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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatataaatacatacatatatgcatacatacatacatacgtgtatatatatatatatatatatattccaatttctatggtggtcctgttataccctgtttggaaatctctcatttagagaacttgtcaaattttatgattaaacccccttttttctgttaacttgcacagCGTGTGGAGCTGGAACGGACATTGACTGATCCACAGAGGGATGAATTTGAGGATATGTTGCGTGCTTTGACATTAGAAAGGAGTCAGATAAAGGAAGCTA

Basic information

species Vitis vinifera
transcript Vv04s0008g06810.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os02g08360.1 (Oryza sativa), 3'ss of exon 14
gtacatataaatacatacatatatgcatacatacatacatacgtgtatatatatatatatatatatattccaatttctatggtggtcctgttataccctgtttggaaatctctcatttagagaacttgtcaaattttatg--attaaacccccttttttctgttaacttgcacagCGTGTGGAGCTGGAACGGACATTGACTGATCCACAGAGGGATGAATTTGAGGATATGTTGCGTGCTTTGACATTAGAAAGGAGTCAGATAAAGGAAGCTA
                                                                               |    |   || |  |   |||| | |   || |   || |  |   ||     |||| |   | || |    |   ||    ||  ||    |||||||| ||  |||| || |||||||||||| ||||| | |||||||||||||| ||| | ||||| |||||||| || || |||||||||||||| ||||
------------------------------------------------------------------------------gtaagagat-tgctgcattttgtt-gaaggccttttgctttgttacggtgaatgtttttgtcctactacaaatacgaattcacattttctctt-cagCGTGTCGAAGTGGAGCGCACATTGACTGATTCACAGCGTGATGAATTTGAGGACATGCTACGTGCATTGACATTGGAGAGAAGTCAGATAAAGGAGGCTA

upper sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G174785_T02 (Zea mays), 3'ss of exon 13
gtacatataaatacatacatatatgcatacatacatacatacgtgtatatatatatatatatatatattccaatttctatggtggtcctgttataccctgtttggaaatctctcatttagagaacttgtcaaattttatgattaaacccccttttttctgttaacttgcacagCGTGTGGAGCTGGAACGGACATTGACTGATCCACAGAGGGATGAATTTGAGGATATGTTGCGTGCTTTGACATTAGAAAGGAGTCAGATAAAGGAAGCTA
                                               || |||  | | || |  || ||  |    ||   | ||  | | ||    ||||||   || ||  ||  | | |   |||    ||  |  | ||||        |||||| |   |    |||||||| ||  |||| || |||||||||||  ||||| | |||||||||||||| ||| |||| |||||||||||||| ||||| || ||||| || || |
----------------------------------------------gtaaataactgt-tagacgtactcagagcatta-aattgttgtttcat----tgtttgttgatgtcaaataaataaatggtgttctgttacaatactaaa--------tttctgatccgtccttcagCGTGTTGAAGTGGAGCGTACATTGACTGACTCACAGCGTGATGAATTTGAGGACATGCTGCGAGCTTTGACATTAGAGAGGAGCCAAATAAAAGACGCCA

upper sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA08G34030.1 (Glycine max), 3'ss of exon 13
gtacatataaatacatacatatatgcatacatacatacatacgtgtatatatatatatatatatatattccaatttctatggtggtcctgttataccctgtttggaaatctctcatttagagaacttgtcaa-attttatgatt---aaacccccttttttctgttaacttgcacagCGTGTGGAGCTGGAACGGACATTGACTGATCCACAGAGGGATGAATTTGAGGATATGTTGCGTGCTTTGACATTAGAAAGGAGTCAGATAAAGGAAGCTA
                                                                                    || || ||      ||| |   ||  |   ||  |   ||  | ||||  | | ||||||   ||    |||| |||   || | |     ||||||| ||||  ||  | ||| |||||||| |||||||||||||||||||||||||| |||||||||| |||||||| ||||| |||||||| || ||||
------------------------------------------------------------------------------------gtactatttattgttgtattttaaattaggatgaatgcaatatctcaatgtctcatgatttataactttccttgttttgattgaatattgtagCGTGTAGAGCCCGACAGAACACTGACTGATGCACAGAGGGATGAATTTGAGGATATGCTGCGTGCTTTAACATTAGAGAGGAGCCAGATAAAAGAGGCTA

upper sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 9
gtacatataaatacatacatatatgcatacatacatacatacgtgtatatatatatatatatatatattccaatttctatggtggtcctgtta--taccctgtttggaaatctctcatttagagaacttgtcaaattttatgattaaacccccttttttctgttaacttgcacagCGTGTGGAGCTGGAACGGACATTGACTGATCCACAGAGGGATGAATTTGAGGATATGTTGCGTGCTTTGACATTAGAAAGGAGTCAGATAAAGGAAGCTA
                                                                       |  || ||| || ||  | | |  ||   ||  || || ||||||| |   |  |  |    | ||||||||         ||| |||   || | |    ||||| || ||||  ||| | ||| |||||||| |||||||||||||||||||||||||| |||||||||| |||||||| ||||| |||||||| || ||||
---------------------------------------------------------------------gtacgttttattgttgtattttcaattaggatgaatgcaa-tctctcaatgtcatgatatactcacttttatga---------cttgttttgattgaatattgcagCGAGTAGAGCCTGAAAGAACACTGACTGATGCACAGAGGGATGAATTTGAGGATATGCTGCGTGCTTTAACATTAGAGAGGAGCCAGATAAAAGAGGCTA

upper sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT5G25060.1 (Arabidopsis thaliana), 3'ss of exon 12
gtacatataaatacatacatatatgcatacatacatacatacgtgtatatatatatatatatatatattccaatttctatggtggtcctgttataccctgtttggaaatctctcatttagagaacttgtcaaattttatgattaaacccccttttttctgttaacttgcacagCGTGTGGAGCTGGAACGGACATTGACTGATCCACAGAGGGATGAATTTGAGGATATGTTGCGTGCTTTGACATTAGAAAGGAGTCAGATAAAGGAAGCTA
                                                                 || ||   || |  |  |  | ||  | ||   | |||     ||| |  || ||  || ||||    ||||    |        | |    ||||||| |   |||||||| |||  | ||  ||||  |||| ||||| ||||||||||| || ||||| |||||||||||| | || |||||||||||||||||||| |||||||
----------------------------------------------------------------gtaatcttcttgcactcttacttctaatttatt-tatttctttttcttttgtt-agctaagttgttc--ttttggtgtgcgggatacctgacactgttaaatcttacagCGTGCGGAAGTTGAGAGGACTCTGACCGATCCTCAGAGGGATGAGTTCGAGGACATGTTGCGTGCTCTTACTTTAGAAAGGAGTCAGATAAAAGAAGCTA

upper sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT5G10800.1 (Arabidopsis thaliana), 3'ss of exon 12
gtacatataaatacatacatatatgcatacatacatacatacgtgtatatatatatatatatatatattccaatttctatggtggtcctgttataccctgtttggaaatctctcatttagagaacttgtcaaattttatgattaaacccccttttttctgttaacttgcacagCGTGTGGAGCTGGAACGGACATTGACTGATCCACAGAGGGATGAATTTGAGGATATGTTGCGTGCTTTGACATTAGAAAGGAGTCAGATAAAGGAAGCTA
                                                           ||      || ||||  |||   |  || | |  |   || ||| | |   | |  ||     |  ||||  |  || ||   | |    |||| |  ||  ||| |   | || |   |||    || |  ||  | || ||| | || ||||||||||||||||| |||||||| ||| | || |||||||||||||| || |  |||||||
----------------------------------------------------------gtaatctccttacaat--ctaacata-tcatatcttcttcttttttgca---tgtttttggagaagtttgttta--ttgatagctga--taccttatcacttataaata--atagTGCACGGAAGCTGAGCAAACTCTAACCGATTCCCAAAGGGATGAATTTGAGGACATGTTGCGCGCTCTAACTTTAGAAAGGAGTCAAATCAGAGAAGCTA

upper sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: PP1S137_118V6.1 (Physcomitrella patens), 3'ss of exon 12
gtacatataaatacatacatatatgcatacatacatacatacgtgtatatatatatatatatatatattccaatttctatggtggtcctgttataccctgtttggaaatctctcatttagagaacttgtcaaattttatgattaaacccccttttttctgttaacttgcacagCGTGTGGAGCTGGAACGGACATTGACTGATCCACAGAGGGATGAATTTGAGGATATGTTGCGTGCTTTGACATTAGAAAGGAGTCAGATAAAGGAAGCTA
                       |   || |  |     | |  |    |  || |     | | |  ||   |||   || ||    |   | |    | |    | | |  |     || |  |  ||  || ||   | |  |    ||| |   | || | ||   ||| |  |||| | ||||||  |||| ||||||   ||| | |||||||||||||| |||||||| || |||||| ||||||| || || ||    |||||||
----------------------gtaagtaaactctctttttctagcccttggattttccagtgtgtcatctgtttttggtgatg----tacaaaaagtggatgttcattatgccgaggtgaaagttgatctgatattcatactttatttgcttgtgggtttttattt-ttcagAGAATGGACCAGGAACGAGCATTAACTGATAGCCAGCGCGATGAATTTGAGGACATGTTGCGGGCATTGACACTAGAAAGAAGCCAAATTCGAGAAGCTA

upper sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: PP1S196_109V6.1 (Physcomitrella patens), 3'ss of exon 12
gtacatataaatacatacatatatgcatacatacatacatacgtgtatatatatatatatatatatattccaatttctatggtggtc--ctgttataccctgtttggaaatctctcatttagagaacttgtcaaattttatgattaaacccccttttttctgttaacttgcacagCGTGTGGAGCTGGAACGGACATTGACTGATCCACAGAGGGATGAATTTGAGGATATGTTGCGTGCTTTGACATTAGAAAGGAGTCAGATAAAGGAAGCTA
                                   ||  |     |   | | ||      |  | | | |||||    | |       || || |  | | |||||  |    || | |        | ||||  || |||||| |      |||||||            ||| |  | || |  || ||  |||| |||||    ||  | ||||||||||||||| ||||||| || |||||| ||||||| ||||| ||    ||||| |
----------------------------------gtaagttgccttcggtttttaacgccttggaaacttcaattcgagtcgcaactaacttttgtgtcgt-tttggggagaattcgtctcacatttatctcaaccttcatgattca------ttttttc------------cagAGAATAGATCACGAGCGAGCATTAACTGACAGCCAACGTGATGAATTTGAGGATGTGTTGCGAGCATTGACACTAGAAAGAAGTCAAATCCGAGAAGCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagaacttgtcaaattttatgattaaacccccttttttctgttaacttgcacagCGTGTGGAGCTGGAACGGACATTGACTGATCCACAGAGGGATGAATTTGAGGATATGTTGCGTGCTTTGACATTAGAAAGGAGTCAGATAAAGGAAGCTA
                                        tgttaac  putative branch site (score: 2)
                            cccccttttttctgtt  CT-rich tract
       ttgtcaaattttatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatataaatacatacatatatgcatacatacatacatacgtgtatatatatatatatatatatattccaatttctatggtggtcctgttataccctgtttggaaatctctcatttagagaacttgtcaaattttatgattaaacccccttttttctgttaacttgcacagCGTGTGGAGCTGGAACGGACATTGACTGATCCACAGAGGGATGAATTTGAGGATATGTTGCGTGCTTTGACATTAGAAAGGAGTCAGATAAAGGAAGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA