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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttggttgatgggtacacaaagttataaatataattctgaaatgaagttgatggctctttttgtgtcactggttcttaacttcggtatttgactgtggcagACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAAGAGGATAACTTCTGGCAGCTATATGGTGATTTTTTACCTAGTGAAGGAG

Basic information

species Vitis vinifera
transcript Vv01s0011g01080.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g01080.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g50980.1 (Oryza sativa), 3'ss of exon 3
ttggttgatgggtacacaaagttataaatataattctgaaatgaagttgatggctcttt--ttgtgtc-actggttcttaacttcggtatttgactgtggcagACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAAGAGGATAACTTCTGGCAGCTATATGGTGATTTTTTACCTAGTGAAGGAG
    ||  |    ||    |    |   |       | |   |  ||  | |  || |   |  |||  ||||  || ||||        |   || | ||||||||||||||||||  ||||||| ||||||||| | | ||||||||||  ||| || ||||| ||||||||||||||||||||||| |||||||  |  |
--tattactcaacacttgcaacc-tgttttcttccttcatgcggtgtcaaagcttcataagtgatgtagactgcatcctaacgcaatctgtaccctcttgcagACAGATTGGGATCTAAGGTTAGCTTGCCTTCTTCTCTATGCATTTGATGTAGAAGACAACTTTTGGCAGCTATATGGTGATTTTTTGCCTAGTGTTGATG

upper sequence: Vv01s0011g01080.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G807767_T03 (Zea mays), 3'ss of exon 3
ttggttgatgggtacacaaagttataaatataattctgaaatgaagttgatggctctttttgtgtcactggttcttaacttcggta-tttg----actgtggcagACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAAGAGGATAACTTCTGGCAGCTATATGGTGATTTTTTACCTAGTGAAGGAG
     |       || |||  | ||   | |  |  | ||   |  || | |   |  |   ||      | |   | ||   ||| ||||    ||| | ||||||||||||||||||  | |||||||| |||||| | | ||||||||||  ||| || ||||| |||||| |||||  ||||||||| || ||||  |  |
---actttcaaaaactcaa--tcatctgtcttttcttcaacaaatattaaagcgccaataaatgatctatgctggaagctgatgtaatttgtattactcttgcagACAGATTGGGATCTAAGATTAGCATGTCTTCTTCTATATGCATTTGATATAGAAGACAACTTTTGGCAGTTATATTCTGATTTTTTGCCAAGTGTTGATG

upper sequence: Vv01s0011g01080.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G16830.1 (Glycine max), 3'ss of exon 4
-------------------------------------------------------------------------------------ttggttgatgggt-acacaaagttataaatataat---tctgaaatgaagttgatggctctttttgtgtcactggttctta-acttcggtatttgactgtggcagACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAAGAGGATAACTTCTGGCAGCTATATGGTGATTTTTTACCTAGTGAAGGAG
                                                                                      |     ||| || || |   ||| ||| | |  |    |||  |  ||  | |    | || | || |  ||| ||  |  | ||  | |  |   ||||||||||||||||||| ||  |||||||||||||||| || | |||||||||    || |  ||||| |||||  | ||||| || || ||||| |||| ||  |
gtaattactattctcttctaagttcatttgttcataataagatataaccaattggttgttttcgcttttcatgataaatacatacgttaccaatgtgtcaccctttgttttaactgtgttgtacctgctacaaaagtaaaaaatgttctggt-tatctgcttaatgtaattgtgcaaatctttgtggcagACAGATTGGGACCTAAGGTTAGCATGCCTTCTCTTATATGCATTTGACTGTGAAGGCAACTTTTGGCAATTGTATGGCGACTTCTTACCGAGTGCAGATG

upper sequence: Vv01s0011g01080.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G05510.1 (Glycine max), 3'ss of exon 4
--------------------------------------------------------------------------------------ttggttgatgggt-acacaaagttataaatataat-tctgaaatgaagttgatggctctttttgtgtcactggttctta-acttcggtatttgactgtggcagACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAAGAGGATAACTTCTGGCAGCTATATGGTGATTTTTTACCTAGTGAAGGAG
                                                                                       |     |||  | || |   ||| ||| |||  |  |||  |  ||  | |    | || | || |  ||| ||  |  | ||  | |  |   ||||||||||||||||||| ||  |||||||||||||||| || |  |||||||||   || |  ||||| |||||  | ||||| || || ||||| |||| ||  |
gtaattacaatctcttctaagttcatttcataataagatataaccaatttgcttggttgttttcacttttcatgataaatacatacattaccaatgtatcaccctttgttttaactattgtacctgctacaaaagtaaaaaatgttctggt-tatctgcttaatgtaattgtgcaaatctttgtggcagACAGATTGGGACCTAAGGTTAGCATGCCTTCTCTTATACGCATTTGATTGCGAAGGCAACTTTTGGCAATTGTATGGCGACTTCTTACCGAGTGCAGATG

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|349826229|gb|FQ416034.1|FQ416034
EST:     TACCAGTGGGACATCCTATATTTGATATTATCAACTCAACCAATCCGGAG                         ACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
genomic: TACCAGTGGGACATCCTATATTTGATATTATCAACTCAACCAATCCGGAGgtaattgtgc ... actgtggcagACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
EST: gi|349830971|gb|FQ418255.1|FQ418255
EST:     TACCAGTGGGACATCCTATATTTGATATTATCAACTCAACCAATCCGGAG                         ACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
genomic: TACCAGTGGGACATCCTATATTTGATATTATCAACTCAACCAATCCGGAGgtaattgtgc ... actgtggcagACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
EST: gi|351025692|gb|FQ426706.1|FQ426706
EST:     TACCAGTGGGACATCCTATATTTGATATTATCAACTCAACCAATCCGGAG                         ACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
genomic: TACCAGTGGGACATCCTATATTTGATATTATCAACTCAACCAATCCGGAGgtaattgtgc ... actgtggcagACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
EST: gi|30327285|gb|CD010547.1|CD010547
EST:     CCAATCCGGAG                         ACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
genomic: CCAATCCGGAGgtaattgtgc ... actgtggcagACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
EST: gi|30325264|gb|CD008526.1|CD008526
EST:     CCAATCCGGAG                         ACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
genomic: CCAATCCGGAGgtaattgtgc ... actgtggcagACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
EST: gi|349824034|gb|FQ417421.1|FQ417421
EST:     TACCAGTGGGACATCCTATATTTGATATTATCAACTCAACCAATCCGGAG                         ACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
genomic: TACCAGTGGGACATCCTATATTTGATATTATCAACTCAACCAATCCGGAGgtaattgtgc ... actgtggcagACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
EST: gi|351019251|gb|FQ429411.1|FQ429411
EST:     TACCAGTGGGACATCCTATATTTGATATTATCAACTCAACCAATCCGGAG                         ACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
genomic: TACCAGTGGGACATCCTATATTTGATATTATCAACTCAACCAATCCGGAGgtaattgtgc ... actgtggcagACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
EST: gi|349832506|gb|FQ421067.1|FQ421067
EST:     TACCAGTGGGACATCCTATATTTGATATTATCAACTCAACCAATCCGGAG                         ACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
genomic: TACCAGTGGGACATCCTATATTTGATATTATCAACTCAACCAATCCGGAGgtaattgtgc ... actgtggcagACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
EST: gi|351048408|gb|FQ448682.1|FQ448682
EST:     TACCAGTGGGACATCCTATATTTGATATTATCAACTCAACCAATCCGGAG                         ACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTCGCATTTGATCAA
genomic: TACCAGTGGGACATCCTATATTTGATATTATCAACTCAACCAATCCGGAGgtaattgtgc ... actgtggcagACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
EST: gi|349821313|gb|FQ404445.1|FQ404445
EST:     TACCAGTGGGACATCCTATATTTGATATTATCAACTCAACCAATCCGGAG                         ACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTCGCATTTGATCAA
genomic: TACCAGTGGGACATCCTATATTTGATATTATCAACTCAACCAATCCGGAGgtaattgtgc ... actgtggcagACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
EST: gi|351053396|gb|FQ455732.1|FQ455732
EST:     TACCAGTGGGACATCCTATATTTGATATTATCAACTCAACCAATCCGGAG                         ACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTCGCATTTGATCAA
genomic: TACCAGTGGGACATCCTATATTTGATATTATCAACTCAACCAATCCGGAGgtaattgtgc ... actgtggcagACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
EST: gi|32248332|gb|CD714151.1|CD714151
EST:     CCAATCCGGAG                         ACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
genomic: CCAATCCGGAGgtaattgtgc ... actgtggcagACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
EST: gi|351028541|gb|FQ444822.1|FQ444822
EST:     TACCAGTGGGACATCCTATATTTGATATTATCAACTCAACCAATCCGGAG                         ACAGATTGGGATCTGCGGTTAGCGTGCCTTCTTTTGTTTGCATTTGATCAA
genomic: TACCAGTGGGACATCCTATATTTGATATTATCAACTCAACCAATCCGGAGgtaattgtgc ... actgtggcagACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
EST: gi|351053071|gb|FQ456678.1|FQ456678
EST:     TACCTGTGGGACATCCTATATTTGATATTATCAACTCAACCAATCCGGAG                         ACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTCGCATTTGATCAA
genomic: TACCAGTGGGACATCCTATATTTGATATTATCAACTCAACCAATCCGGAGgtaattgtgc ... actgtggcagACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
EST: gi|351016333|gb|FQ446193.1|FQ446193
EST:     TACCAGTGGGACATCCTATATTTGATATTATCAACTCAACCAATCCGGAG                         ACAGATTGGGATCTGCAGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
genomic: TACCAGTGGGACATCCTATATTTGATATTATCAACTCAACCAATCCGGAGgtaattgtgc ... actgtggcagACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
EST: gi|30328160|gb|CD011422.1|CD011422
EST:     CCAATCCGGAG                         ACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
genomic: CCAATCCGGAGgtaattgtgc ... actgtggcagACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
EST: gi|32247267|gb|CD713086.1|CD713086
EST:     CCAATCCGGAG                         ACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
genomic: CCAATCCGGAGgtaattgtgc ... actgtggcagACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
EST: gi|351013379|gb|FQ425410.1|FQ425410
EST:     TACCAGTGGGACATCCTATATTTGATATTATCAACTCAACCAATCCGGAG                         ACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
genomic: TACCAGTGGGACATCCTATATTTGATATTATCAACTCAACCAATCCGGAGgtaattgtgc ... actgtggcagACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
EST: gi|351015737|gb|FQ431692.1|FQ431692
EST:     TACCAGTGGGACATCCTATATTTGATATTATCAACTCAACCAATCCGGAG                         ACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
genomic: TACCAGTGGGACATCCTATATTTGATATTATCAACTCAACCAATCCGGAGgtaattgtgc ... actgtggcagACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA
EST: gi|351034855|gb|FQ458212.1|FQ458212
EST:     TACCAGTGGGACATCCTATATTTGATATTATCAACTCAACCAATCCGGAG                         ACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTCGCATTTGATCAA
genomic: TACCAGTGGGACATCCTATATTTGATATTATCAACTCAACCAATCCGGAGgtaattgtgc ... actgtggcagACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgatggctctttttgtgtcactggttcttaacttcggtatttgactgtggcagACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAAGAGGATAACTTCTGGCAGCTATATGGTGATTTTTTACCTAGTGAAGGAG
         tcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttggttgatgggtacacaaagttataaatataattctgaaatgaagttgatggctctttttgtgtcactggttcttaacttcggtatttgactgtggcagACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAAGAGGATAACTTCTGGCAGCTATATGGTGATTTTTTACCTAGTGAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - ttgatgg
- - -tgatggg
- - - - - - -acacaaa
- - - - - - - - - - - - -aaatata
- - - - - - - - - - - - - - - - - - - aaatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctggttc