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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGAAAGTTTGGATCCAGCTTTGCTTCGGCCTGGTCGAATAGATAGGAAGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAGgtacatgtgtgtttaagattatgcaaatgcaatattcactatattttcatccgacttcttgtgacaactgaatcaccaaacctggcttgattactattactaagcaaatctcatttatttaaattgcag

Basic information

species Vitis vinifera
transcript Vv07s0005g05160.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 5'ss of exon 4
AATTGAAAGTTTGGATCCAGCTTTGCTTCGGCCTGGTCGAATAGATAGGAAGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAGgtacatgt-----gtgtttaagattatg-caaatgcaatattcactatattttcatccgacttcttgtgacaactgaatcaccaaacctggcttgattactattactaagcaaatctcatttatttaaattgcag
 ||||||||| | || |||||||||||||| |||||||| ||||| || ||||||||||| ||  | || || |||||||| || || || || |||||||| | | |      ||||| |  || || |  ||   | |    ||   || | |||  |    || ||    | |                                                           
CATTGAAAGTCTTGACCCAGCTTTGCTTCGACCTGGTCGGATAGACAGAAAGATTGAATTTCCGTTACCAGATATTAAAACCAGGAGGCGGATCTTCCAGgtgcttttctacaatgtttcaagttctgtcttattggaaacctgcttcgttcttatc-aatagtttttgggtgcag-----------------------------------------------------------

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G056569_T01 (Zea mays), 5'ss of exon 3
AATTGAAAGTTTGGATCCAGCTTTGCTTCGGCCTGGTCGAATAGATAGGAAGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAGgtacatgtgtgttta-agattatgcaaatgcaatattcactatattttcatccgacttcttgtgacaactgaatcaccaaacctggcttgattactattactaagcaaatctcatttatttaaattgcag
 ||||||||| | ||||| |||||||||||||| || || |||||  ||||||||||||||||||| || || |||||||| ||||||||||| |||||||| |       | |  |||   |   | |   ||  ||| | |   |    ||   || |  | | ||   |      |||||  ||                                           
CATTGAAAGTCTTGATCCTGCTTTGCTTCGGCCAGGCCGTATAGACCGGAAGATTGAATTCCCTCTCCCAGATATTAAAACTAGAAGACGCATCTTCCAGgtgctgtaacatctgtagacagtaatatttgcattatcaatgttcgtaatacctttttgtccttataatgaaggttgtaaaccgtgcag-----------------------------------------

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G095593_T01 (Zea mays), 5'ss of exon 3
AATTGAAAGTTTGGATCCAGCTTTGCTTCGGCCTGGTCGAATAGATAGGAAGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAGgtacatgtgtgtttaagattatgcaaatgcaatattcactatattttca-tccgacttcttgtgacaactgaatcaccaaacctggcttgattactattactaagcaaatctcatttatttaaattgcag
 ||||||||| | |||||||| ||||||||||| || || |||||  ||||||||||||| ||||| || || |||||||| ||| ||||||| ||||||||||      || |   | |    | ||     ||| || || || | | | |   || || | |  |  |||      || || |                                            
CATTGAAAGTCTTGATCCAGCCTTGCTTCGGCCAGGCCGTATAGACCGGAAGATTGAATTTCCTCTACCAGATATTAAAACTAGACGACGCATCTTCCAGgtactgtgacgtctgtaaatgataatatttg-cattaacaatgttcttaataccctttgttcttattatagaaggttgtaaacttgtgcag---------------------------------------

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 4
AATTGAAAGTTTGGATCCAGCTTTGCTTCGGCCTGGTCGAATAGATAGGAAGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAGgtacatgtgtgtt-taagattatgcaaatgcaatattcactatattttcatccgacttcttgtgacaactgaatcaccaaacctggcttgattactattactaagcaaatctcatttatttaaattgcag
 ||||||||| | |||||||| |||||||| || |||||||| || || ||||||||||||||| | |||||  | || || ||  | ||||| |||||||| | | | |||  | | |   |   | | |  |  |    ||          || || |||| || |          ||   ||  ||||| |  |                                 
TATTGAAAGTCTTGATCCAGCCTTGCTTCGCCCAGGTCGAATTGACAGAAAGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctatgtgatgaaagcttctgagtcctgttcttttaattaaaaagcatgatttgttgttaccaa---------aattttgttttgatgagcag--------------------------------

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA03G32800.1 (Glycine max), 5'ss of exon 4
AATTGAAAGTTTGGATCCAGCTTTGCTTCGGCCTGGTCGAATAGATAGGAAGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAGgtacatgtgtgtttaagattatgcaaatgcaatattcactatattttcatccgacttcttgtgacaactgaatcaccaaacctggcttgattactattactaagcaaatctcatttatttaaattgcag
|||||||||  | |||||||||||||| || ||||||||||| || |||||||||||||| ||||| ||||| ||||||||||||||||||||||||||||||              ||| ||  || ||||  ||      | ||||| | |  |   ||| | | || |||   |  |     ||| |||| ||| |||||  |  ||| ||   | | || |  ||
AATTGAAAGCCTTGATCCAGCTTTGCTGCGACCTGGTCGAATTGACAGGAAGATTGAATTTCCTCTCCCTGATATTAAAACAAGAAGACGCATTTTCCAGgtaggcac---------attttgtgaaagcaagtttt----cagtttca-ctgcttcactgttatatcttaatatgcttattctacttaatta-tatgactaaa-aggtcttatacttctgaaatttag

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA10G04920.1 (Glycine max), 5'ss of exon 4
AATTGAAAGTTTGGATCCAGCTTTGCTTCGGCCTGGTCGAATAGATAGGAAGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAGgtacatgtgtgtttaagattatgcaaatgcaatattcactatattttcatccgacttcttgtgacaactgaatcaccaaacctggcttgattactattactaagcaaatctcatttatttaaattgcag
|||||||||| | |||||||||||||| |||||||||||||| || |||||||| ||||| ||||||||||| || |||||||| |||||||| || ||||||   |  ||  |||  || || ||     | |   || || | ||            || || | ||  ||       |||||     ||  | ||  |     | | |  ||| |||         
AATTGAAAGTCTTGATCCAGCTTTGCTACGGCCTGGTCGAATTGACAGGAAGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTTCAGgtag--gcatgactaattttgtgaaagcaatacacctaccatgtgtt------------tgggaaatcttgat-----ggcctggtccatttg-tgttctttctttatttttgttttttt---------

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA13G19280.1 (Glycine max), 5'ss of exon 4
AATTGAAAGTTTGGATCCAGCTTTGCTTCGGCCTGGTCGAATAGATAGGAAGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAGgtacatgtgtgtttaagattatgcaaatgcaatattcactatattttcatccgacttcttgtgacaactgaatcaccaaacctggcttgattactattactaagcaaatctcatttatttaaattgcag
|||||||||| | |||||||||||||| || ||||||||||| || |||||||| ||||| ||||||||||| || |||||||| |||||||| |||||||||    ||  |     ||| ||  || ||||||             || ||   |  ||| || | ||  ||  ||    |    |||  | || |   ||      | |   || |           
AATTGAAAGTCTTGATCCAGCTTTGCTACGACCTGGTCGAATTGACAGGAAGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAGgtaggcatgact----aattttgtgaaagcaata-------------cacccatgtgtttgggaaagcttgatggcctggtcca-tttgtgttctttctttagttttgtttttgtttt-----------

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA19G35510.1 (Glycine max), 5'ss of exon 4
AATTGAAAGTTTGGATCCAGCTTTGCTTCGGCCTGGTCGAATAGATAGGAAGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAGgtacatgtgtgtttaagattatgcaaatgcaatattcactatattttcatccgacttcttgtgacaactgaatcaccaaacctggcttgattac-tattactaagcaaatctcatttatttaaattgcag
|||||||||  | ||||||||  |||| || ||||||||||| || |||||||||||||| ||||| ||||| || ||||||||||||||||||||||||||     ||  |      || ||  ||   || ||    |   |||||| | |||        | | || |||   |  |     |||  |||  | | |||||  |  ||| ||   ||| |  |  ||
AATTGAAAGCCTTGATCCAGCCCTGCTGCGACCTGGTCGAATTGACAGGAAGATTGAATTTCCTCTCCCTGATATCAAAACAAGAAGACGCATTTTCCAGgtcggaatgact----agttctgtgaa---aacatgtttttggttttca-ctgac--------atatcttaatattcctattctacttagttatatctcactaaa-aggtcttatacttttgatatttag

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT2G20140.1 (Arabidopsis thaliana), 5'ss of exon 4
AATTGAAAGTTTGGATCCAGCTTTGCTTCGGCCTGGTCGAATAGATAGGAAGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAGgtacatgtgtgtttaagattatgcaaatgcaatattcactatattttcatccgacttcttgtgacaactgaatcaccaaacctggcttgattactattactaagcaaatctcatttatttaaattgcag
 || || ||| | || || ||  | ||| | || || || || || ||||| || |||||||||||||| || || |||||||||||||| || ||||||||         |  |  | |  |  |     |  ||  || | ||||  |  || || |   || |  |   | | |     |   |||  | | |||| ||                           
GATCGAGAGTCTTGACCCGGCACTTCTTAGACCAGGCCGGATCGACAGGAAAATCGAATTCCCTCTTCCAGATATCAAAACAAGAAGACGTATCTTCCAGgt---------tccacaactg-gtgatccttaagttttctttctttttttgtgaattttctagaaagatc--tgatcggtttttaattgcatgccattattag--------------------------

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT4G29040.1 (Arabidopsis thaliana), 5'ss of exon 4
AATTGAAAGTTTGGATCCAGCTTTGCTTCGGCCTGGTCGAATAGATAGGAAGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAGgtacatgtgtgtttaagattatgcaaatgcaatattcactatattttcatccgacttcttgtgacaactgaatcaccaaacctggcttgattactattactaagcaaatctcatttatttaaattgcag
||| || ||| | || |||||  ||||||| ||||| || || |||||||| || || |||||||| || || || |||||||||||||| || |||||||||      | | |||   ||   | |||  | ||  |  |  | |||     |  | |  ||   | |||             | ||    | ||                                 
AATCGAGAGTCTTGACCCAGCACTGCTTCGACCTGGACGGATTGATAGGAAAATCGAGTTCCCTCTCCCAGATATCAAAACAAGAAGACGTATCTTCCAGgta-----atatataattctactgagatggcaaatcaatgacttgttcg---aaactttcttgttcattgaggttgtgggttctgtttataaaatag--------------------------------

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|229418620|gb|GO652857.1|GO652857
EST:     AGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAG                         ATACATACATCAAGGATGACATTGGCTGATGATGTTAACTTGGAAGAATTT
genomic: AGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAGgtacatgtgt ... taaattgcagATACATACATCAAGGATGACATTGGCTGATGATGTTAACTTGGAAGAATTT
EST: gi|27580875|gb|CB003570.1|CB003570
EST:     AGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAG                         ATACACACATCAAGGATGACATTGGCTGATGATGTTAACTTGGAAGAATTT
genomic: AGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAGgtacatgtgt ... taaattgcagATACATACATCAAGGATGACATTGGCTGATGATGTTAACTTGGAAGAATTT
EST: gi|110703456|gb|EE080320.1|EE080320
EST:     AGATTGAATTCCCTCT-CCTGACATTAAAACAAGAAGACGCATTTTCCAG                         ATACACACATCAAGGATGACATTGGCTGATGATGTTAACTTGGAAGAATTT
genomic: AGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAGgtacatgtgt ... taaattgcagATACATACATCAAGGATGACATTGGCTGATGATGTTAACTTGGAAGAATTT
EST: gi|30321368|gb|CD004630.1|CD004630
EST:     AGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAG                         ATACACACATCAAGGATGACATTGGCTGATGATGTTAACTTGGAAGAATTT
genomic: AGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAGgtacatgtgt ... taaattgcagATACATACATCAAGGATGACATTGGCTGATGATGTTAACTTGGAAGAATTT
EST: gi|26264508|gb|CA815571.1|CA815571
EST:     AGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAG                         ATACATACATCAAGGATGACATTGGCTGATGATGTTAACTTGGAAGAATTT
genomic: AGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAGgtacatgtgt ... taaattgcagATACATACATCAAGGATGACATTGGCTGATGATGTTAACTTGGAAGAATTT
EST: gi|27580357|gb|CB003052.1|CB003052
EST:     AGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAG                         ATACACACATCAAGGATGACATTGGCTGATGATGTTAACTTGGAAGAATTT
genomic: AGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAGgtacatgtgt ... taaattgcagATACATACATCAAGGATGACATTGGCTGATGATGTTAACTTGGAAGAATTT
EST: gi|27580606|gb|CB003301.1|CB003301
EST:     AGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAG                         ATACACACATCAAGGATGACATTGGCTGATGATGTTAACTTGGAAGAATTT
genomic: AGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAGgtacatgtgt ... taaattgcagATACATACATCAAGGATGACATTGGCTGATGATGTTAACTTGGAAGAATTT
EST: gi|30131170|gb|CB916509.1|CB916509
EST:     AGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAG                         ATACACACATCAAGGATGACATTGGCTGATGATGTTAACTTGGAAGAATTT
genomic: AGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAGgtacatgtgt ... taaattgcagATACATACATCAAGGATGACATTGGCTGATGATGTTAACTTGGAAGAATTT
EST: gi|110392599|gb|EC958132.1|EC958132
EST:     AGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAG                         ATACATACATCAAGGATGACATTGGCTGATGATGTTAACTTGGAAGAATTT
genomic: AGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAGgtacatgtgt ... taaattgcagATACATACATCAAGGATGACATTGGCTGATGATGTTAACTTGGAAGAATTT
EST: gi|71881961|gb|DT031016.1|DT031016
EST:     AGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAG                         ATACACACATCAAGGATGACATTGGCTGATGATGTTAACTTGGAAGAATTT
genomic: AGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAGgtacatgtgt ... taaattgcagATACATACATCAAGGATGACATTGGCTGATGATGTTAACTTGGAAGAATTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTGAAAGTTTGGATCCAGCTTTGCTTCGGCCTGGTCGAATAGATAGGAAGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAGgtacatgtgtgtttaagattatgcaaatgcaatattcactatattttcatccgacttcttgtgacaactgaatcaccaaacctggcttgattactattactaagcaaatctcatttatttaaattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG