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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggaactccaaaatgtttaattccaaatattttctgattgtctgcagttattcctgcataaatctcatgtatataaccatttcttgtgttgccatgacagGATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATTCGACCAGCAGTTCAAGATGATGGTGGGGACATCGAGTATCGGGGATTTG

Basic information

species Vitis vinifera
transcript Vv13s0106g00620.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0106g00620.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g06330.1 (Oryza sativa), 3'ss of exon 3
tggaactccaaaatgtttaattccaaatattttctgattgtctgcagtta-----ttcctgcataaatctcatgtatataaccatttcttgtgttgccatgacagGATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATTCGACCAGCAGTTCAAGATGATGGTGGGGACATCGAGTATCGGGGATTTG
                 |  ||     ||| |||  | | ||  || |       | |    | | | |  | |||| |   ||| | ||   |       | |||||||||| ||||  || |||||||| |||||  || |||||||||| ||||||||||| ||||||||||||||||| ||||| || ||||| |||||||
-----taatggctcacctcgttttgcgtatcttcctaatctcctcaatcccctcctcctcaaacacaccctaagtattttcacatatttttcctctatgccatagGATGATTCAGAAATAGTTGCAATGATAAAAGAGTTGCTGGAGACTCGCATTCGACCAGCTGTTCAAGATGATGGTGGTGACATTGAATATCGAGGATTTG

upper sequence: Vv13s0106g00620.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G131249_T03 (Zea mays), 3'ss of exon 3
tggaactccaaaatgtttaattccaaat--attttctgat-tgtctgcagttattc-ctgcataaatctcatgtatataaccatttcttg---tgttgccatgacagGATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATTCGACCAGCAGTTCAAGATGATGGTGGGGACATCGAGTATCGGGGATTTG
         | ||  |  | ||| ||||   |||| || | |||  ||   ||||  |    |  |  |    ||   || | | || ||   |||| ||     |||||||||||||||  || || ||||| |||||| | ||||||||||||||||||||||| ||||||||||| || || ||||| || || || ||||| |
-------tgacaacatacatttcaaaatcagttttatgttatgttggcctctattttccttgtggagttgtgatactgaatcttctcctgcactgtttcccccctagGATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGAGACTCGTATTCGACCAGCTGTTCAAGATGACGGCGGTGACATTGAATACCGAGGATTCG

upper sequence: Vv13s0106g00620.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA20G38630.1 (Glycine max), 3'ss of exon 2
tggaactcc--aaaatgtttaattccaaatattttctgattgtctgcagttattcctgcataaatctcatgtatataaccatttcttgtgttgccatgacagGATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATTCGACCAGCAGTTCAAGATGATGGTGGGGACATCGAGTATCGGGGATTTG
|   |||    |||||| |  |         |  ||     ||    ||  | |  ||   |      |  || ||      |     | || |||| | |||||||||||||||| || ||||||||||| ||| |||| |||||||| |||||||| ||||| ||||||||||| |||||||| || ||| | || ||||
taagactttgtaaaatggtccaagtttgtcttactcatggagtacataggaagtt-tgagaaggcgaaaactaaatggtacatatacatttttccat-atagGATGATTCTGAAACAGTTGCAATGATCAAGGAATTGTTAGAGACTCGAATTCGACCTGCAGTGCAAGATGATGGCGGGGACATTGAATATAGAGGTTTTG

upper sequence: Vv13s0106g00620.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G51390.1 (Arabidopsis thaliana), 3'ss of exon 3
tggaactccaaaatgtttaattccaaatattttctgattgtctgcagttattcctgcataaatctcatgtatataaccatttcttgtgttgccatgacagGATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATTCGACCAGCAGTTCAAGATGATGGTGGGGACATCGAGTATCGGGGATTTG
             |       | | ||| ||| ||          | |||  | |  | ||| | ||  ||  ||| || |  |||| |  |      ||||||| |||||||||||||||||||| || ||||| |||||||| ||||| |||||| |||| ||||||||||| ||||||||||||||| | ||||| |
------------gtaggctgctgccaatgtttgctag--------acttagacttttaaaaagc-caaatac-taatcaatgattgtttctc------agGATGACTCTGAAACTGTAGCAATGATTAAGGAACTCTTGGAGACGCGTATCCGACCATCAGTCCAAGATGATGGAGGGGACATCGAGTATTGTGGATTCG

upper sequence: Vv13s0106g00620.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G20970.1 (Arabidopsis thaliana), 3'ss of exon 3
tggaactccaaaatgtttaattccaaatattttctgattgtctg-cagttattcctgcataaatctcatgtatataaccatttcttgtgttgccatga--cagGATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATTCGACCAGCAGTTCAAGATGATGGTGGGGACATCGAGTATCGGGGATTTG
      ||   |||| |   | | |  | ||    |||   ||    || |    || | |  |  |   |   |   ||||  |     |    |||  |||||||| |||||||| |||||||||||||| ||||| || || || || ||  ||||||||||||||||||||||||||||||| |||||| | || ||||
-aacgttctgcaatgctc--tccaaggttttggtagataagctaatggtgacaagtgtaaatgttgctatttcttgctcattggtgaaacttttgtgattcagGATGACTCTGAAACAGTAGCAATGATCAAGGAACTCTTAGAAACACGCATCAGACCAGCAGTTCAAGATGATGGTGGGGACATTGAGTATTGTGGGTTTG

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|110721131|gb|EE097777.1|EE097777
EST:     TGTTCCTTGACTCCAATACTGCAGCAGCAATGGACACAGCTATTCATGAA                         GATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATT
genomic: TGTTCCTTGACTCCAATACTGCAGCAGCAATGGACACAGCTATTCATGAAgtatctcctt ... gccatgacagGATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATT
EST: gi|349819400|gb|FQ412294.1|FQ412294
EST:     TGTTCCTTGACTCCAATACTGCAGCAGCAATGGAGACAGTTATTCATGAA                         GATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATT
genomic: TGTTCCTTGACTCCAATACTGCAGCAGCAATGGACACAGCTATTCATGAAgtatctcctt ... gccatgacagGATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATT
EST: gi|30128878|gb|CB914217.1|CB914217
EST:     TGTTCCTTGACTCCAATACTGCAGCAGCAATGGACACAGCTATTCATGAA                         GATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATT
genomic: TGTTCCTTGACTCCAATACTGCAGCAGCAATGGACACAGCTATTCATGAAgtatctcctt ... gccatgacagGATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATT
EST: gi|349819125|gb|FQ412019.1|FQ412019
EST:     TGTTCCTTGACTCCAATACTGCAGCAGCAATGGACACAGCTATTCATGAA                         GATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATT
genomic: TGTTCCTTGACTCCAATACTGCAGCAGCAATGGACACAGCTATTCATGAAgtatctcctt ... gccatgacagGATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATT
EST: gi|349813184|gb|FQ411424.1|FQ411424
EST:     TGTTCCTTGACTCCAATACTGCAGCAGCAATGGACACAGCTATTCATGAA                         GATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATT
genomic: TGTTCCTTGACTCCAATACTGCAGCAGCAATGGACACAGCTATTCATGAAgtatctcctt ... gccatgacagGATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATT
EST: gi|110417947|gb|EC984052.1|EC984052
EST:     TGTTCCTTGACTCCAATACTGCAGCAGCAATGGACACAGCTATTCATGAA                         GATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATT
genomic: TGTTCCTTGACTCCAATACTGCAGCAGCAATGGACACAGCTATTCATGAAgtatctcctt ... gccatgacagGATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATT
EST: gi|110413185|gb|EC978962.1|EC978962
EST:     TGTTCCTTGACTCCAATACTGCAGCAGCAATGGACACAGCTATTCATGAA                         GATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATT
genomic: TGTTCCTTGACTCCAATACTGCAGCAGCAATGGACACAGCTATTCATGAAgtatctcctt ... gccatgacagGATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATT
EST: gi|349820680|gb|FQ408509.1|FQ408509
EST:     TGTTCCTTGACTCCCATACTGCAGCAGCAATGGACACAGCTATTCATGAA                         GATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATT
genomic: TGTTCCTTGACTCCAATACTGCAGCAGCAATGGACACAGCTATTCATGAAgtatctcctt ... gccatgacagGATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATT
EST: gi|349824783|gb|FQ414641.1|FQ414641
EST:     TGTTCCTTGACTCCAATACTGCAGCAGCAATGGACACAGCTATTCATGAA                         GATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATT
genomic: TGTTCCTTGACTCCAATACTGCAGCAGCAATGGACACAGCTATTCATGAAgtatctcctt ... gccatgacagGATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATT
EST: gi|110426203|gb|EC992603.1|EC992603
EST:     TGTTCCTTGACTCCAATACTGCAGCAGCAATGGACACAGCTATTCATGAA                         GATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATT
genomic: TGTTCCTTGACTCCAATACTGCAGCAGCAATGGACACAGCTATTCATGAAgtatctcctt ... gccatgacagGATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATT
EST: gi|161716019|gb|FC068772.1|FC068772
EST:     TGTTCCTTGACTCCAATACTGCAGCAGCAATGGACACAGCTATTCATGAA                         GATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATT
genomic: TGTTCCTTGACTCCAATACTGCAGCAGCAATGGACACAGCTATTCATGAAgtatctcctt ... gccatgacagGATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttattcctgcataaatctcatgtatataaccatttcttgtgttgccatgacagGATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATTCGACCAGCAGTTCAAGATGATGGTGGGGACATCGAGTATCGGGGATTTG
                         atataac  putative branch site (score: 3)
                     atgtatataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggaactccaaaatgtttaattccaaatattttctgattgtctgcagttattcctgcataaatctcatgtatataaccatttcttgtgttgccatgacagGATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATTCGACCAGCAGTTCAAGATGATGGTGGGGACATCGAGTATCGGGGATTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - -ctccaaa
- - - - - - - - - - - ccaaata
- - - - - - - - - - - - - - - - -ctgattg
- - - - - - - - - - - - - - - - - - - - tctgcag
- - - - - - - - - - - - - - - - - - - - - - - - - -tcctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgta