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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtcacatggagcaatcttctgtttaaattattacgaagatgtgagaatagttgcatgaagggatgatatctaacctacaattctctgcttttgtccagCCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCAGGTTTGGCGTCTGATCTCTTGTATATGGCTACATGCTGGGGTGTTCCAT

Basic information

species Vitis vinifera
transcript Vv06s0004g04890.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g04890.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA15G04230.1 (Glycine max), 3'ss of exon 1
-------------------------------------------------atgtcaca-tggagcaatcttctgtt-taaattattacgaagatgtgagaatagttgcatgaagggatgatatctaacctacaattctctgcttttgtccagCCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCAGGTTTGGCGTCTGATCTCTTGTATATGGCTACATGCTGGGGTGTTCCAT
                                                 |  | | | |  |  |||| | |||  || ||| || | | ||     ||||| ||   || ||| |  |||  |     ||| || |    |||| |  ||  ||||||||||||||||||| ||||||  ||| ||| | |||||||| ||||||||||| ||  |||||||||||||| | || | ||||||  | |||
gtgagttcttcttctctcatcacctaaaagcacaattttattttcattgagattataatttaaaaatcatgtgtcatacattgttgcaatgactaatgaatactt---tgtaggtac-atacgttgttgacattttttaatttttatttagATTAGAGAAGATGGGTGCTCTTGAAGTGGGTAAAGTGATTCATAGACACCAGGTTTGGCGCCTTTTCTCTTGTATATGGTTGCACGGTGGGGTTGTTCAT

upper sequence: Vv06s0004g04890.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA13G41170.1 (Glycine max), 3'ss of exon 1
-----------atgtcacatggagcaatcttctgtttaaattattacgaagatgtgaga-atagttgca-tgaa---gggatgatatctaacctacaattctct--------gcttttgtccagCCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCAGGTTTGGCGTCTGATCTCTTGTATATGGCTACATGCTGGGGTGTTCCAT
            | || ||| |  |||         |  ||| | |   |  ||| | | || |||||| ||||    ||||  || | |  ||  |||| | |           ||| |  ||  ||||||||||||||||||| |||||   ||| ||| | ||| |||| ||||||||||| ||  |||||||||||||| | || | ||||||  | || 
gtgagttcttcgtctctcatcgcccaaaaacacaactttatt-tcattcatgtgtcatacattgttgcaatgaataatggattgtaccaatactgaaattttttttatttttatatttatttagATTAGAGAAGATGGGTGCTCTTGAAGTTGGTAAAGTGATTCATGGACACCAGGTTTGGCGGCTCTTCTCTTGTATATGGTTGCACGGTGGGGTTGTTCAC

upper sequence: Vv06s0004g04890.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT2G29050.2 (Arabidopsis thaliana), 3'ss of exon 1
--atgtcacatggagcaatcttctgtttaaattattacgaagatgtgagaatagttgcatgaagggatgatatctaacctacaattctctgcttttgt-ccagCCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCAGGTTTGGCGTCTGATCTCTTGTATATGGCTACATGCTGGGGTGTTCCAT
   ||   | | ||   |  || || | |||||||      |   |  | || ||  || | |   || |  | | |     |  | | | ||||  | ||||  | ||||||||||| ||| |||| || || | |||||| ||||  ||  |||| |||||  || || ||||||||||||||||||||||||| || |||
ttgtggggcttagaatgaaatt-tggtgaaattatacttgtggcatt-gcattgtaaca-gtaaatatcaagtgttatagttatgtgtattctttgataccagATTGGAGAAGATGGGGGCTTTAGATGTATCAATGGTGGTTCATAAGCACGAGGTGTGGCGCTTGTTCACTTGTATATGGCTACATGCTGGGGTTTTTCAT

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|349829002|gb|FQ419534.1|FQ419534
EST:     TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCAC                         CCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCA
genomic: TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCACgtgagttttc ... ttttgtccagCCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCA
EST: gi|110701018|gb|EE078179.1|EE078179
EST:     TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCAC                         CCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCA
genomic: TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCACgtgagttttc ... ttttgtccagCCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCA
EST: gi|110412849|gb|EC978612.1|EC978612
EST:     TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCAC                         CCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCA
genomic: TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCACgtgagttttc ... ttttgtccagCCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCA
EST: gi|349825356|gb|FQ418077.1|FQ418077
EST:     TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCAC                         CCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCA
genomic: TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCACgtgagttttc ... ttttgtccagCCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCA
EST: gi|351012669|gb|FQ430232.1|FQ430232
EST:     TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCAC                         CCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCA
genomic: TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCACgtgagttttc ... ttttgtccagCCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCA
EST: gi|110689118|gb|EE065062.1|EE065062
EST:     TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCAC                         CCTAGAGAAGATGGGTGATCTAGAAGTGTCTAAGGTGGTCCATAGACATCA
genomic: TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCACgtgagttttc ... ttttgtccagCCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCA
EST: gi|351016069|gb|FQ432024.1|FQ432024
EST:     TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCAC                         CCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCA
genomic: TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCACgtgagttttc ... ttttgtccagCCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCA
EST: gi|161721553|gb|FC070095.1|FC070095
EST:     TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCAC                         CCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCA
genomic: TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCACgtgagttttc ... ttttgtccagCCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCA
EST: gi|351031206|gb|FQ445033.1|FQ445033
EST:     TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCAC                         CCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCA
genomic: TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCACgtgagttttc ... ttttgtccagCCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCA
EST: gi|351025014|gb|FQ433431.1|FQ433431
EST:     TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCAC                         CCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCA
genomic: TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCACgtgagttttc ... ttttgtccagCCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCA
EST: gi|110702261|gb|EE080769.1|EE080769
EST:     TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCAC                         CCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCA
genomic: TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCACgtgagttttc ... ttttgtccagCCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCA
EST: gi|351023516|gb|FQ432899.1|FQ432899
EST:     TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCAC                         CCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCA
genomic: TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCACgtgagttttc ... ttttgtccagCCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCA
EST: gi|351042831|gb|FQ434393.1|FQ434393
EST:     TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCAC                         CCTAGAAAAAATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCAT
genomic: TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCACgtgagttttc ... ttttgtccagCCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCAT
EST: gi|71869620|gb|DT018675.1|DT018675
EST:     TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCAC                         CCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCA
genomic: TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCACgtgagttttc ... ttttgtccagCCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCA
EST: gi|110382751|gb|EC947072.1|EC947072
EST:     TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCAC                         CCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCA
genomic: TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCACgtgagttttc ... ttttgtccagCCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCA
EST: gi|349826702|gb|FQ418793.1|FQ418793
EST:     TCGTTTCAGCCACTCAAGGGGAATCCACTACTCGGCCCGTCTTCGTCCAC                         CCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCA
genomic: TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCACgtgagttttc ... ttttgtccagCCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCA
EST: gi|349828349|gb|FQ416302.1|FQ416302
EST:     TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCAC                         CCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCA
genomic: TCGTTTCAGCCACTCAAGGAGAATCCACTACTCGGCCCGTCTTCGTCCACgtgagttttc ... ttttgtccagCCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaatagttgcatgaagggatgatatctaacctacaattctctgcttttgtccagCCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCAGGTTTGGCGTCTGATCTCTTGTATATGGCTACATGCTGGGGTGTTCCAT
                        atctaac  putative branch site (score: 2)
                                     ttctctgcttttgtcc  putative PPT
                      atatctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtcacatggagcaatcttctgtttaaattattacgaagatgtgagaatagttgcatgaagggatgatatctaacctacaattctctgcttttgtccagCCTAGAGAAGATGGGTGCTCTAGAAGTGTCTAAGGTGGTCCATAGACATCAGGTTTGGCGTCTGATCTCTTGTATATGGCTACATGCTGGGGTGTTCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- -tcacatg
- - - - - - - - -cttctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctacaa