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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtacaacttgtggcagttcatcctcaagaatcatatatttctattgaaatcttaacacagatctttgggttttttagGAACTCACAAAGATGGAAACACAAGAGCTACTAAAGCATCGCATGCTGAAATTCCGAAAAATTGGTGGGTTTCAGGAAGGTATCCCAGTTGATCCTGAAA

Basic information

species Vitis vinifera
transcript Vv08s0007g01750.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g01750.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA18G42310.2 (Glycine max), 3'ss of exon 9
-gtgagtacaacttgtggcagttcatcctcaagaatcatatatttctattgaaatcttaacacaga-----tctttgg---gttttttagGAACTCACAAAGATGGAAACACAAGAGCTACTAAAGCATCGCATGCTGAAATTCCGAAAAATTGGTGGGTTTCAGGAAGGTATCCCAGTTGATCCTGAAA
 || |||    |  |  |||  |  |   |   || || |||| |  |   |  | |||||   |      ||| | |    || | ||||||||||| |||||| | ||| |||| ||  |||| ||||||||||| || ||| |||| |||||||| || ||||||||||| ||  | |||||  |  
tgtaagttttgcaggcagcaagtgttatactgaaaacaaatatgttaacgcatgtgttaactttggaactttctcttgtccattatgtaGGAACTCACGAAGATGAACACAGAAGAACTGTTAAAACATCGCATGCTTAAGTTCAGAAAGATTGGTGGATTCCAGGAAGGTATTCCTATAGATCCCAAG-

upper sequence: Vv08s0007g01750.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA18G42310.1 (Glycine max), 3'ss of exon 13
gtgagtacaacttgtggcagttcatcctcaagaatcatatatttctattgaaatcttaacacaga-----tctttgg---gttttttagGAACTCACAAAGATGGAAACACAAGAGCTACTAAAGCATCGCATGCTGAAATTCCGAAAAATTGGTGGGTTTCAGGAAGGTATCCCAGTTGATCCTGAAA
|| |||    |  |  |||  |  |   |   || || |||| |  |   |  | |||||   |      ||| | |    || | ||||||||||| |||||| | ||| |||| ||  |||| ||||||||||| || ||| |||| |||||||| || ||||||||||| ||  | |||||  | |
gtaagttttgcaggcagcaagtgttatactgaaaacaaatatgttaacgcatgtgttaactttggaactttctcttgtccattatgtagGAACTCACGAAGATGAACACAGAAGAACTGTTAAAACATCGCATGCTTAAGTTCAGAAAGATTGGTGGATTCCAGGAAGGTATTCCTATAGATCCCAAGA

upper sequence: Vv08s0007g01750.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA18G42280.1 (Glycine max), 3'ss of exon 9
gtgagtacaacttgtggcagttcatcctcaagaatcatatatttctattgaaatcttaacacaga-----tctttgg---gttttttagGAACTCACAAAGATGGAAACACAAGAGCTACTAAAGCATCGCATGCTGAAATTCCGAAAAATTGGTGGGTTTCAGGAAGGTATCCCAGTTGATCCTGAAA
|| |||    |  |  |||  |  ||  |   || || |||| |  |   |  | |||||   |      ||| | |    || | ||||| ||||| |||||| | ||| |||| ||  |||| ||||||||||| || ||| |||| ||||||||||| ||||||||||| ||  | |||||| | |
gtaagttttgcaggcagcaagtgttctactgaaaacaaatatgttaacgcatgtgttaactttggaactttctcttgtccattatgtagGAGCTCACGAAGATGAACACAGAAGAACTGTTAAAACATCGCATGCTTAAGTTCAGAAAGATTGGTGGGTTCCAGGAAGGTATTCCTATAGATCCTAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcaagaatcatatatttctattgaaatcttaacacagatctttgggttttttagGAACTCACAAAGATGGAAACACAAGAGCTACTAAAGCATCGCATGCTGAAATTCCGAAAAATTGGTGGGTTTCAGGAAGGTATCCCAGTTGATCCTGAAA
                           tcttaac  putative branch site (score: 2)
                                               tttttt  putative PPT
      aatcatatatttctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtacaacttgtggcagttcatcctcaagaatcatatatttctattgaaatcttaacacagatctttgggttttttagGAACTCACAAAGATGGAAACACAAGAGCTACTAAAGCATCGCATGCTGAAATTCCGAAAAATTGGTGGGTTTCAGGAAGGTATCCCAGTTGATCCTGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG