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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttgttagttacctttctggatgtatcatgccaatcttttggatgctgtactttggtttaacacactttaaattgtgtttgaaatatctacagGAGGAAAGAAGGATGTCATTACTGAAGTATCAGGTGCATGATGAAACTAGCCAG

Basic information

species Vitis vinifera
transcript Vv03s0017g02160.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0017g02160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os09g38790.1 (Oryza sativa), 3'ss of exon 5
-------------------gttagttgttagttacctttctggatgtatcatgccaatcttttggatgctgtactttggtttaaca--cactttaaattgtgtttgaaatatctacagGAGGAAAGAAGGATGTCATTACTGAAGTATCAGGTGCATGATGAAACTAGCCAG----------------------------------------------
                    |||||||||| |  | ||   |    | |  |    || ||     | ||  |  |  |||| |     |  | ||||  |  ||||  | | ||  ||||||||||||  ||||  |||  ||||||||||||||||||||||||||||||                                              
gtatattttccatcctctctttagttgttattctcattagagatcatttggtatatatgttacat-tactagatatgagtttgagggttatctcaaatatttgttgacttgtgta--gGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTCTGATTTTTATAATTTTATATCTGTAATATTAATGATAT

upper sequence: Vv03s0017g02160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os09g38790.3 (Oryza sativa), 3'ss of exon 5
-------------------gttagttgttagttacctttctggatgtatcatgccaatcttttggatgctgtactttggtttaaca--cactttaaattgtgtttgaaatatctacagGAGGAAAGAAGGATGTCATTACTGAAGTATCAGGTGCATGATGAAACTAGCCAG
                    |||||||||| |  | ||   |    | |  |    || ||     | ||  |  |  |||| |     |  | ||||  |  ||||  | | ||  ||||||||||||  ||||  |||  ||||||||||||||||||||||||||||||
gtatattttccatcctctctttagttgttattctcattagagatcatttggtatatatgttacat-tactagatatgagtttgagggttatctcaaatatttgttgacttgtgta--gGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAG

upper sequence: Vv03s0017g02160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G081812_T02 (Zea mays), 3'ss of exon 5
gttagttgttagttacctttctggatgtatcatgccaatcttttggatgctgtactttggtttaac-----acactttaaattgtgtttgaaatatctacagGAGGAAAGAAGGATGTCATTACTGAAGTATCAGGTGCATGATGAAACTAGCCAG
||  | |  ||   | | | ||  |||| |  |      ||| || ||   |   | || || ||      | | | | |||| | |      | | |  |||||||||||||| |||| || |  ||||||||||||||||||||||||||||||
gtatgcttctaaccatcat-ctatatgtcttttagtttacttgtgcatagcgatatatgattgaaatgttaataatctcaattttttgctgtct-tttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG

upper sequence: Vv03s0017g02160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G081812_T01 (Zea mays), 3'ss of exon 5
gttagttgttagttacctttctggatgtatcatgccaatcttttggatgctgtactttggtttaac-----acactttaaattgtgtttgaaatatctacagGAGGAAAGAAGGATGTCATTACTGAAGTATCAGGTGCATGATGAAACTAGCCAG----------------------------------------------
||  | |  ||   | | | ||  |||| |  |      ||| || ||   |   | || || ||      | | | | |||| | |      | | |  |||||||||||||| |||| || |  ||||||||||||||||||||||||||||||                                              
gtatgcttctaaccatcat-ctatatgtcttttagtttacttgtgcatagcgatatatgattgaaatgttaataatctcaattttttgctgtct-tttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTGTGTTTCTTATGATACTATTATTGTAGTTTCTCAAACAA

upper sequence: Vv03s0017g02160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G05390.2 (Glycine max), 3'ss of exon 5
gttagttgttagttacctttctggatgtatcatgcca-atcttttggatgctgtactttggtttaacacactttaaattgtgtttgaaatatctacagGAGGAAAGAAGGATGTCATTACTGAAGTATCAGGTGCATGATGAAACTAGCCAG
      ||||   | | |      || | |  ||    || |    | || |||   ||||||    |   | | |    || |||   |  ||  ||||||||||||| ||||| || |  || ||||||||||||||||||| |||||||
---gtgtgttgtgttcttgagaaaatatgtagtgtttcatttgactgctgttgtttcttggttggtaatgttatga----tgcttgg--ttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAG

upper sequence: Vv03s0017g02160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G05390.1 (Glycine max), 3'ss of exon 5
gttagttgttagttacctttctggatgtatcatgcca-atcttttggatgctgtactttggtttaacacactttaaattgtgtttgaaatatctacagGAGGAAAGAAGGATGTCATTACTGAAGTATCAGGTGCATGATGAAACTAGCCAG----------------------------------------------
      ||||   | | |      || | |  ||    || |    | || |||   ||||||    |   | | |    || |||   |  ||  ||||||||||||| ||||| || |  || ||||||||||||||||||| |||||||                                              
---gtgtgttgtgttcttgagaaaatatgtagtgtttcatttgactgctgttgtttcttggttggtaatgttatga----tgcttgg--ttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAGGTAAGTCATACTACCTCTTTAATAGATGGAGTTGCTTTCACATCTA

upper sequence: Vv03s0017g02160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA05G34280.1 (Glycine max), 3'ss of exon 5
gttagttgttagttacctttctggatgtatcatgc-caatcttttggatgctgtactttggtttaacacactttaaattgtgtttgaaatatctacagGAGGAAAGAAGGATGTCATTACTGAAGTATCAGGTGCATGATGAAACTAGCCAG
|| ||||||  ||| | |      || | |  ||  | || |      || |||   ||||||    | | | | |    || |||   |  ||  ||||||||||||| ||||| || |  || ||||||||||||||||||| |||||||
gtgagttgt--gtt-cttgagaaaatatgtagtgttccatttgactactgttgtttcttggttggtaatattatga----tgcttgg--ttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggatgctgtactttggtttaacacactttaaattgtgtttgaaatatctacagGAGGAAAGAAGGATGTCATTACTGAAGTATCAGGTGCATGATGAAACTAGCCAG
                 gtttaac  putative branch site (score: 3)
                            tttaaattgtgtttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttgttagttacctttctggatgtatcatgccaatcttttggatgctgtactttggtttaacacactttaaattgtgtttgaaatatctacagGAGGAAAGAAGGATGTCATTACTGAAGTATCAGGTGCATGATGAAACTAGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG