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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactaggatgtgagtccatcacatgcatacatgctttgtcattttaaatcgtccgcgtaacattagatggtccaatgctatctgtattttgtgttcacagAAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACTCCTCCCACCAATGAGGACAGATATTTGCTGTTCATTGATGAGTTACGTG

Basic information

species Vitis vinifera
transcript Vv06s0004g06120.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g06120.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os02g43350.1 (Oryza sativa), 3'ss of exon 10
tactaggatgtgagtccatcacatgcatacatgctttgtcattttaaatcgtccgcgtaacattagatggtccaatgctatctgtattttgtgttcacagAAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACTCCTCCCACCAATGAGGACAGATATTTGCTGTTCATTGATGAGTTACGTG
   | | | |  || | |  |     | | |   |||   |    ||||  ||  | |    ||| ||  |  | || | |   | |||        ||||| ||||| ||||||||||| ||||| || |||||||| |||||||| || |||||||| |  || || ||||||||||| ||  |||||||  | ||||
-gtttgaacgcaag-caactatcgataga-acagtttaaga----aaatgttcgtcttgggcttacat--tttagtgttgttcttttttc----caccagAAATTGAGTATATTGCCAAGGTCAGGTGGTGCATTGGGCTTTACATACACCCCTCCCACAACAGAAGATAGATATTTGCTCTTTGTTGATGAACTGCGTG

upper sequence: Vv06s0004g06120.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G163193_T03 (Zea mays), 3'ss of exon 9
tactaggatgtgagtccatcacatgcatacatgctttgtcattttaaatcgtccgcgtaacattagatggtccaatgctatctgtattttgtgttca-cagAAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACTCCTCCCACCAATGAGGACAGATATTTGCTGTTCATTGATGAGTTACGTG
                       || |   | ||  |  |   |  ||   || | |  |   |  |   |    | || | |  ||  ||  || | ||||| ||||| ||||||||||| |||||||| ||||| || |||||||| || ||||||||||  ||||| |||||||| || ||  |||||||  ||||||
--------------------gtttgaacttaagcaattactgatagaacaatctgagagaagatgtaatttgacttactttttcaatgctgaatttaacagAAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACCCCTCCCACCACAGAGGATAGATATTTACTCTTTGTTGATGAACTACGTG

upper sequence: Vv06s0004g06120.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA14G37090.1 (Glycine max), 3'ss of exon 11
tactaggatgtgagt-ccatcacatgcatacatgctttgtcattttaaatcgtccgcgtaacattagatggtccaatgctatctgtattttg-tgttcacagAAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACTCCTCCCACCAATGAGGACAGATATTTGCTGTTCATTGATGAGTTACGTG
 | |  | | |||    |||        | | |  ||  | ||| |  ||        |   || ||    | ||   ||  || | |   | ||||  |||||  | ||||||||||| || ||||||||||| ||||| ||||| || |||||||| || |||||||||||||| ||||| |||||||||||||| ||||
-attgtgttatgaaaatcattgttaagtttcttatttgtttattgtttattaagaagatc-tataaggatattcatgccttactatctcgggatgttatcagAAACTAAGCATATTGCCTAGGTCAGGAGGGGCTTTGGGATTTACTTACACTCCTCCAACAAATGAGGACAGATACTTGCTTTTCATTGATGAGTTGCGTG

upper sequence: Vv06s0004g06120.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA02G39040.1 (Glycine max), 3'ss of exon 11
tactaggatgtgagtccatcacatgcatacatgctttgtcattttaaatcgtccgcgtaacattagatggtccaatgctatctgtattttgtgttcacagAAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACTCCTCCCACCAATGAGGACAGATATTTGCTGTTCATTGATGAGTTACGTG
|   ||  |    ||  ||   |       | | ||  |  || |  ||        |       |||  ||      ||      |  | ||||  |||||  | ||||||||||| || ||||||||||| ||||| ||||| || |||||||| || |||||||||||||| ||||| |||||||||||||| ||||
ttggagcctacttgtgtattgaaaatcattaagtttcttatttgtttattaagaaaatctataaggatattcatgccttactctcttggtatgttatcagAAACTAAGCATATTGCCTAGGTCAGGAGGGGCTTTGGGATTTACTTACACTCCTCCAACAAATGAGGACAGATACTTGCTTTTCATTGATGAGTTGCGTG

upper sequence: Vv06s0004g06120.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA0028S00210.1 (Glycine max), 3'ss of exon 10
tactaggatgtgagtc-catcacatgcatacatgctttgt-cattttaaatcgtccgcgtaacattag-atggtccaatgctatctgtattttgtgttca----cagAAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACTCCTCCCACCAATGAGGACAGATATTTGCTGTTCATTGATGAGTTACGTG
     | || | |||   |||      ||   |   |||  |||| | | || |     ||   | || ||| | || |||  |   ||| |||||||      |||||  | || ||||||||||| ||||||||||| ||||| ||||| |||| |||||| || | |||||| ||||| ||||| ||  | |||||||| | ||
-----gtatataagttgtatcttggaaatctctatgttgcacattattagtccttaa-atactttaaggatgattcagtgcc-ttaatatcttgtgtttgtcatcagAAACTAAGTATATTGCCAAGGTCAGGAGGGGCTTTGGGCTTTACTTATATTCCTCCAACAACTGAGGATAGATACTTGCTATTTGTCGATGAGTTGCATG

upper sequence: Vv06s0004g06120.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA18G07280.1 (Glycine max), 3'ss of exon 10
tactaggatgtgagtc-catcacatgcatacatgctttgt-cattttaaatcgtccgcgtaacattag-atggtccaatgctatctgtattttgtgttca----cagAAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACTCCTCCCACCAATGAGGACAGATATTTGCTGTTCATTGATGAGTTACGTG
     | || | |||   |||      ||   |   |||  |||  | | || |     ||   | || ||| | ||||||  |   ||| |||||||      |||||  | || ||||||||||| ||||||||||| ||||| ||||| |||| |||||| || | |||||| ||||| ||||| ||  | |||||||| | ||
-----gtatataagttgtatcttggaaatctctatgttgcacatcattagtccttaa-atactttaaggatgattcaatgcc-ttaatatgttgtgtttgtcatcagAAACTAAGTATATTGCCAAGGTCAGGAGGGGCTTTGGGCTTTACTTATATTCCTCCAACAACTGAGGATAGATACTTGCTATTTGTCGATGAGTTGCATG

upper sequence: Vv06s0004g06120.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 10
tactaggatgtgagtccatcacatgcatacatgctttgtcattttaaatcgtccgcgtaacattagatggtccaa-tgctatctgtatttt--gtgttcacagAAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACTCCTCCCACCAATGAGGACAGATATTTGCTGTTCATTGATGAGTTACGTG
   ||  |||  |   | |    | |||  | |||   |   ||||  | ||    |||     | ||| | ||| |  |     | |||   |||||  ||||| || ||||||||||||||| |||||||||||||||| |||||||| | |||||| || | ||| ||||||||||| || |||||||||||| | | ||
--gtaaaatgcaaaaactttgtctacatttacgctcattg--tttatgttgttta-gtacgtgcaaatgattcaagttttgctcatctttgtggtgttgtcagAAATTAAGCATATTGCCAAGAACAGGAGGGGCATTGGGATTTACATACATTCCTCCTACTAGTGAAGACAGATATTTACTCTTCATTGATGAGCTGCTTG

upper sequence: Vv06s0004g06120.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT5G58870.1 (Arabidopsis thaliana), 3'ss of exon 10
tactaggatgtgagtccatcacatgcatacatgctttgtcattttaaatcgtccgcgtaacattagatggtccaatgctatctgtattttgtgttcacagAAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACTCCTCCCACCAATGAGGACAGATATTTGCTGTTCATTGATGAGTTACGTG
         || |  |  | | |  |  |  |   |||  | |    ||  |   | |    ||| ||| ||   |||||  |  || |||| ||   |||| || |||||||| ||||||||||||||||||||||| |||||||| | ||| || ||  |||| |||||||||||||| || ||||||||  ||| ||
---------gtaaagcagtgagaaccgcatgttgcttgatactc---attttttacatg-tgtta-atgctc---tgctaa-tacatattgtatttttagAAATTAAGCATATTACCAAGATCAGGAGGGGCATTGGGCTTTACATACATTCCCCCAACGCATGAAGACAGATATTTGCTCTTTATTGATGAACTACATG

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|30325592|gb|CD008854.1|CD008854
EST:     TAGTGGGAACTGCTGTTGCTAATCTTCTTTGTGGACAGCCACGTGTTGAG                         AAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACT
genomic: TAGTGGGAACTGCTGTTGCTAATCTTCTTCCTGGACAGCCACGTGTTGAGgtaagttatt ... gtgttcacagAAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACT
EST: gi|32270442|gb|CD719601.1|CD719601
EST:     TAGTGGGAACTGCTGTTGCTAATCTTCTTTGTGGACAGCCACGTGTTGAG                         AAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACT
genomic: TAGTGGGAACTGCTGTTGCTAATCTTCTTCCTGGACAGCCACGTGTTGAGgtaagttatt ... gtgttcacagAAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACT
EST: gi|32247509|gb|CD713328.1|CD713328
EST:     TAGTGGGAACTGCTGTTGCTAATCTTCTTTGTGGACAGCCACGTGTTGAG                         AAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACT
genomic: TAGTGGGAACTGCTGTTGCTAATCTTCTTCCTGGACAGCCACGTGTTGAGgtaagttatt ... gtgttcacagAAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACT
EST: gi|32248091|gb|CD713910.1|CD713910
EST:     TAGTGGGAACTGCTGTTGCTAATCTTCTTTGTGGACAGCCACGTGTTGAG                         AAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACT
genomic: TAGTGGGAACTGCTGTTGCTAATCTTCTTCCTGGACAGCCACGTGTTGAGgtaagttatt ... gtgttcacagAAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACT
EST: gi|22012057|gb|BQ797091.1|BQ797091
EST:     GGACAGCCACGTGTTGAG                         AAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACT
genomic: GGACAGCCACGTGTTGAGgtaagttatt ... gtgttcacagAAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACT
EST: gi|32247574|gb|CD713393.1|CD713393
EST:     TAGTGGGAACTGCTGTTGCTAATCTTCTTTGTGGACAGCCACGTGTTGAG                         AAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACT
genomic: TAGTGGGAACTGCTGTTGCTAATCTTCTTCCTGGACAGCCACGTGTTGAGgtaagttatt ... gtgttcacagAAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACT
EST: gi|30325618|gb|CD008880.1|CD008880
EST:     TAGTGGGAACTGCTGTTGCTAATCTTCTTTGTGGACAGCCACGTGTTGAG                         AAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACT
genomic: TAGTGGGAACTGCTGTTGCTAATCTTCTTCCTGGACAGCCACGTGTTGAGgtaagttatt ... gtgttcacagAAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACT
EST: gi|32271685|gb|CD720844.1|CD720844
EST:     TAGTGGGAACTGCTGTTGCTAATCTTCTTTGTGGACAGCCACGTGTTGAG                         AAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACT
genomic: TAGTGGGAACTGCTGTTGCTAATCTTCTTCCTGGACAGCCACGTGTTGAGgtaagttatt ... gtgttcacagAAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACT
EST: gi|30135654|gb|CB920992.1|CB920992
EST:     TAGTGGGAACTGCTGTTGCTAATCTTCTTTGTGGACAGCCACGTGTTGAG                         AAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACT
genomic: TAGTGGGAACTGCTGTTGCTAATCTTCTTCCTGGACAGCCACGTGTTGAGgtaagttatt ... gtgttcacagAAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACT
EST: gi|30324236|gb|CD007498.1|CD007498
EST:     TAGTGGGAACTGCTGTTGCTAATCTTCTTTGTGGACAGCCACGTGTTGAG                         AAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACT
genomic: TAGTGGGAACTGCTGTTGCTAATCTTCTTCCTGGACAGCCACGTGTTGAGgtaagttatt ... gtgttcacagAAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACT
EST: gi|30327438|gb|CD010700.1|CD010700
EST:     TAGTGGGAACTGCTGTTGCTAATCTTCTTTGTGGACAGCCACGTGTTGAG                         AAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACT
genomic: TAGTGGGAACTGCTGTTGCTAATCTTCTTCCTGGACAGCCACGTGTTGAGgtaagttatt ... gtgttcacagAAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACT
EST: gi|30131038|gb|CB916377.1|CB916377
EST:     TAGTGGGAACTGCTGTTGCTAATCTTCTTTGTGGACAGCCACGTGTTGAG                         AAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACT
genomic: TAGTGGGAACTGCTGTTGCTAATCTTCTTCCTGGACAGCCACGTGTTGAGgtaagttatt ... gtgttcacagAAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACT
EST: gi|30326116|gb|CD009378.1|CD009378
EST:     TAGTGGGAACTGCTGTTGCTAATCTTCTTTGTGGACAGCCACGTGTTGAG                         AAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACT
genomic: TAGTGGGAACTGCTGTTGCTAATCTTCTTCCTGGACAGCCACGTGTTGAGgtaagttatt ... gtgttcacagAAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatcgtccgcgtaacattagatggtccaatgctatctgtattttgtgttcacagAAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACTCCTCCCACCAATGAGGACAGATATTTGCTGTTCATTGATGAGTTACGTG
         gcgtaac  putative branch site (score: 3)
            taacatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactaggatgtgagtccatcacatgcatacatgctttgtcattttaaatcgtccgcgtaacattagatggtccaatgctatctgtattttgtgttcacagAAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACTCCTCCCACCAATGAGGACAGATATTTGCTGTTCATTGATGAGTTACGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - -ggatgtg
- - - - - - - -ccatcac
- - - - - - - - - - - - - - acatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tagatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaatgc