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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttattccattacatctctctctctctgtgatgtagccaatttctgttatgctattcttctccttgtttttttgccactgttcttattttatattgactgctgttttttattgtgggatgtagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGC

Basic information

species Vitis vinifera
transcript Vv06s0004g00180.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 6
gtatttattccattacatctctctctctctgtgatgtagccaatttctgttatgctattcttctccttgtttttttgccactgttcttattttatattgactg-ctgttt--tttattgtgggatgt-agGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGC
                              || |      |||  | || | || | ||| |||     | |   | |||      || | | ||  |  ||  ||||||   | ||||    ||   ||||||| |||||||||||||| |||||||| |||||||||||||| || || ||||| || || |||||||||||||||||||| || || || 
------------------------------gtaactatttcaagct-tgct-tgattttcatctgtgcatgtgcctaccaaatacattctgtaattgtacctaactgtttaactcattgcactataccagGATTTCAAGATTCAGAACATTGTTGGCTCTTGTGATGTTAAATTTCCAATCAGGCTGGAGGGACTTGCATATTCTCATGGTGCTTTCTCAAGT

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os12g39070.1 (Oryza sativa), 3'ss of exon 5
gtatttattccattacatctctctctctctgtgatgtagccaatttctgt-tatgctattcttctccttgtttttttgccactgttcttattttatattgactgctgttttttattgtgggatgtagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGC
                     |  || | |  |   |    |||||   | | ||| | |     || | ||  ||    |   || |   |  || || |   ||  |||  | | |       |||| || |||||||||||||| ||||| || |||||||||||||| || || ||||| || || |||||||||||||||||||| || || || 
--------------------gtaactatttcaggcttgattaattttcatctgtgcaaatgcctaccattttcattctgtaagattgtacctaaatgttta--actcatttgcactatac----cagGACTTCAAGATTCAGAACATTGTTGGTTCTTGTGATGTTAAATTTCCAATCAGGCTGGAGGGACTTGCATATTCTCATGGTGCTTTCTCAAGT

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 3
gtatttattccattacatctctctctctctgtgatgtagccaatttctgttatgctattcttctccttgtttttttgccactgttcttattttatattgactgctgttttttattgtgggatgtagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGC
                                  |   |||| | |   | |    | |    ||   | ||  ||| |  ||  ||||| | |  |||||    |  ||  |   ||  ||| ||||||| ||||| |||||||| ||||| || |||||||| ||||| || ||  | || || |||||||| ||||||||||| || || || || 
---------------------------------gtaatgccactctagctcacatcaattcattca--gattgattgtccttg--cttatatcagcttgac----gcattggaacatg--atgcagGATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGT

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 6
gtatttattccattacatctctctctctctgtgatgtagccaatttctgttatgctattcttctccttgtttttttgccactgttcttattttatattga-ctgctgttttttattgtgggatgtagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGC
                                   ||| |   |||   |  |  | | | |   | |||| |||   || | |    ||    |  | |  ||||||| |          |   ||||||||||||||||||| || |||||||| |||||||| || || || || |||||||| |||||||||||||||||||||||||| || || 
-----------------------------------gtaact--ttttcatacttgtgtacattgacctgttctttgaacaatatgtacatcagttgctaagttgctgttct---------aagccagGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTCAAGTTTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGT

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G149238_T04 (Zea mays), 3'ss of exon 5
gtatttattccattacatctctctctctctgtgatgtagccaatttctgttatgctattcttctccttgtttttttgccactgttcttattttatattgactgctgttttttattgtgggatgt-agGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGC
                                           |  || || |  || || | | |   | |      |  ||  |   || || ||      ||   ||    |||   |||  |||| |||||||||||||| || |||||||| |||||||| || || || || |||||||| |||||||| ||||||||||||||||| || || 
------------------------------------------gtagctattttcatactcgtgtacagatctg---agctttgaacaatttgtacatcagtcactaagtt--gctgttctatgccagGACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGT

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA09G41330.1 (Glycine max), 3'ss of exon 6
gtatttattccattacatctctctctctctgtgatgtagccaatttctgttatgctattcttctccttgtttttttgccactgttcttattttatattgactgctgttt-tttattgtgggatgtagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGC
                             |   |  |  ||||    | |||| |  || || |||    |       || | || |  |  |  ||| | | || ||| |||||| ||   | ||||||||||||||||||||||| |||||||| |||||||| || ||||||||  | ||||| || ||||| ||||| |||||||| || || || 
----------------------------gttcaacatctccaaaaatt-ttat-cagttgttttccactctacagaagcagt-ttgtggtcattgatttattcctttttctttattctgc--tttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 5
gtatttattccattacatctctctctctctgtgatgtagccaatttctgttatgctatt--cttctccttgtttttttgccactgttcttattttatattgactgctgttttttattgtgggatgtagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGC
                           | |  | |  | | |  | |    ||  |||    |  |      | |   |   | |||  |  |   |  |   | |  |||| | |  |  | | ||||||||||||||||||||||| |||||||| |||||||| || ||||||||  | ||||| || ||||| ||||| |||||||| || || || 
---------------------------tttaaggttcaac-atctccaaaaattttatcagttgttttccactctacagaagcagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA03G04500.1 (Glycine max), 3'ss of exon 6
----------------------------gtatttattccattacatctctctctctctgtgatgtagccaatttctgttatgctattc-ttctccttgtttttttgccactgttcttattttatatt-gactgctgttttttattgtggg----atg---tagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGC
                             |  | |    |||  |   | || | |     || |  | | ||||    ||   || | || |  | ||| ||||  |||| |  |||| |  | || || | ||  ||  |  | ||||    |||   |||||||| || ||||||||||| || ||||| |||||||| || ||||||||| |||| || || ||||||||||| |||||||| || || || 
gtactgcttctgctctttctcataatctttgctgaaattattgaaaagcgctattttaaaaatttt-ctattttcccccatttaatccattttggtcgttcttttctcactataattatgtagtgtttgattactaattggttctttgggtattatgctttagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA19G28780.1 (Glycine max), 3'ss of exon 6
gtatttattccattacatctctctctctctgtgatgtagccaatttctgttatgctattcttctccttgtttttttgccactgttcttattttatattgactgctgttttttattgtgggatgtagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGC
                      |    |||    || |     | || ||| |  |   ||   |     |  ||||     ||  ||  |||||         | || |||||| ||   | ||||||||||||||||||||||| |||||||| |||||||| || ||||||||  | ||||| || ||||| ||||| ||| |||| || || || 
-------------------gtacaacatctactctgaaaattttatcagttgttttccactctacagaagtagtttgtg---gtcattgatttattcc-----tttttctttattctgc--tttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATAGTGCTTTCTCAAGT

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA16G25450.3 (Glycine max), 3'ss of exon 6
gtatttattccattacatctctctctctctgtgatgtagccaatttctgttatgctattcttctccttgtttttttgccactgttcttattttatattgactgctgttttttattgtgggatgtagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGC
             |||  || |  |||| | |     |  | || | | || | ||    |||||  |||   | ||    ||| |||  ||   | | | || |   ||   |  |  | | |||||||| || ||||||||||| || ||||| |||||||| || ||||||||| |||| || || ||||||||||| |||||||| || || || 
------------gtactgcttttgctctttct----caatccatgttttttgttct---tttctcactgtaactatgt---tgtgcttgatt---actaattggttccttgggtattatgctctagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA18G44460.1 (Glycine max), 3'ss of exon 5
gtatttattccattacatctctctctctctgtgatgt-agccaatttctgttatgctattcttctccttgtttttttgccactgttcttattttatattgactgctgttttttattgtgggatgtagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGC
             |||| |   | ||||      ||| ||    ||||   | | |     |  |   || |  ||  |   | ||| | ||||             || ||| |||||   | |||||||||||||||||||| || |||||||| |||||||| || ||||||||  | || || || ||||| ||||| |||||||| || || || 
-----------ggtacaacatccgctctgaaaattgtcagttgttttccactctacagaagtagtttgtgatcattgact--tattcctttttt-------------ttcttttttgtgc--tttaGGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTCCCCATTCGACTGGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAG-

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA02G06370.1 (Glycine max), 3'ss of exon 2
gtatttattccattacatctctctctctctgtgatgtagccaatttctgttatgctattcttctccttgtttttttgccactgttcttattttatattgactgctgttttttattgtgggatgtagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGC
                       ||| |    ||  |    |||   |||| |||| ||||| ||    |   | |  |  |||  |  ||   || | | || |   ||   |  |  | | |||||||| || ||||||| ||| || ||||| |||||||| || ||||||||| | || || || ||||||||||| |||||||| || || || 
---------------------aatctttgctggaactgtttaatccatgtt-tgctgttcttttc----tcactgtaactatgtagtgtttgattactaattggttccttgggtattatgctttagGATTTCAAAATTCAGATCATTGTCGGCTCTTGTGATGTCAAGTTCCCCATATG-CTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G55520.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatttattccattacatctctctctctctgtgatgtagc-caatttctgttatgctattcttctcc--ttgtttttttgccactgttcttatt---------------ttatattgactgctg------ttttttattgtgggatgtagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGC
       | |   ||  |||||||||     ||||  ||| ||   | |||||| |  || |    |  |      || |    | || ||||                 ||||  | ||  |       ||  | |||      || ||||||||||||| |||||||| || ||||| |||||||| ||||||||||| ||||||||||| |||||||| |||||| |||| || || || 
------gtactcatatgtctctctctggtcctgatccagcacacactgtgttattcatttttatctcaatcaacaattcgtgtgtatttttatcggaaggaaaaattacgtataaagtctagtaataaaattgctgattacattttgcagGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGT

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT3G13445.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatttattccattacatctctctctctctgtgatgtagccaatttctgttatgctattcttctccttgtttttttgccactgttcttattttatattgactgctgttttttattgtgggatgtagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGC
                                   |||  |||||||| | |  || |||     |     |||||     |  | ||  || ||| | | |    |   || ||      || ||||||| ||||||||||| || || || || |||||||| |||||||| ||||| |||||||| ||||| || ||||| | ||| || || || 
-----------------------------------gta--caatttctttaaaccttttccctatccaacattttttttcttacttttgctt-atactaaatatattcaattgttacatcctgcagGATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGT

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ36040 (Selaginella moellendorffii), 3'ss of exon 5
gtatttattccattacatctctctctctctgtgatgtagccaatttctgttatgctattcttctccttgtttttttgccactgttcttattttatattgactgctgttttttattgt--gggat-gtagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGC
                                                                    || |     | |     | | | |  | |   ||     ||  ||  ||  | ||| | ||||||||||||| |||||||| |||||||||||||| ||||| ||||| || ||  | || ||||| || ||  |||| |||  ||| || |||
--------------------------------------------------------------------gtatgaagacgaaaacacat-tgtggtctgagctcaaacttagtaacgtccgtgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGTGACGTTAAGTTCCCGATCAGATTGGAGGGCCTGGCGTACGCTCACGGTCACTTCTCAAGC

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ04980 (Selaginella moellendorffii), 3'ss of exon 5
gtatttattccattacatctctctctctctgtgatgtagccaatttctgttatgctattcttctccttgtttttttgccactgttcttattttatattgactgctgttttttattgtgggatgtagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGC
                                                             |      |            || ||| |  | | | | | |   ||   | ||        | ||||||||||||| |||||||| ||||||||||| || ||||| ||||| || ||  | || ||||| || ||  |||| |||  ||| || |||
----------------------------------------------------------gtatgaagaagaaaacacattg-tggtctgagctcaaacttagtaacgtccatgatc-------gcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATCAGATTGGAGGGCCTGGCGTACGCTCACGGTCACTTCTCAAGC

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|161713889|gb|FC062573.1|FC062573
EST:     TATGCTCGAATTATTCAGAAGCTCGGTTTTCCAGCTAAATTTAAG                         GATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATA
genomic: TATGCTCGAATTATTCAGAAGCTCGGTTTTCCAGCTAAATTTAAGgtatttattc ... tgggatgtagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATA
EST: gi|349817400|gb|FQ405404.1|FQ405404
EST:     TATGCTCGAATTATTCAGAAGCTCGGTTTTCCAGCTAAATTTAAA                         GATTTTAAGATTCAGAACATAGTTGGCTCCAGTGATGTTAAATTCCCCATA
genomic: TATGCTCGAATTATTCAGAAGCTCGGTTTTCCAGCTAAATTTAAGgtatttattc ... tgggatgtagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATA
EST: gi|110721938|gb|EE097741.1|EE097741
EST:     TATGCTCGAATTATTCAGAAGCTCGGTTTTCCAGCTAAATTTAAG                         GATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATA
genomic: TATGCTCGAATTATTCAGAAGCTCGGTTTTCCAGCTAAATTTAAGgtatttattc ... tgggatgtagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATA
EST: gi|71881466|gb|DT030521.1|DT030521
EST:     TATGCTCGAATTATTCAGAAGCTCGGTTTTCCAGCTAAATTTAAG                         GATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCC
genomic: TATGCTCGAATTATTCAGAAGCTCGGTTTTCCAGCTAAATTTAAGgtatttattc ... tgggatgtagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCC
EST: gi|110724394|gb|EE100183.1|EE100183
EST:     TATGCTCGAATTATTCAGAAGCTCGGTTTTCCAGCTAAATTTAAG                         GATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATA
genomic: TATGCTCGAATTATTCAGAAGCTCGGTTTTCCAGCTAAATTTAAGgtatttattc ... tgggatgtagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgccactgttcttattttatattgactgctgttttttattgtgggatgtagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGC
                       tattgac  putative branch site (score: 2)
          tgttcttattttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttattccattacatctctctctctctgtgatgtagccaatttctgttatgctattcttctccttgtttttttgccactgttcttattttatattgactgctgttttttattgtgggatgtagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG