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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAGgtttttaaactcttcagtattattgtcttgatgtcgcacaagttcatgggaatttagggttttctggaactcaggcttttctgtttcttttttttttcgt...

Basic information

species Vitis vinifera
transcript Vv07s0104g00160.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0104g00160.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os04g39444.1 (Oryza sativa), 5'ss of exon 2
GTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAGgt----ttttaaactcttcagta--ttattgtcttgatgtcgcacaagttcatgggaatttagggttttctggaactcaggcttttctgtttcttttttttttcgt
||||||||||||| |||||||||| || ||  | |||||||||||||| || ||||| || || || ||||| || |||    |||| | |||  |   |    |  |     | || |   || ||      |||||||||  |       | | ||   || |||| ||    ||| |  |
GTTTCTGATGAAGCTGAACAACGAGACGGTCACCATCGAGCTCAAGAACGGCACCGTCGTCCACGGAACCATCACCGgtaagcttttcacctcgcccacaggccacaggtcgcaagtaggg-aatttttgaaaaatttaggggctct-----ccctggtgcttgtgttcctaggatttattat

upper sequence: Vv07s0104g00160.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA03G30880.1 (Glycine max), 5'ss of exon 2
GTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAGgtttt-taaactcttcagtattatt----gtcttgatgtcgcacaa-gttcatgggaatttagggttttctggaactcaggcttttctgtttcttttttttttcgt
|||||| |||||| |||||||||||||||| || |||||||||||||| ||||| || |||||||||||||| ||||||| | |   |||||| ||  |  |     ||||  |||    ||  | ||       ||   | |||| |  ||| |  | ||    |||||    ||       
GTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAGgttctcttctctcttccgtccttctccgaatctttttgttcttcaccgctccattttgttgctgcttttgttaaaccctagtttc---gtttcgcgcttaaac---

upper sequence: Vv07s0104g00160.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA19G33700.1 (Glycine max), 5'ss of exon 2
GTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAGgt-ttttaaactcttcagtattattgtcttgatgtcgcacaagttcatgggaatttagggttttctggaactcaggcttttctgtttcttttttttttcgt-----
||||||||||||| |||||||||||||||| || |||||||||||||| || || || ||||| |||||||| ||||||  | |   | |||| |   | ||  | |   ||       |||| | |    || |  |||  ||   ||   | |   |   |  |||  |||  ||      
GTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAGgtactcttctcccttccgctcttttcccgtatcgtttt----gttcttcgccgctt-gattttgttgctgcttttgttaaacc-ctagtttggtttcgcgcttaaa

upper sequence: Vv07s0104g00160.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA18G52210.1 (Glycine max), 5'ss of exon 3
GTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAGgtttttaaactcttcagtattattgtcttgatgtcgcacaagttcatgg-gaatttag--ggttttctggaactcaggcttttc-tgtttcttttttttttcgt
 ||| | |||||||||||||| ||||||||||| || |||||||||||||| ||  | |||||||||||||| |||||||| |   ||  |   | |       || |       || |||  ||  | ||| ||  || ||  | |   | |   |  || ||   | |||  || |   
-TTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGGtttcttttcttcttcttgtagagccgtttacaaacatcatgttagtgttggattcagttgggttattagttttgaacttgatcgtgaggcatttaattat---

upper sequence: Vv07s0104g00160.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA02G10640.1 (Glycine max), 5'ss of exon 3
GTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAGgtttttaaactct-tcagtattattgtcttgatgtcgcacaagttcatgggaatttagggttttctggaactcaggctt--ttctgtttcttttttttttcgt
|||| | |||||||||||||| ||||||||||| || |||||||||||||| ||  | |||||||||||||| |||||||| |   || | ||    || ||  |    ||| | ||||||  |     |||||       |    | |   | |   ||| || |  |||     | | 
GTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGgtttcttttctttctctaattttttcccccagtgttgtacaagtgtagaaccatttacaagcaac--atattagagttgaattcagtgtagtttcgagcttg-

upper sequence: Vv07s0104g00160.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT4G02840.1 (Arabidopsis thaliana), 5'ss of exon 2
GTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAGgtttttaaactcttcagtattattgtcttgatgtcgcacaagttcatggg---aatttagggt---tttctggaactcaggcttttctgtttcttttttttttcgt
|||| ||||||| |||||||||||||| || || |||||||| ||||| |||||| | |||||||| ||||| || |||       ||||| |  |      |||    |  |   | | |  || |   ||| || | |   |  ||| ||   | | ||    |  | ||           
GTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTGgtacgctt-ctcttaaaaacccagctctattcgctgtttagggttttgtgtaaaatctacgatgcttacctgtaatcgatggttactcgcgtattcacaaa-----

upper sequence: Vv07s0104g00160.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT4G02840.2 (Arabidopsis thaliana), 5'ss of exon 2
GTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAGgtttttaaactcttcagtattattgtcttgatgtcgcacaagttcatggg---aatttagggt---tttctggaactcaggcttttctgtttcttttttttttcgt----------------------------------------------------------------------------------------
|||| ||||||| |||||||||||||| || || |||||||| ||||| |||||| | |||||||| ||||| || |||       ||||| |  |      |||    |  |   | | |  || |   ||| || | |   |  ||| ||   | | ||    |  | ||      |||                                                                                          
GTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTGgtacgctt-ctcttaaaaacccagctctattcgctgtttagggttttgtgtaaaatctacgatgcttacctgtaatcgatggttactcgcgtattcacaaattctgatggtgtagtttgagtttagctagtgtctttcccctaataatgctttgttggtattaaccctagtgacactggtcaagtcagatgcag

upper sequence: Vv07s0104g00160.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: EFJ29766 (Selaginella moellendorffii), 5'ss of exon 2
GTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAGgtttttaaactcttcagtattattgtcttgatgtcgcacaagttcatgggaatttagggttttctggaactcaggcttttctgtttcttttttttttcgt
 |||||||||||| | |||||||| || || || ||||||||||||||||| ||  | ||  |||| || || ||||||||      |||  ||   || | ||| |   | |       | ||  |  |      || |||||     ||                          
ATTTCTGATGAAGCTAAACAACGAGACAGTATCCATCGAGCTCAAGAATGGGACTATTGTGAATGGAACAATCACAGgttt----gatctctag-gctagtttctagcgattgttttctctgataagtttccctttttctctggtgtgtag--------------------------

upper sequence: Vv07s0104g00160.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: EFJ08912 (Selaginella moellendorffii), 5'ss of exon 2
GTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAGgtttttaaactcttcagtattattgtcttgatgtcgcacaagttcatgggaatttagggttttctggaactcaggcttttctgtttcttttttttttcgt
 |||||||||||| | |||||||| || || || ||||||||||||||||| ||  | ||  |||| || || ||||||   | |  |||  ||   || | ||| |   | |       | ||  |  |      |  |||||     ||                          
ATTTCTGATGAAGCTAAACAACGAGACGGTATCGATCGAGCTCAAGAATGGGACTATTGTGAATGGAACAATCACAGgtg--tgatgtctctag-gctagtttctagcgattgttttctctgataagtttcccttttcctctggtgtgtag--------------------------

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|77578860|gb|DV218230.1|DV218230
EST:     TGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAG                         GTGTTGATATTAGTATGAACACACATTTGAAGACAGTGAAACTTACGTTGA
genomic: CGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAGgtttttaaac ... cttgttatagGTGTTGATATTAGTATGAACACACATTTGAAGACAGTGAAACTTACGTTGA
EST: gi|110715316|gb|EE093229.1|EE093229
EST:     TGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAG                         GTGTTGATATTAGTATGAACACACATTTGAAGACAGTGAAACTTACGTTGA
genomic: CGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAGgtttttaaac ... cttgttatagGTGTTGATATTAGTATGAACACACATTTGAAGACAGTGAAACTTACGTTGA
EST: gi|32246247|gb|CD712066.1|CD712066
EST:     TGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAG                         GTGTTGATATTAGTATGAACACACATTTGAAGACAGTGAAACTTACGTTGA
genomic: CGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAGgtttttaaac ... cttgttatagGTGTTGATATTAGTATGAACACACATTTGAAGACAGTGAAACTTACGTTGA
EST: gi|71873275|gb|DT022330.1|DT022330
EST:     TGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAG                         GTGTTGATATTAGTATGAACACACATTTGAAGACAGTGAAACTTACGTTGA
genomic: CGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAGgtttttaaac ... cttgttatagGTGTTGATATTAGTATGAACACACATTTGAAGACAGTGAAACTTACGTTGA
EST: gi|27583587|gb|CB006282.1|CB006282
EST:     TGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAG                         GTGTTGATATTAGTATGAACACACATTTGAAGACAGTGAAACTTACGTTGA
genomic: CGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAGgtttttaaac ... cttgttatagGTGTTGATATTAGTATGAACACACATTTGAAGACAGTGAAACTTACGTTGA
EST: gi|110726188|gb|EE101761.1|EE101761
EST:     TGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAG                         GTGTTGATATTAGTATGAACACACATTTGAAGACAGTGAAACTTACGTTGA
genomic: CGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAGgtttttaaac ... cttgttatagGTGTTGATATTAGTATGAACACACATTTGAAGACAGTGAAACTTACGTTGA
EST: gi|77578278|gb|DV217913.1|DV217913
EST:     TGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAG                         GTGTTGATATTAGTATGAACACACATTTGAAGACAGTGAAACTTACGTTGA
genomic: CGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAGgtttttaaac ... cttgttatagGTGTTGATATTAGTATGAACACACATTTGAAGACAGTGAAACTTACGTTGA
EST: gi|110717228|gb|EE092911.1|EE092911
EST:     TGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAG                         GTGTTGATATTAGTATGAACACACATTTGAAGACAGTGAAACTTACGTTGA
genomic: CGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAGgtttttaaac ... cttgttatagGTGTTGATATTAGTATGAACACACATTTGAAGACAGTGAAACTTACGTTGA
EST: gi|30131461|gb|CB916800.1|CB916800
EST:     TGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAG                         GTGTTGATATTAGTATGAACACACATTTGAAGACAGTGAAACTTACGTTGA
genomic: CGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAGgtttttaaac ... cttgttatagGTGTTGATATTAGTATGAACACACATTTGAAGACAGTGAAACTTACGTTGA
EST: gi|110690320|gb|EE067314.1|EE067314
EST:     ATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAG                         GTGTTGATATTAGTATGAACACACATTTGAAGACAGTGAAACTTACGTTGA
genomic: ATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAGgtttttaaac ... cttgttatagGTGTTGATATTAGTATGAACACACATTTGAAGACAGTGAAACTTACGTTGA
EST: gi|110419993|gb|EC986253.1|EC986253
EST:     TGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAG                         GTGTTGATATTAGTATGAACACACATTTGAAGACAGTGAAACTTACGTTGA
genomic: CGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAGgtttttaaac ... cttgttatagGTGTTGATATTAGTATGAACACACATTTGAAGACAGTGAAACTTACGTTGA
EST: gi|71872888|gb|DT021943.1|DT021943
EST:     TGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAG                         GTGTTGATATTAGTATGAACACACATTTGAAGACAGTGAAACTTACGTTGA
genomic: CGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAGgtttttaaac ... cttgttatagGTGTTGATATTAGTATGAACACACATTTGAAGACAGTGAAACTTACGTTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAGgtttttaaactcttcagtattattgtcttgatgtcgcacaagttcatgggaatttagggttttctggaactcaggcttttctgtttcttttttttttcgt

- - - - - - - - - - - - - - - - - - - AGCTCA