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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattatcatcttggcttaaaaaattactgaatatggtataaacattcatcgacctctcttcactattgtaattttttgaaaagtaaatgttcattaagttactgttggatttgtacagGTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACCCTGGCAGCTTTTGGTGGTGATGAAAACTTGGCTCTTGAAAAGCTCTGCT

Basic information

species Vitis vinifera
transcript Vv17s0000g00610.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g00610.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G37620.3 (Glycine max), 3'ss of exon 5
gtattatcatcttggcttaaaaaattactgaatatggtataaac-attcatcgacctctcttcactattgta-attttttgaaaagtaaatgttcattaagttactgttggatttg-tacagGTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACCCTGGCAGCTTTTGGTGGTGATGAAAACTTGGCTCTTGAAAAGCT-CTGCT
                    | |||||   ||| |  |||  |    | ||    |     | || || ||| || |  | |      || | |     |||| || ||   |||| |||||||||| ||||| || |||||||| || || ||||||  ||||||||| |   ||| |||| |||||||||||||||||||||||||||||| | | |||  
--------------------ataattatgaaatttaatatccattgctaatgagtcaaatatgaccatagtatatatgataattttctaacgcttgc--agtttcttttatttttgctacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCAAGTAAGGAGCATTTTGGAAGCTGTTGGTGGTGATGAAAACTTGGCTCTTGAAAGGTTGCTGT-

upper sequence: Vv17s0000g00610.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G17470.3 (Glycine max), 3'ss of exon 4
gtattatcatcttggcttaaaaaattactgaa-tatggtata-aacattcatcgacctctcttcactattgtaattttttgaaaagtaaatgttcattaagttactgttggatttg-tacagGTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACCCTGGCAGCTTTTGGTGGTGATGAAAACTTGGCTCTTGAAAAGCT-CTGCT
                      |||||   || | |  |||  |   || ||  | |  |  | || ||    || | |   ||  |     | | || | || || ||   |||| |||||||||| ||||| || |||||||| || || ||||||  ||||||||| |   ||| |||| ||||||||||||||||| |||| ||||||| | | |||  
----------------------aattatgaaaatttaatatccattgttaatgaatcaattatgacaatacgtatatatgataattttgtaatgcttttaatttcttttatttttggtacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCGAGTAAGGAGCATTTTGGAAGCTGTTGGTGGTGATGAAAACATGGCCCTTGAAAGGTTGCTGT-
















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|161716905|gb|FC068127.1|FC068127
EST:     CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAG                         GTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
genomic: CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAGgtattatcat ... atttgtacagGTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
EST: gi|30298293|gb|CB975087.1|CB975087
EST:     CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAG                         GTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
genomic: CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAGgtattatcat ... atttgtacagGTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
EST: gi|110428546|gb|EC995021.1|EC995021
EST:     TTGCATCTTCTCGTGGACTTGAGGAAAAG                         GTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
genomic: TTGCATCTTCTCGTGGACTTGAGGAAAAGgtattatcat ... atttgtacagGTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
EST: gi|30298360|gb|CB975154.1|CB975154
EST:     CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAG                         GTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
genomic: CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAGgtattatcat ... atttgtacagGTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
EST: gi|110391172|gb|EC956130.1|EC956130
EST:     CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAG                         GTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
genomic: CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAGgtattatcat ... atttgtacagGTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
EST: gi|110396526|gb|EC962216.1|EC962216
EST:     CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAG                         GTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
genomic: CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAGgtattatcat ... atttgtacagGTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
EST: gi|77583489|gb|DV220783.1|DV220783
EST:     CTCGATATTGGACAGAAAATTTTGCATCTTTTCGTGGACTTGAGGAAAAG                         GTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
genomic: CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAGgtattatcat ... atttgtacagGTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
EST: gi|110401583|gb|EC968197.1|EC968197
EST:     CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAG                         GTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
genomic: CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAGgtattatcat ... atttgtacagGTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
EST: gi|32460677|gb|CD801851.1|CD801851
EST:     CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAG                         GTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
genomic: CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAGgtattatcat ... atttgtacagGTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
EST: gi|30295997|gb|CB972791.1|CB972791
EST:     CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAG                         GTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
genomic: CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAGgtattatcat ... atttgtacagGTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
EST: gi|161714263|gb|FC064160.1|FC064160
EST:     CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAG                         GTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
genomic: CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAGgtattatcat ... atttgtacagGTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
EST: gi|83274440|gb|DV938537.1|DV938537
EST:     CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAG                         GTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
genomic: CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAGgtattatcat ... atttgtacagGTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
EST: gi|83275178|gb|DV939274.1|DV939274
EST:     CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAG                         GTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
genomic: CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAGgtattatcat ... atttgtacagGTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
EST: gi|351028328|gb|FQ427224.1|FQ427224
EST:     CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAG                         GTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
genomic: CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAGgtattatcat ... atttgtacagGTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
EST: gi|77581774|gb|DV219842.1|DV219842
EST:     CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAG                         GTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
genomic: CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAGgtattatcat ... atttgtacagGTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
EST: gi|77583170|gb|DV220622.1|DV220622
EST:     CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAG                         GTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
genomic: CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAGgtattatcat ... atttgtacagGTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
EST: gi|71890757|gb|DT039812.1|DT039812
EST:     CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAG                         GTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
genomic: CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAGgtattatcat ... atttgtacagGTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
EST: gi|77588446|gb|DV223434.1|DV223434
EST:     CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAG                         GTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
genomic: CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAGgtattatcat ... atttgtacagGTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
EST: gi|77578362|gb|DV217970.1|DV217970
EST:     CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAG                         GTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
genomic: CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAGgtattatcat ... atttgtacagGTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
EST: gi|110412172|gb|EC977911.1|EC977911
EST:     CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAG                         GTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC
genomic: CTCGATATTGGACAGAAAATTTTGCATCTTCTCGTGGACTTGAGGAAAAGgtattatcat ... atttgtacagGTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgtaattttttgaaaagtaaatgttcattaagttactgttggatttgtacagGTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACCCTGGCAGCTTTTGGTGGTGATGAAAACTTGGCTCTTGAAAAGCTCTGCT
     taattttttgaaaagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattatcatcttggcttaaaaaattactgaatatggtataaacattcatcgacctctcttcactattgtaattttttgaaaagtaaatgttcattaagttactgttggatttgtacagGTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACCCTGGCAGCTTTTGGTGGTGATGAAAACTTGGCTCTTGAAAAGCTCTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG