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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgtagttagtaagaggacaaaataagttcttgtgtgtgtgtgtgtgtgagtgagtgagtgagagagagagagaggacagacaatttggtttatgactttagtttactactcttatcttctacttcctgatgatttcatgctgatgcttattgatgtatgtttgggatgccaaatcatttcttttgcagTTTCATTTCAACTGTATGATCTAAAGCAACAAGGGTTCATTGAAAGACAGGAG

Basic information

species Vitis vinifera
transcript Vv00s1569g00020.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g42840.1 (Oryza sativa), 3'ss of exon 4
gtaagttgtagttagtaagaggacaaaataagttcttgtgtgtgtgtgtgtgtgagtgagtgagtgagagagagagagaggacagacaatttggtttatgactttagtttactactcttatcttctacttcctgatgatttcatgctgatgcttattgatgtatgtttgggatgccaaatcatttcttttgcagTTTCATTTCAACTGTATGATCTAAAGCAACAAGGGTTCATTGAAAGACAGGAG
                                                                                          || |  ||||  ||  |     |  | || | |    ||| ||  |   ||||   |  ||  |    |   ||  |||   |  |  |  | | |||  |||||||| || || || ||||| || |||||||||||||||||||||||||| |||
------------------------------------------------------------------------------------------ttagcatatg--ttatgccctttttttttctgtgtctcttgcttttatcttcaatgttgtgtgtgaaaagaaattcttgcattaactcaataatcctt--gcagTTTCTTTCCAGCTATATGACCTCAAGCAACAAGGGTTCATTGAAAGACAAGAG

upper sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 4
gtaagttgtagttagtaagaggacaaaataagttcttgtgtgtgtgtgtgtgtgagtgagtgagtgagagagagagagaggacagacaatttggtttatgactttagtttactactcttatcttctacttcctgatgatttcatgctgatgcttattgatgtatgtttgggatgccaaatc-atttcttttgcagTTTCATTTCAACTGTATGATCTAAAGCAACAAGGGTTCATTGAAAGACAGGAG
                                                                                               || |  ||||  | |      |||||       ||  || |  |||  |  |  |  ||   |    |   |     | |  | || |      ||||||||||||| ||||| ||||| || ||||||||||| ||||||||||||||||||
-----------------------------------------------------------------------------------------------ttctttctttcttctctgtgccttatgcctgctttagtgttttttttttttttgtatttgagggcaaaaaatatcccttctgactctacaatccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGGAG

upper sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G39940.1 (Glycine max), 3'ss of exon 5
gtaag--ttgtagttagtaagaggacaaaataagttcttgtgtgtgtgtgtgtgtgagtgagtgagtgagagagagagagaggacagaca-atttggtttatgactttagtttactactcttatcttctacttcctgatg-atttcatgctgatgcttattgatgtatgtttgggatgccaaatcatttctttt-gcagTTTCATTTCAACTGTATGATCTAAAGCAACAAGGGTTCATTGAAAGACAGGAG
|||||  |   |  |  | ||| |||   |    | || || |     | | | || ||   ||| || ||  |  |   |    | |   |  | | | ||   ||| ||||       |||| |  |  | | | ||| ||||  |  ||||  | ||     |||||| ||||| || ||   || ||||| ||||||||||| ||| |||||||||| || |||||||| || |||||||||||||||
gtaagaatgacaaatgtttagaagactttagctat-ctggtctactgttttatctgggttt-tgaatgggaagggcatttattgtaaagggagctagatcattttttttgtttctgtagtttatttatt--tccttaatgcatttgttattgatagtaat--gcatatgttggggattcccaactcttcctttttgcagTTTCATTCCAATTGTATGATCTCAAACAACAAGGTTTTATTGAAAGACAGGAG

upper sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G00830.1 (Glycine max), 3'ss of exon 5
gtaag--ttgtagttagtaagaggacaaaataagttcttgtgtgtgtgtgtgtgtgagtgagtgagtgagagagagagagaggacagacaatttggtttatgactttagtttactactcttatcttctacttcctgatg-atttcatgctgatgcttattgatgtatgtttgggatg-ccaaatcatttcttttgcagTTTCATTTCAACTGTATGATCTAAAGCAACAAGGGTTCATTGAAAGACAGGAG
|||||  |   |  |  | ||| |||   |    |  | || |   | | | | || ||     |  |  ||||        |       |  | | | |||  ||| ||||       |||| |  |  | | | ||| |||   |  | ||  | ||     |||||| || ||  |||| |  | | ||||||||||||||| ||| |||||||||| || || ||||| || |||||||| ||||||
gtaagaatgacaaatgtttagaagactttagctatg-tggtctacttttttatctgggttttgaataggaagagcatttattggagagggagctagatcatg--ttttgtttctgtagtttatttatt--tccttaatgcattagttattaatagtaat--gcatatgttgggcatttccaacttttcttttttgcagTTTCATTCCAATTGTATGATCTCAAACAGCAAGGTTTTATTGAAAGGCAGGAG

upper sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagttgtagttagtaagaggacaaaataagttcttgtgtgtgtgtgtgtgtgagtgagtgagtgagagagagagagaggacagacaatttggtttatgactttagtttactactcttatcttctacttcctga-tgatttcatgctgatgcttattgatgtatgtttgggatgccaaatcatttcttttgcagTTTCATTTCAACTGTATGATCTAAAGCAACAAGGGTTCATTGAAAGACAGGAG
                                                                                                          ||      || ||| ||| ||  ||   |   |  |   | | |  |  ||| ||| || |     || | |      || |||||||||||||||||| || |||||||| || || |||||||| || ||| | || |||
----------------------------------------------------------------------------------------------------------gtacgtcccttttagcttgtatctcaaaaacaagattgggataacac--attaatg-atat-----atacta------tttttttgcagTTTCATTTCAGCTATATGATCTTAAACAGCAAGGGTTTATCGAACGGCAAGAG

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|110380717|gb|EC946005.1|EC946005
EST:     TGCCCTCTCTGTCTTTCATCCCAATGCACCCATTGAAGACAAAATTGACT                         TTTCATTTCAACTGTATGATCTAAAGCAACAAGGGTTCATTGAAAGACAGG
genomic: TGCCCTCTCTGTCTTTCATCCCAATGCACCCATTGAAGACAAAATTGACTgtaagttgta ... tcttttgcagTTTCATTTCAACTGTATGATCTAAAGCAACAAGGGTTCATTGAAAGACAGG
EST: gi|77582686|gb|DV220332.1|DV220332
EST:     TGCCCTCTCTGTCTTTCATCCCAATGCACCCATTGAAGACAAAATTGACT                         TTTCATTTCAACTGTATGATCTAAAGCAACAAGGGTTCATTGAAAGACAGG
genomic: TGCCCTCTCTGTCTTTCATCCCAATGCACCCATTGAAGACAAAATTGACTgtaagttgta ... tcttttgcagTTTCATTTCAACTGTATGATCTAAAGCAACAAGGGTTCATTGAAAGACAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatgctgatgcttattgatgtatgtttgggatgccaaatcatttcttttgcagTTTCATTTCAACTGTATGATCTAAAGCAACAAGGGTTCATTGAAAGACAGGAG
              tattgat  putative branch site (score: 3)
                                        tcatttctttt  putative PPT
                                     aaatcatttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgtagttagtaagaggacaaaataagttcttgtgtgtgtgtgtgtgtgagtgagtgagtgagagagagagagaggacagacaatttggtttatgactttagtttactactcttatcttctacttcctgatgatttcatgctgatgcttattgatgtatgtttgggatgccaaatcatttcttttgcagTTTCATTTCAACTGTATGATCTAAAGCAACAAGGGTTCATTGAAAGACAGGAG

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