCATTACTTGGGTTCAAATACTTGCAGCCAC

upper sequence: Vv08s0007g04290.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA19G37310.3 (Glycine max), 3'ss of exon 13
-ccttctgaaccatatatcctgattgagg---acaccttctaaaactggttagtgtaatatattttatgtttctattgaacttgttctgattattatgtcacagGTCATTACAGGTTTTGAACCAAAAGAACGCTGTATGCTTCTTAAATTTGTGACAAGTTGTTCTCGAGCTCCATTACTTGGATTTAAACACCTGCAGCCAA
 |||  |||   ||||       || | |    |   || |  |  ||   | | ||| |||| | |||||| | ||   |||  ||||   | | ||| |||||| |||| ||| |||||||| ||||| ||||||||||||||||||||||| || ||||||||||| || ||||||||||| || ||| || |||||||| 
gcctcatgagttatattgaagagttcatgcatgctatttgtgcagatgccaattttaagatatct-atgtttattttctgctt--tctgccaactgtgt-acagGTAATTAAAGGCTTTGAACCTAAAGAGCGCTGTATGCTTCTTAAATTTGTCACCAGTTGTTCTCGTGCCCCATTACTTGGGTTCAAATACTTGCAGCCAC

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|110373009|gb|EC937214.1|EC937214
EST:     ACACAGGCGGTTATAGTGAGGGCAGCCGGACAGTTAAACTCTTTTGGGAG                         GTCATTACAGGTTTTGAACCAAAAGAACGCTGTATGCTTCTTAAATTTGTG
genomic: ACACAGGCGGTTATACTGAGGGCAGCCGGACAGTTAAACTCTTTTGGGAGgtattgatac ... tatgtcacagGTCATTACAGGTTTTGAACCAAAAGAACGCTGTATGCTTCTTAAATTTGTG
EST: gi|110380386|gb|EC945648.1|EC945648
EST:     ACACAGGCGGTTATAGTGAGGGCAGCCGGACAGTTAAACTCTTTTGGGAG                         GTCATTACAGGTTTTGAACCAAAAGAACGCTGTATGCTTCTTAAATTTGTG
genomic: ACACAGGCGGTTATACTGAGGGCAGCCGGACAGTTAAACTCTTTTGGGAGgtattgatac ... tatgtcacagGTCATTACAGGTTTTGAACCAAAAGAACGCTGTATGCTTCTTAAATTTGTG
EST: gi|110363275|gb|EC926852.1|EC926852
EST:     ACACAGGCTGTTATACTGAGGGCAGCCGGACAGTTAAACTCTTTTGGGAG                         GTCATTACAGGTTTTGAACCAAAAGAACGCTGTATGCTTCTTAAATTTGTG
genomic: ACACAGGCGGTTATACTGAGGGCAGCCGGACAGTTAAACTCTTTTGGGAGgtattgatac ... tatgtcacagGTCATTACAGGTTTTGAACCAAAAGAACGCTGTATGCTTCTTAAATTTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagtgtaatatattttatgtttctattgaacttgttctgattattatgtcacagGTCATTACAGGTTTTGAACCAAAAGAACGCTGTATGCTTCTTAAATTTGTGACAAGTTGTTCTCGAGCTCCATTACTTGGATTTAAACACCTGCAGCCAA
                                   ttctgat  putative branch site (score: 3)
      taatatattttatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccttctgaaccatatatcctgattgaggacaccttctaaaactggttagtgtaatatattttatgtttctattgaacttgttctgattattatgtcacagGTCATTACAGGTTTTGAACCAAAAGAACGCTGTATGCTTCTTAAATTTGTGACAAGTTGTTCTCGAGCTCCATTACTTGGATTTAAACACCTGCAGCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
ccttctg
- - - -aaccata
- - - - - - - - -cctgatt
- - - - - - - - - - - - - - -caccttc
- - - - - - - - - - - - - - - - - - - - - tggttag