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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatttaaataaatgtctttaagttggggaccatttcatttaaattgatagcttcttagttgatttaacggcttcatcaatagGTGAAAAGTGAGCTGCCTAGTACTTTCAAGGCCTTCCGCTTTCAGCAACACAGGTGGTCCTGTGGTCCAGCCAATTTGTTCAGAAAAATGGTGATGGAGA

Basic information

species Vitis vinifera
transcript Vv06s0061g01230.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0061g01230.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os02g09930.2 (Oryza sativa), 3'ss of exon 5
---------------------------------------------------------------------------------------gtacatttaaataaatgtctttaagttggggaccatttcatttaaattgatagcttcttag------------ttgatttaacg------gcttcatcaatagGTGAAAAGTGAGCTGCCTAGTACTTTCAAGGCCTTCCGCTTTCAGCAACACAGGTGGTCCTGTGGTCCAGCCAATTTGTTCAGAAAAATGGTGATGGAGA
                                                                                        | |||||   |   | |  ||    | | |   ||   |  |  ||| ||     || ||            |   ||||||       || || |    |||| |||||||||||||| ||||||||||| ||||| || |||||||| ||||||||||| ||||| || || ||  ||||||| || ||| |||||||||
gtacacaccaatcatggatatcctacacatgatcagcttgagatagcatccaatgcatcctttgtcattgctcttgctaagttgctattgcatttcccttctttttctttttcttgaggaaatagtacattgattcatgttgcctaagagagaaaaaaaatgagtttaacaagaattgcgtcgttttcagGTCAAAAGTGAGCTGCCAAGTACTTTCAAAGCCTTTCGGTTTCAGCAGCACAGGTGGTCATGTGGGCCGGCAAACCTGTTCAGGAAGATGCTGATGGAGA

upper sequence: Vv06s0061g01230.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os06g42020.1 (Oryza sativa), 3'ss of exon 5
-----------------------------------------gtacatttaaataaatgtctttaagttggggaccatttcatttaaattgatagcttcttagttgatttaacggcttcatcaatagGTGAAAAGTGAGCTGCCTAGTACTTTCAAGGCCTTCCGCTTTCAGCAACACAGGTGGTCCTGTGGTCCAGCCAATTTGTTCAGAAAAATGGTGATGGAGA
                                          | |||  |  |     ||| ||  ||         || |  || ||    |      ||  | |  |       |  |    ||||||||||||| || || ||||| ||||| || ||||| | ||| |||||||| |||||||| || || || ||  ||||||| |||||| || ||||||
gtaaatatgcactagtagcctaacaattcatgcaatatccaatgcatcaatttgcgcttctatatattacattgttattaagctatataaggaaggatgtaactaacctggtaatgttgtttgaagGTGAAAAGTGAACTTCCAAGTACATTCAAAGCATTCCGGTATCAACAACACAGATGGTCCTGCGGACCGGCAAACCTGTTCAGGAAAATGTTGGTGGAGA

upper sequence: Vv06s0061g01230.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G105631_T05 (Zea mays), 3'ss of exon 1
-------------------gtacattta-aataaatgtctttaagttggggaccatttcatttaaattgatagc-ttcttagttgatttaacggcttcatcaatagGTGAAAAGTGAGCTGCCTAGTACTTTCAAGGCCTTCCGCTTTCAGCAACACAGGTGGTCCTGTGGTCCAGCCAATTTGTTCAGAAAAATGGTGATGGAGA
                   |  |||| | |||    | ||  |   || | |  |  | |  |  |   ||    | | |    ||||| |   || ||      ||||||||| |||||||| ||||| |||||||||||||| || ||||| ||||||||||| || || || || ||  ||||||| || ||| | |||||||
tttttttgttgagacgatggcgcattcagaatttcagactgcacagtgagaagaaagtgaaattcacccatgatgtgcctgcccgatttgattcctgca------gGTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCACAGGTGGTCGTGCGGCCCGGCGAACCTGTTCAGGAAGATGCTCATGGAGA

upper sequence: Vv06s0061g01230.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA12G08990.1 (Glycine max), 3'ss of exon 5
----------------------------------------------------------------------------gtacatttaa-ataaatgtctttaagttgg-ggaccatttcatttaaattga--tagcttcttagttgatttaacggcttcatca-atagGTGAAAAGTGAGCTGCCTAGTACTTTCAAGGCCTTCCGCTTTCAGCAACACAGGTGGTCCTGTGGTCCAGCCAATTTGTTCAGAAAAATGGTGATGGAGA
                                                                            | | ||| |  | |  ||  | | | ||       || ||   ||| | | |   |   | ||  ||  || || |||  | | | |||||  ||||||||||| ||||||||||| |  |||||| | || ||||| ||||| ||||| |||||||| || ||||||||| | ||||||||||||||||
gtgaatgaatgttccatctacttacttattagtacttccaaagtcagcaattaatgttctgcatgcaattaatggagaatattaattacatgtgattatgaattatcatttcaattttcttatactaagtcatggtgttttttttttcaatggcaactttatatagGCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCACAGATGGTCTTGTGGTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGA

upper sequence: Vv06s0061g01230.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G19490.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------------gtacatttaaataa---atgtctttaagttgg-----ggaccatttcatttaaattgatagcttcttagttgatttaacggcttcatca-atagGTGAAAAGTGAGCTGCCTAGTACTTTCAAGGCCTTCCGCTTTCAGCAACACAGGTGGTCCTGTGGTCCAGCCAATTTGTTCAGAAAAATGGTGATGGAGA
                                                        |   || | ||| |   |||  | | | ||         |   | | ||   || | || |   |||  ||  || || ||   | | | |||||  ||||||||||| || |||||||| |  |||||| | || ||||| ||||| ||||| |||||||| || ||||||||| | ||||||||||||||||
gttaatcaatgctccatctacttacctattagtacttccaaagttaacaattaacggagaatatgaatgacatatgattatgaattatcatttcaattttcttatactaagtaatggtgcctttttt--ttaaatggtaactttatatagGCCAAAAGTGAGCTTCCCAGTACTTTGAGAGCCTTCAGATTCCAGCAGCACAGATGGTCATGTGGTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGA

upper sequence: Vv06s0061g01230.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA17G05350.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------------------------------------gtacatttaaataaatgtctttaagttggggaccatttcatttaaattgata-gcttcttagttg--attta----acggcttcatcaatagGTGAAAAGTGAGCTGCCTAGTACTTTCAAGGCCTTCCGCTTTCAGCAACACAGGTGGTCCTGTGGTCCAGCCAATTTGTTCAGAAAAATGGTGATGGAGA
                                                                                            ||  |||  |       | ||||  ||         |  |||   | || |  | |||| | | |  |||||    ||      ||  ||||| |||||||||||| || |||||| | |  ||||||||||| ||||| ||  | ||||| |||||||| || ||| | ||| | ||||||||||||||||
gtatacattttttttataccaacgcgaccttattaattccaatcaattgtatatactacatgcttataatggatgatatgaagcatggttttgttaattctatcggcaatatttatctttacattttgtgtattagtaatgttctgtttctcattagtcatttacaaaaccaaactatgtatagGCGAAAAGTGAGCTTCCAAGTACTCTTAGAGCCTTCCGCTTCCAGCAGCATCGATGGTCTTGTGGTCCTGCTAATCTATTCCGCAAAATGGTGATGGAGA

upper sequence: Vv06s0061g01230.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G22740.1 (Arabidopsis thaliana), 3'ss of exon 5
--------------gtacatttaaataaatgtcttta--agttggggaccatttcatttaaattgatagcttcttagttgatttaacggcttcatcaatagGTGAAAAGTGAGCTGCCTAGTACTTTCAAGGCCTTCCGCTTTCAGCAACACAGGTGGTCCTGTGGTCCAGCCAATTTGTTCAGAAAAATGGTGATGGAGA
                | |  |||| | || |  |||  | |||  ||  | ||  | || ||    |   | | |||   ||| ||    |   || ||||||||||||||||| || |||||||| |  |||||||| ||||||||||| || ||||| ||||| || || ||| | || || |||||||| |||||||
tcattttacctttttaagaagtaaagatattttgttattacttgttgaaaaattggtatacatcataaatatatgagtcctttttactttctttgca-tagGTGAAAAGTGAGCTTCCAAGTACTTTTAGAGCCTTCCGTTTTCAGCAACATAGATGGTCTTGTGGACCTGCAAATCTCTTTAGGAAAATGGTTATGGAGA

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|110419935|gb|EC986193.1|EC986193
EST:     TCCGTGCTAGTCTCAAGGGCTGGAAATTCGTTTATCTTGGTGATCTTCAG                         GTGAAAAGTGAGCTGCCTAGTACTTTCAAGGCCTTCCGCTTTCAGCAACAC
genomic: TCCGTGCTAGTCTCAAGGGCTGGAAATTCGTTTATCTTGGTGATCTTCAGgtacatttaa ... tcatcaatagGTGAAAAGTGAGCTGCCTAGTACTTTCAAGGCCTTCCGCTTTCAGCAACAC
EST: gi|110719707|gb|EE095069.1|EE095069
EST:     TCCGTGCTAGTCTCAAGGGCTGGAAATTCGTTTATCTTGGTGATCTTCAG                         GTGAAAAGTGAGCTGCCTAGTACTTTCAAGGCCTTCCGCTTTCAGCAACAC
genomic: TCCGTGCTAGTCTCAAGGGCTGGAAATTCGTTTATCTTGGTGATCTTCAGgtacatttaa ... tcatcaatagGTGAAAAGTGAGCTGCCTAGTACTTTCAAGGCCTTCCGCTTTCAGCAACAC
EST: gi|34543478|gb|CF511710.1|CF511710
EST:     TCCGTGCTAGTCTCAAGGGCTGGAAATTCGTTTATCTTGGTGATCTTCAG                         GTGAAAAGTGAGCTGCCTAGTACTTTCAAGGCCTTCCGCTTTCAGCAACAC
genomic: TCCGTGCTAGTCTCAAGGGCTGGAAATTCGTTTATCTTGGTGATCTTCAGgtacatttaa ... tcatcaatagGTGAAAAGTGAGCTGCCTAGTACTTTCAAGGCCTTCCGCTTTCAGCAACAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaccatttcatttaaattgatagcttcttagttgatttaacggcttcatcaatagGTGAAAAGTGAGCTGCCTAGTACTTTCAAGGCCTTCCGCTTTCAGCAACACAGGTGGTCCTGTGGTCCAGCCAATTTGTTCAGAAAAATGGTGATGGAGA
                                  atttaac  putative branch site (score: 3)
                                           cttcatc  putative PPT
     tttcatttaaattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatttaaataaatgtctttaagttggggaccatttcatttaaattgatagcttcttagttgatttaacggcttcatcaatagGTGAAAAGTGAGCTGCCTAGTACTTTCAAGGCCTTCCGCTTTCAGCAACACAGGTGGTCCTGTGGTCCAGCCAATTTGTTCAGAAAAATGGTGATGGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA