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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgttttaaggaaaatatcattttattttaaccatttctcccttgacctagatatcatactccattactatttattaggcaagtgtctgcttcttttgttactgaacttgaggttatattgttggacgtggaactaacatttatactttatatatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA

Basic information

species Vitis vinifera
transcript Vv00s0211g00080.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0211g00080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 9
gtgagttgttttaaggaaaatatcattttattttaaccatttctcccttgacctagatatcatactccattactatttattaggcaagtgtctgcttcttttgttactgaacttgaggttatattgttggacgtggaactaacatttatactttatatatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA
                                        |     ||||| |   | |  |  |   ||       ||    |   ||  ||| ||||| |    |          || |  ||     |  |  || |  |   |  ||  | ||   ||  ||||| ||||||||| ||| ||||| ||||||   |||||||| || || || |||||||| || || ||||| || ||| ||||||||||||||||  | |
---------------------------------------gtatatacttgagcagaacaata-gcaagatagtagcgtagggtgttggta-ctgtttcttctccatcctgtgactctgtgagcttcaaaaaaataaaaatgcctaatg-accctctac-cgtctagGTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTGCAAGGTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTA

upper sequence: Vv00s0211g00080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 8
gtgagttgttttaaggaaaatatcattttattttaaccatttctcccttgacctagatatcatactccattactatttattaggcaagtgtctgcttcttttgttactgaacttgaggttatattgttggacgtggaactaacatttatactttatatatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA
                                         | |  | |||   | |    | |    | ||  |  | ||   |      |||||||||   |||   |||   ||||| || || |  ||            || ||| | ||||        |||| ||||||| | ||| ||||||||||||   |||||||||||||| || |||||||| ||||| || || || ||| ||||||| ||||||||  | |
----------------------------------------gtatggcatgatgaaaacgataaaaaaaactagcaggtgttgaac------ctgcttcttgcattaa-aaaccaaaggtt-tagtgatatac------------ttaatattctata--------gGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTGCAAGGTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCA

upper sequence: Vv00s0211g00080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G37270.1 (Glycine max), 3'ss of exon 9
gtgagttgttttaaggaaaatatcattttattttaaccatttctcccttgacctagatatcatactccattactatttattaggcaagtgtctgcttcttttgttactgaacttgaggttatattgttggacgtggaactaacatttatactt-tatatatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA
        ||  ||||||||  |  ||| |  ||     ||  |    |  |     | ||| | | ||||   ||  |  |||  ||| | || |  ||          ||||||  |||| |   |  |      | ||||| || | ||| | |  || ||||||| ||||||||||| |||||||||||||| || ||||| || |||||||| ||||||||||||||||| ||||| ||| |||| ||||||||||| ||||
---gtcaattccaaggaaaaagttctttgacatttttgtttattttaatttctgtactctcagatttcattctcatcaac-aggatagtatgtgttgtttccc-------acttgaatttatgtaaattcataaatca-taacagttgttcttctttcaatttgaagGTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGA

upper sequence: Vv00s0211g00080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA18G27710.1 (Glycine max), 3'ss of exon 10
gtgagttgttttaaggaaaatatcattttattttaaccatttctcccttgacctagatatcatactccattactatttattaggcaagtgtctgcttcttttgttactgaacttgaggttatattgttggacgtggaactaacatttatactttatata-tgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA
|| |||  |  |   |||||||   |   |||||      || |    |  |     | ||  | | ||||   ||  ||  |  |   || ||  |  |||  ||||  | |||| || |  |  |    | |      |||| || | |||  |  | | ||||| | |||||||||||||| ||||||||||| || ||||| || |||||||| ||||| ||||||||||| ||||| ||| |||| ||||||||||||||||
gtaagt-atcctggagaaaataatttgacatttttgtttattttgatct--ctgtactctcggatttcattctgatcaataggata---gtttgtgttgtttcctacttgagttgatgtaaattcataaatcat------aacagttgttcttcttgcaatttgaagCTATTGTATGACTATGAGGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGGGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCATTGA

upper sequence: Vv00s0211g00080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G33480.1 (Glycine max), 3'ss of exon 9
gtgagttgttttaaggaaaatatcattt--tattttaac---catttctcccttgacctagatatcatactccattactatttattaggcaagtgtctgcttcttttgttactgaacttgaggttatattgttggacgtggaactaacatttatacttt--atatatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA
      | ||       |||| | ||||   |||||  |   | |||  |  ||   |||  |||||   ||  ||   ||   || |||| ||   |      ||    | |  |  | |  | ||    |  | |    | | |||  | ||  ||   |  ||| |||||||  ||||||||||||||||||||||||||   ||||| ||||||||||| ||| |||| ||||||   ||| | ||| |||| ||||||||||||||||
-----gtattcctgaacaaattttatttgacattttggcatacttttggcttttatactatctatcaagttctgttttcatgattttggcatgttgttctagtcttcaaaaatttatgtaaattcatggcatgagccaaacagc-aaccctaatttttctaacttatttgaagGTGATGTATGACTATGAAGACAAAATCAATAGAGCTGTGTTTCCTGGACTGCAAAGTGGTCCTCACTTCCACTCTATTACTGGTTTAGCTGTTGCATTGA

upper sequence: Vv00s0211g00080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S79_54V6.1 (Physcomitrella patens), 3'ss of exon 9
gtgagttgttttaaggaaaatatcattttattttaaccatttctcccttgacctagatatcat-actccattactatttattaggcaagtgtctgcttcttttgttactgaacttgaggttatattgttggacgtggaactaacatttatactttatatatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA
                                                         | || | ||||||     |   ||  ||    ||   |  ||   | |  | ||  ||  ||||| ||| |  |  |      |   ||  || ||       |||| || |||| || ||||||||||||||||| |||   ||||| ||||| ||||| ||||| || |||||||| ||||| ||||| ||  | |||||||| ||||
---------------------------------------------------------tgtcttcactccaacga-aagcataggggcgatgctggtctcgcgtat-gcggaggtt--ggttacatt-tcagctgaatgtttctgatccatcctgc-----tgtgcagATTTTCTACGACTATGAAGACAAAATTAATGCTGCTGTTTTTCCAGGACTACAAGGGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGA

upper sequence: Vv00s0211g00080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ32604 (Selaginella moellendorffii), 3'ss of exon 9
gtgagttgttttaaggaaaatatcattttattttaaccatttctcccttgacctagatatcatactccattactatttattaggcaagtgtctgcttcttttgttactgaacttgaggttatattgttggacgtggaactaacatttatactttatatatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA
                                                                                                                         ||   ||        || | || |   |      |   |  | ||||| | || ||||| |  || ||||| |||   || || || ||||| ||||||||||| ||||||||||||||||||||||   | || || ||  | |
------------------------------------------------------------------------------------------------------------------------gtacgtttactttcccaagttacctccttgaca-gtgcct-cgcagGTTCTATACGACTACGCTGAGAAAATAAATGCTGCAGTGTTCCCTGGGCTTCAAGGTGGTCCTCACAATCACACAATTGCTGCGCTTGCCGTGGCTCTTA

upper sequence: Vv00s0211g00080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ16660 (Selaginella moellendorffii), 3'ss of exon 9
gtgagttgttttaaggaaaatatcattttattttaaccatttctcccttgacctagatatcatactccattactatttattaggcaagtgtctgcttcttttgttactgaacttgaggttatattgttggacgtggaactaacatttatactttatatatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA
                                                                                                                         ||   ||        || | || |   |     |       | ||||| | || ||||| |  || ||||| |||   || || || ||||| ||||||||||| ||||||||||||||||||||||   | || || ||  | |
------------------------------------------------------------------------------------------------------------------------gtacgtttactttcccaagttacctccttga--cagcgcctcgcagGTTCTATACGACTACGCTGAGAAAATAAATGCTGCAGTGTTCCCTGGGCTTCAAGGTGGTCCTCACAATCACACAATTGCTGCGCTTGCCGTGGCTCTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgaggttatattgttggacgtggaactaacatttatactttatatatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA
                         aactaac  putative branch site (score: 1)
                         aactaacatttatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttgttttaaggaaaatatcattttattttaaccatttctcccttgacctagatatcatactccattactatttattaggcaagtgtctgcttcttttgttactgaacttgaggttatattgttggacgtggaactaacatttatactttatatatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT