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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaattttttactatttgtactattttcattgttttgtgtttgcttcatctgcagcttttttattttttattttttgaattctgtggtggatgtagGGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATGCTGTTTTGCTTGTGTAAGAGGATTATCAACAGCAACAAGAATATGGTGG

Basic information

species Vitis vinifera
transcript Vv08s0105g00280.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0105g00280.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os07g47580.1 (Oryza sativa), 3'ss of exon 8
gtaagaaattttttactatttgtactattttcattgttttgtgtttgcttcatctgcagcttttttattttttattttttgaattctgtggtggatgtagGGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATGCTGTTTTGCTTGTGTAAGA--GGATTATCAACAGCAACAAGAATATGGTGG
|||||  || | ||      ||| ||  ||   ||| ||| |   | || |  ||| | |||     ||   ||         |  ||| |||     ||| ||||| |||||||| ||||| ||||||||||||||||| ||||| |||||||| || || |||||||   | | |   |    |  ||    | | ||  
gtaaggcatctgttgaa---tgttctgcttattttgctttttaacttctcc--ctggaactt----gttccataaaacagcgttcttgtcgtg----cagGTAAATATGCACAAGTTACAAACAACCCAGAGAATGATGGCTGTATCAATGCTGTCTTACTCGTGTAAGGACGCAATGCTATACACTTCATTCTTCTCGT--

upper sequence: Vv08s0105g00280.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G174204_T01 (Zea mays), 3'ss of exon 8
gtaagaaattttttactatttgtactattttcattgttttgtgtttgcttcatctgcagcttttttattttttattttttgaattctgtggtggatgtagGGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATGCTGTTTTGCTTGTGTAAGAGGATTATCAACAGCAACAAGAATATGGTGG----
|| ||||||||   |             |||| |   ||  || |      | ||  ||   ||||       ||      ||||   ||   | || ||||||||| || ||||| ||||| ||||| ||||||||||| ||||| |||||||||||||| |||||  |  ||  | |     |    |  |||||||     
gtgagaaatttgcca-----------gctttcttctcttcttgctcaacctaccttgagtcctttt-----caataaaccaaattgcttgt--gttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAATGATGGGTGTATCAATGCTGTTTTGCTAGTGTAGAACCATAGTGAG----ATTTTGTTTATGGTGATGAA

upper sequence: Vv08s0105g00280.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G009876_T01 (Zea mays), 3'ss of exon 8
gtaagaaattttttactatttgtactattttcattgttttgtgtttgcttcatctgcagcttttttattttttattttttgaattctgtggtggatgtagGGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATGCTGTTTTGCTTGTGTAAGAGGATTATCAACAGCAACAAGAATATGGTGG-
             |   |  | | | |  |    |||  | | ||| |   | || |  |||     | ||  |||    |||||   ||   | || ||||||||| || ||||| ||||| ||||| ||||| ||||| ||||| |||||||||||||| ||||| |||   ||   | |       ||   |||||  
------------gtgagaaatctgccaactcttctgtgctctttttacccaacctac--cttgaccctgttcaattaacagaatttcttgt--gttgcagGGAAATATGCTCAAGTTACAAACAACCCGGAGAACGATGGCTGTATCAATGCTGTTTTGCTAGTGTA-GAGCCATAGTGAGATTTTGTTGATGGTGGTGAA

upper sequence: Vv08s0105g00280.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA10G00490.1 (Glycine max), 3'ss of exon 8
gtaagaaattttttactatttgtactattttcattgttttgtgtttgcttcatctgcagcttttttattttttattttttgaattctgtggtggatgtagGGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATGCTGTTTTGCTTGTGTAAGAGGATTATCAACAGCAACAAGAATATGGTGG---
||||||  || |||  |  ||||  | |  | |   ||   ||     || | ||| |   ||  | | ||  | ||||     | ||  ||||||| ||| |||||||| || || |||||||||||||| |||||||| ||||||||||||||||||||||| ||||   || | ||||  || || |  |   |      
gtaaga--ttattttttccttgtgttttgcttaccattgactgaa-attttaactgaaa--ttgatgtgttggaattttg----tttgccgtggatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATGCTGTTTTGCTTGTTTAAGGTCAT-AGCAAC--CATCAGGGTTCCAGCTTGAT

upper sequence: Vv08s0105g00280.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA02G35500.1 (Glycine max), 3'ss of exon 8
gtaagaaattttttactatttgtactattttcattgttttgtgtttgcttcatctgcagcttttttattttttattttttgaattctgtggtggatgtagGGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATGCTGTTTTGCTTGTGTAAGA--GGATTATCAACAGCAACAAGAATATGGTGG
||||||  || |||  |  ||||  | |  |  ||    |    |    || |        ||  | | ||  | ||||     | ||  | | ||| ||| |||||||| || || |||||||||||||| || ||||| ||||||||||||||||||||||| ||||   | || |       ||||  || |   | | 
gtaaga--ttatttgttccttgtgttttgcttgttaccattgactcaaatcttaactgaaattgatgtgttggaattttg----tttgccgggaatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAACGATGGTTGTATAAATGCTGTTTTGCTTGTTTAAGGTCGCATCAG-GGTTCCAACTTGATTTCAGAG-

upper sequence: Vv08s0105g00280.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA10G10000.1 (Glycine max), 3'ss of exon 8
gtaagaaattttttactatttgtactattt-tcattgttttgtgtttgcttcatctgcagcttttttattttttattttttgaattctgtggtggatgtagGGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATGCTGTTTTGCTTGTGTAAGAGGATTATCAACAGCAACAAGAATATGGTGG---
||||||   ||| | | || |||  || ||  |||||  |    ||| ||  |  ||  |  ||   ||||| |             ||  ||| ||| ||| |||||||| || || |||||||||||||| |||||||| ||||||||||| ||||||||||| ||||    | ||    |||| || |  |   |      
gtaagattatttgttccatgtgttttacttaccattgactgaaattttctgaaattgatgtgttggaattttgt------------ttgccgtgaatgcagGTAAATACGCTCAGGTCACAAATAACCCAGAAAATGATGGTTGTATAAATGCCGTTTTGCTTGTTTAAGG---TCATAGCAAGCATCAGGGTTCCAGCTTGAT

upper sequence: Vv08s0105g00280.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT5G06360.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaagaaattttttactatttgtactattttcattgttttgtgtttgcttcatctgcagcttttttattttttattttttgaattctgtggtggatgtagGGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATGCTGTTTTGCTTGTGTAAGAGGATTATCAACA--GCAACAAGAATATGGTGG
        |   | || || |  || |  || | ||     | |    || || | |||  | || | | | | ||     ||||      ||  |  ||| |||||||| ||||||||||| || |||||||| || |||||||||||||||||||| |||||||||    ||   |  ||  |    |  | |||||   
-------gtaagtgacaatatacacaacctt-agtgcaaactataattttgattt-cagagtcttaactctctcttc----aatt------tgacttcagGAAAATACGCTCAAGTGACAAACAATCCAGAGAACGACGGATGTATAAATGCTGTTTTACTTGTGTAACCAAATGTCCGGCACTGTCGTAGAAGTATGGA--

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|351034903|gb|FQ458260.1|FQ458260
EST:     AATGTGAGTGAACTAGGTTTGGTCACACCCGGCAGGGAAAGTTGTATGGG                         GGAAATACGCACAAGTGA
genomic: AATGTGAGTGAACTAGGTTTGGTCACACCAG-CAGGGAAAGTTGTATGGGgtaagaaatt ... gtggatgtagGGAAATACGCACAAGTGA
EST: gi|110388463|gb|EC953218.1|EC953218
EST:     AAATGTGAGTGAACTAGGTTTGGTCACACCAGCTGGGAAAGTTGTATGGG                         GGAAATACGCACAAGTGACAAATAACCCATAGAATGATGGATGTATAAATG
genomic: AAATGTGAGTGAACTAGGTTTGGTCACACCAGCAGGGAAAGTTGTATGGGgtaagaaatt ... gtggatgtagGGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATG
EST: gi|351034907|gb|FQ458264.1|FQ458264
EST:     AAATGTGAGTGAACTAGGTTTGGTCACACCGGCCGGGAAAGTTGTATGGG                         GGAAATACCCACAAGTGACAAATAACCC
genomic: AAATGTGAGTGAACTAGGTTTGGTCACACCAGCAGGGAAAGTTGTATGGGgtaagaaatt ... gtggatgtagGGAAATACGCACAAGTGACAAATAACCC
EST: gi|71886734|gb|DT035789.1|DT035789
EST:     AAATGTGAGTGAACTAGGTTTGGTCACACCAGCTGGGAAAGTTGTATGGG                         GGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATG
genomic: AAATGTGAGTGAACTAGGTTTGGTCACACCAGCAGGGAAAGTTGTATGGGgtaagaaatt ... gtggatgtagGGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATG
EST: gi|351012282|gb|FQ429967.1|FQ429967
EST:     AAATGTGAGTGAACTAGGTTTGGTCACACCAGCAGGGAAAGTTGTATGGG                         GGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATG
genomic: AAATGTGAGTGAACTAGGTTTGGTCACACCAGCAGGGAAAGTTGTATGGGgtaagaaatt ... gtggatgtagGGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATG
EST: gi|351053282|gb|FQ459150.1|FQ459150
EST:     AAATGTGAGTGAACTAGGTTTGGCCACACCAGCAGGGAAAGTTGTATGGG                         GGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAAAT
genomic: AAATGTGAGTGAACTAGGTTTGGTCACACCAGCAGGGAAAGTTGTATGGGgtaagaaatt ... gtggatgtagGGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAA-T
EST: gi|110691373|gb|EE069403.1|EE069403
EST:     AAATGTGAGTGAACTAGGTTTGGTCACACCAGCTGGGAAAGTTGTATGGG                         GGAAATACGCACAAGTGACAAATTACCCAGAGAAT
genomic: AAATGTGAGTGAACTAGGTTTGGTCACACCAGCAGGGAAAGTTGTATGGGgtaagaaatt ... gtggatgtagGGAAATACGCACAAGTGACAAATAACCCAGAGAAT
EST: gi|351025564|gb|FQ426380.1|FQ426380
EST:     AAATGTGAGTGAACTAGGTTTGGTCACACCAGCAGGGAAAGTTGTATGGG                         GGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATG
genomic: AAATGTGAGTGAACTAGGTTTGGTCACACCAGCAGGGAAAGTTGTATGGGgtaagaaatt ... gtggatgtagGGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATG
EST: gi|110686904|gb|EE063847.1|EE063847
EST:     AA-TGTGAGTGAACTANGTTTGGTCACACCAGCTGGGAAAGTTGTATGGG                         GGAAATACGNCACA-GTGACAAATAACCCAGAGAAT
genomic: AAATGTGAGTGAACTAGGTTTGGTCACACCAGCAGGGAAAGTTGTATGGGgtaagaaatt ... gtggatgtagGGAAATACG-CACAAGTGACAAATAACCCAGAGAAT
EST: gi|351035636|gb|FQ463481.1|FQ463481
EST:     AAATGTGAGTGAACTAGGTTTGGTCACACCAGCAGGGAAAGTTGTATGGG                         GGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATG
genomic: AAATGTGAGTGAACTAGGTTTGGTCACACCAGCAGGGAAAGTTGTATGGGgtaagaaatt ... gtggatgtagGGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATG
EST: gi|349827505|gb|FQ422373.1|FQ422373
EST:     AAATGTGAGTGAACTAGGTTTGGTCACACCAGCAGGGAAAGTTGTATGGG                         GGAAATACGCACAAGTGACAAATAACC
genomic: AAATGTGAGTGAACTAGGTTTGGTCACACCAGCAGGGAAAGTTGTATGGGgtaagaaatt ... gtggatgtagGGAAATACGCACAAGTGACAAATAACC
EST: gi|351056948|gb|FQ443575.1|FQ443575
EST:     AAATGTGAGTGAACTAGGTTTGGTCACACCCGCAGGGAAAGTTGTATGGT                         GGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATG
genomic: AAATGTGAGTGAACTAGGTTTGGTCACACCAGCAGGGAAAGTTGTATGGGgtaagaaatt ... gtggatgtagGGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATG
EST: gi|351049548|gb|FQ429170.1|FQ429170
EST:     AAATGTGAGTGAACTAGGTTTGGTCACACCAGCTGGGAAAGTTGTATGGG                         GGAAATACGCAC
genomic: AAATGTGAGTGAACTAGGTTTGGTCACACCAGCAGGGAAAGTTGTATGGGgtaagaaatt ... gtggatgtagGGAAATACGCAC
EST: gi|349830525|gb|FQ416835.1|FQ416835
EST:     AAATGTGAGTGAACTAGGTTTGGTCACACCAGCAGGGAAAGTTGTATGGG                         GGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATG
genomic: AAATGTGAGTGAACTAGGTTTGGTCACACCAGCAGGGAAAGTTGTATGGGgtaagaaatt ... gtggatgtagGGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATG
EST: gi|351049014|gb|FQ431558.1|FQ431558
EST:     AAATGTGAGTGAACTAGGTTTGGTCACACCAGCTGGGAAAGTTGTATGGG                         GGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATG
genomic: AAATGTGAGTGAACTAGGTTTGGTCACACCAGCAGGGAAAGTTGTATGGGgtaagaaatt ... gtggatgtagGGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATG
EST: gi|351056833|gb|FQ443460.1|FQ443460
EST:     AAATGTGAGTGAACTAGGTTTGGTCACACCAGCAGGGAAAGTTGTATGGG                         GGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATG
genomic: AAATGTGAGTGAACTAGGTTTGGTCACACCAGCAGGGAAAGTTGTATGGGgtaagaaatt ... gtggatgtagGGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATG
EST: gi|110701282|gb|EE078674.1|EE078674
EST:     AAATGTGAGTGAACTAGGTTTGGTCACACCAGCTGGGAAAGTTGTATGGG                         GGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATG
genomic: AAATGTGAGTGAACTAGGTTTGGTCACACCAGCAGGGAAAGTTGTATGGGgtaagaaatt ... gtggatgtagGGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttcatctgcagcttttttattttttattttttgaattctgtggtggatgtagGGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATGCTGTTTTGCTTGTGTAAGAGGATTATCAACAGCAACAAGAATATGGTGG
               ttttttattttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaaattttttactatttgtactattttcattgttttgtgtttgcttcatctgcagcttttttattttttattttttgaattctgtggtggatgtagGGAAATACGCACAAGTGACAAATAACCCAGAGAATGATGGATGTATAAATGCTGTTTTGCTTGTGTAAGAGGATTATCAACAGCAACAAGAATATGGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG