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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAAAATAGCATCTCTGTTGGGGCTTCTGGTGCTCTTTTTGGGCTTTTGGGAGCAATGCTTTCAGAGCTTATTACAAACTGGTCCATGTATACAAACAGGgtgagcaatctagcccactgttgtcttactccttaccctttgagataattagccttgtttgttgcttttgtag

Basic information

species Vitis vinifera
transcript Vv16s0100g00640.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0100g00640.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA16G32150.1 (Glycine max), 5'ss of exon 3
TCAAAATAGCATCTCTGTTGGGGCTTCTGGTGCTCTTTTTGGGCTTTTGGGAGCAATGCTTTCAGAGCTTATTACAAACTGGTCCATGTATACAAACAGGgtga-gcaatctagcccactgttgtctt------actccttacccttt---------gagataattagccttgtttgttgcttttgtag-----------
|  ||| | ||| |||||||| |||||||||||||||||||| ||| | ||||||||||||||||| ||||| ||||| |||   || ||||| || | ||||  |    | | || | | |||| ||        |  |||    ||          | || ||||   || |     | |||||              
TAGAAACAACATTTCTGTTGGTGCTTCTGGTGCTCTTTTTGGACTTCTTGGAGCAATGCTTTCAGAACTTATCACAAATTGGAGTATTTATACTAATAAGgtgttggttcccatcctatttttgtattctgtgtgtttgttagttctttttaaaaggaaaattattaatgttatgaaaagattttgacaaattcctgtat

upper sequence: Vv16s0100g00640.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA09G26610.2 (Glycine max), 5'ss of exon 3
TCAAAATAGCATCTCTGTTGGGGCTTCTGGTGCTCTTTTTGGGCTTTTGGGAGCAATGCTTTCAGAGCTTATTACAAACTGGTCCATGTATACAAACAGGgtgagca--atctagcccactgttgtcttactcct-taccctttgagataattagccttgtttgttgcttttgtag------------------------
|  ||| |  ||||||||||| |||||||||||||| ||||| ||| | || |||||||||||||| ||||| |||||||||   || ||||| || | |||||| |  |  |       |    || || |  | |   || || | |  ||||   | ||           |                          
TAGAAACAATATCTCTGTTGGTGCTTCTGGTGCTCTATTTGGACTTCTTGGTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAGgtgagtataaagtcattggttcccatcctatttttgttttctgtgtgtttgttagttcttttgaaaaggaaaatgattaatgttatgaaaagattgacaa

upper sequence: Vv16s0100g00640.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA20G29570.1 (Glycine max), 5'ss of exon 3
TCAAAATAGCATCTCTGTTGGGGCTTCTGGTGCTCTTTTTGGGCTTTTGGGAGCAATGCTTTCAGAGCTTATTACAAACTGGTCCATGTATACAAACAGGgtgagca-atctagcccact--gttgtcttactccttac--cctttgagataattagccttgtttgttgcttttgtag----------------------------------------------------------------------------------------------------------
   | |   |||||||||||| ||||||||||| |||||||| ||| | || |||||||| || || ||||| ||||||||| | || ||| | || |  |||||   | |||   |  |  ||   | || |  |||   | ||    ||  |||    | ||| |   | |   ||                                                                                                          
CAGAGACCACATCTCTGTTGGTGCTTCTGGTGCCCTTTTTGGACTTCTTGGCGCAATGCTGTCTGAACTTATCACAAACTGGACTATATATTCCAATAAAgtgagtgtacctaattctttaggtcagcctaatttttatggctttctgcatggttattaatttttttcaatataagagacacctcaaatcttctacactttggctcattgtaatcaattagtttcatatctttaaattatattaacatggcacaagttaacttttttttttactcttgttgtag

upper sequence: Vv16s0100g00640.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA09G26620.1 (Glycine max), 5'ss of exon 6
-----------------------------------------------------------------------------TCAAAATAGCATCTCTGT------TGGGGCTTCTGGTGCTCTTTTTGGGCTTTTGGGAGCAATGCTTTCA----GAGCTTATTACAAACTGGTCCATGTATACAAACAG--Ggtgagcaatctagcccac-tgttgtcttactccttaccctttgagataatta--gccttgtttgttgcttttgtag
                                                                             |    ||   || | |||      |  |  |  | || || |  || |         |  | |  ||| |    ||| || |  | || |  |  ||| || ||  | |  | |  ||||  |  |   | |  | | ||     ||    | | || |  | |  | ||| |||  |  ||| | ||
TGGACTTGGAGCAATGCTTTCAGAACTTATTACAAACTGGAGTATTCATACAAATAAGGTGAGAATAGAGTTATCAGTTCTTATGCTATTTTTGTATTCTgtatgattgttagttctttaatttgaaaaggaaaatgattaattttacgaagagattttggcgaagtcctgtatgcatgcatcccgttgattggcaaaatgacttgcatagtatatttaagattcatttataagtttctaaccgtcttttttcatattttggcag

upper sequence: Vv16s0100g00640.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA10G38290.1 (Glycine max), 5'ss of exon 3
TCAAAATAGCATCTCTGTTGGGGCTTCTGGTGCTCTTTTTGGGCTTTTGGGAGCAATGCTTTCAGAGCTTATTACAAACTGGTCCATGTATACAAACAGGgtgagca-atctagcccact--gttgtcttactcctta---ccctttgagataattag--ccttgtttgttgcttttgtag-----------------------------------------------------------------------------------
   | |   ||||||||| || ||||||||||| |||||||| ||| | || |||||||| || || ||||| ||||||||| | || ||| | || |  |||||   | |||   |  |  ||   | |  |   |      |||  | | ||      |||    | ||  |  | | |                                                                                   
CAGAGACCACATCTCTGTGGGTGCTTCTGGTGCCCTTTTTGGACTTCTTGGCGCAATGCTGTCTGAACTTATCACAAACTGGACTATATATTCCAATAAAgtgagtgtacctaattctttaagtcaccctgatttatgggtttcttcaatacaagagacacctcaaatcttcttcattttggctcattgcaatcaattagttttataccttcaaaatagattaacattgtacgagttaacttttgtttttcactctttttgcag

upper sequence: Vv16s0100g00640.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT5G07250.1 (Arabidopsis thaliana), 5'ss of exon 3
TCAAAATAGCATCTCTGTTGGGGCTTCTGGTGCTCTTTTTGGGCTTTTGGGAGCAATGCTTTCAGAGCTTATTACAAACTGGTCCATGTATACAAACAGGgtgag---caatctagcccactgttgtcttactccttaccctttgagataattagccttgtttgttgcttttgtag---------
   ||| || ||||||||||| |||||||||||||||||||| ||  | ||  ||||||| || || ||| | || |||||| | || ||  | |||| ||| |    ||||||      |  ||     |  |    | ||     ||  |    | ||||| |    |  | |          
CAGAAACAGTATCTCTGTTGGAGCTTCTGGTGCTCTTTTTGGCCTCCTTGGCTCAATGCTCTCTGAACTTTTCACCAACTGGACAATCTACTCTAACAAGgttaataccaatctgcttttcatttcaaacatacaaatcactccatcatgttggctcatgtttctgatctgagcatatgtaccag

upper sequence: Vv16s0100g00640.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT5G07250.2 (Arabidopsis thaliana), 5'ss of exon 3
TCAAAATAGCATCTCTGTTGGGGCTTCTGGTGCTCTTTTTGGGCTTTTGGGAGCAATGCTTTCAGAGCTTATTACAAACTGGTCCATGTATACAAACAGGgtgag---caatctagcccactgttgtcttactccttaccctttgagataattagccttgtttgttgcttttgtag------------------------
   ||| || ||||||||||| |||||||||||||||||||| ||  | ||  ||||||| || || ||| | || |||||| | || ||  | |||| ||| |    ||||||      |  ||     |  |    | ||     ||  |    | ||||| |    |  | |                         
CAGAAACAGTATCTCTGTTGGAGCTTCTGGTGCTCTTTTTGGCCTCCTTGGCTCAATGCTCTCTGAACTTTTCACCAACTGGACAATCTACTCTAACAAGgttaataccaatctgcttttcatttcaaacatacaaatcactccatcatgttggctcatgtttctgatctgagcatatgtaccagattgctgcactcctg

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|352789912|gb|FQ478727.1|FQ478727
EST:     AGCAAATGCTTTCAGAGCTTATTACAAACTGGTCCATGTATACAAACAGG                         GCTGCAGCACTACTCACACTCTTGGTCAT
genomic: AGCAA-TGCTTTCAGAGCTTATTACAAACTGGTCCATGTATACAAACAGGgtgagcaatc ... gcttttgtagGCTGCAGCACTACTCACACTCTTGGTCAT
EST: gi|351055425|gb|FQ442023.1|FQ442023
EST:     GAGCAATGCTTTCAGAGCTTATTACAAACTGGTCCATGTACACAAACAGG                         GCTGCAGCACTACTCACACTCTT
genomic: GAGCAATGCTTTCAGAGCTTATTACAAACTGGTCCATGTATACAAACAGGgtgagcaatc ... gcttttgtagGCTGCAGCACTACTCACACTCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAAAATAGCATCTCTGTTGGGGCTTCTGGTGCTCTTTTTGGGCTTTTGGGAGCAATGCTTTCAGAGCTTATTACAAACTGGTCCATGTATACAAACAGGgtgagcaatctagcccactgttgtcttactccttaccctttgagataattagccttgtttgttgcttttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT