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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaggagttattaatataaccttaacctatttctgtataatgcttacttggttttgaacttttattctttcgtctgcagTTGTTTCCTAGTCTTAACAAGATAGTGTTCCTCGACGATGACATCGTGGTTCAAACTGATCTTACACCTCTGTGGGACATTGACATGGAAGGGAAAGTGA

Basic information

species Vitis vinifera
transcript Vv19s0014g05130.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0014g05130.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G36280.1 (Glycine max), 3'ss of exon 4
-------------------------gtaaaggagttatt-aatataaccttaacctatttctgtataatgcttacttggttttgaacttttattctttcgtct--gcagTTGTTTCCTAGTCTTAACAAGATAGTGTTCCTCGACGATGACATCGTGGTTCAAACTGATCTTACACCTCTGTGGGACATTGACATGGAAGGGAAAGTGA
                          |||||   |||||  ||||    | | |   |   | | |  ||  |     | ||    |  |||| ||||  |||  ||||||||| || |||||||||||| | || |||||||| |||||||| ||||| |||||||||||| ||||||||||||||||||| ||| | || ||||| |
gtaaaaataaggcatagtatagcaaataaagcttttatttgatatcttataaccaagtaagtctttggtgtctgtgatgcttattgccattatgcttttttcttagcagTTGTTCCCAAGTCTTAACAAGTTGGTCTTCCTCGATGATGACATTGTGGTACAAACTGATCTTTCACCTCTGTGGGACATTGAAATGAATGGAAAAGTAA

upper sequence: Vv19s0014g05130.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA12G34280.1 (Glycine max), 3'ss of exon 4
---------------------------gtaaaggagttatt-aatataaccttaacctatttctgtataatgcttacttggttt--tgaacttttattctttcgtctgcagTTGTTTCCTAGTCTTAACAAGATAGTGTTCCTCGACGATGACATCGTGGTTCAAACTGATCTTACACCTCTGTGGGACATTGACATGGAAGGGAAAGTGA
                           ||||||   |||||  |||     | | |   |     | |  | | |     | ||  ||   |  | || |||      ||||||||||| ||| |||||||| | || ||||| || |||||||||||||| |||||||||||| ||||| ||||||||||||| ||| | || ||||| |
gtaatatatatatatagcaattagcaagtaaagcttttatttgatagcttataagctggtaaacctttggttcctgtgatgcttattgtcatgatgtttttttcataacagTTGTTTCCAAGTATTAACAAGGTGGTCTTCCTTGATGATGACATCGTGGTACAAACTGATCTTTCACCTTTGTGGGACATTGAAATGAATGGAAAAGTAA

upper sequence: Vv19s0014g05130.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G41630.1 (Glycine max), 3'ss of exon 4
-------------gtaaaggagttattaatataacct--taacctatttctgtataatgcttacttggttttga-----acttttattctttcgtctgcagTTGTTTCCTAGTCTTAACAAGATAGTGTTCCTCGACGATGACATCGTGGTTCAAACTGATCTTACACCTCTGTGGGACATTGACATGGAAGGGAAAGTGA
               |||  | |||| |||  ||  |  |    |||  |||  |||   ||  ||   | |||     ||||  ||  |    | | ||||||||  | |||||||||||| | || ||||| || |||||||| ||||| |||||||||||| |||||||||||||||||||| || | || ||||| |
gtaaaaatgatggaaaaaaaaattatgaatcaaagttatttttgtataactgattaaccttttttttcctgtgatgcttacttccataatacatttttcagTTGTTCTCAAGTCTTAACAAGGTGGTCTTCCTTGATGATGACATTGTGGTACAAACTGATCTTTCACCTCTGTGGGACATTGACTTGAATGGAAAAGTCA

upper sequence: Vv19s0014g05130.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA12G16550.1 (Glycine max), 3'ss of exon 4
----------------------gtaaaggagttatta-atataaccttaacctatttctgtataatgcttacttggttttgaacttttattctttcgtctgcagTTGTTTCCTAGTCTTAACAAGATAGTGTTCCTCGACGATGACATCGTGGTTCAAACTGATCTTACACCTCTGTGGGACATTGACATGGAAGGGAAAGTGA
                      | |||    || ||   ||   | ||||||| |||   | | ||||||||||   | |||   | |    |||| |   ||||||||  | |||||||||||| | || |||||||| |||||||  ||||| |||||||||||| |||||||||||||||||||| |  | || ||||| |
gtaaaagtgatagaattatgaagcaaaattatttttgtgtagttcattaaccttttttcctgtgatgcttactt--ctgtgatactct----tttcattaacagTTGTTCTCAAGTCTTAACAAGGTGGTCTTCCTCGATGATGACACTGTGGTACAAACTGATCTTTCACCTCTGTGGGACATTGACTTAAATGGAAAAGTTA

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|110424737|gb|EC991107.1|EC991107
EST:     GTCCAAAGTATAATTCAGTGATGAATCACATCAGGATACATCTACCTGAG                         TTGTTTCCTAGTCTTAACAAGATAGTGTTCCTCGACGATGACATCGTGGTT
genomic: GTCCGAAGTATAATTCAGTGATGAATCACATCAGGATACATCTACCTGAGgtaaaggagt ... tcgtctgcagTTGTTTCCTAGTCTTAACAAGATAGTGTTCCTCGACGATGACATCGTGGTT
EST: gi|122690411|gb|EC952332.1|EC952332
EST:     CAGTGATGAATCACATCAGGATACATCTACCTGAG                         TTGTTTCCTAGTCTAAACAAGATAGTGTTCCTCGACGATGACATCGTGGTT
genomic: CAGTGATGAATCACATCAGGATACATCTACCTGAGgtaaaggagt ... tcgtctgcagTTGTTTCCTAGTCTTAACAAGATAGTGTTCCTCGACGATGACATCGTGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctatttctgtataatgcttacttggttttgaacttttattctttcgtctgcagTTGTTTCCTAGTCTTAACAAGATAGTGTTCCTCGACGATGACATCGTGGTTCAAACTGATCTTACACCTCTGTGGGACATTGACATGGAAGGGAAAGTGA
                tgcttac  putative branch site (score: 2)
                                  cttttattctttcgtc  putative PPT
                           ttttgaacttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaggagttattaatataaccttaacctatttctgtataatgcttacttggttttgaacttttattctttcgtctgcagTTGTTTCCTAGTCTTAACAAGATAGTGTTCCTCGACGATGACATCGTGGTTCAAACTGATCTTACACCTCTGTGGGACATTGACATGGAAGGGAAAGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG