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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttttagttgtagtattttgctggagcttaagtatcataagcttttattaatttgattttgatttctttataacagGGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAAACTTTGCTTGCAAGGGCAGTAGCTCATCATACTGACTGTACTTTCATCAGGGTTTCTGGTTCTG

Basic information

species Vitis vinifera
transcript Vv09s0002g05800.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 3'ss of exon 4
--gtagttttagttgtagtattttgctggagcttaagtatcataagcttttattaatttgattttgatttctttataacagGGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAAACTTTGCTTGCAAGGGCAGTAGCTCATCATACTGACTGTACTTTCATCAGGGTTTCTGGTTCTG
   |    ||  |   | |||  | ||  | |     |||  | |  | |||  |     || || | |   || |  ||||| ||||| || ||||| || || || ||||| ||||| ||| | ||| | ||||| |||||||| |||||||| || ||||||||||| |||||||| |
gtttgaacttcttaacaatatcat-cttaaacgatcctatttttaagtattagcagaa-aatattaactctcttttttcagGGTGTCCTTCTCTATGGCCCTCCAGGCACAGGAAAAACATTGTTGGCACGTGCAGTTGCTCATCACACTGACTGCACCTTCATCAGGGTGTCTGGTTCCG

upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G137528_T01 (Zea mays), 3'ss of exon 4
---------gtagttttagttgtagtattttgctggagcttaagtatcataagcttttattaatttgattttgat----ttctttataacagGGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAAACTTTGCTTGCAAGGGCAGTAGCTCATCATACTGACTGTACTTTCATCAGGGTTTCTGGTTCTG
          |   || ||   |         ||  | |||  | |   ||    |   |  |   || |  |||    ||  || |  ||||| ||||| || ||||| || || || ||||| || || ||||| ||| | || || |||||||| |||||||| || ||||||||||| ||||||||||
gtttattttctctcttgaggcttgaagaccatcttaaccttttgaactttacatgtaggtggagaagactgagatcttatttattttttcagGGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGTGCGGTTGCTCATCACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTG

upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 4
----gtagttttagttgtagtattttgctggagcttaagtatcataagcttttattaatt-tgattttgatttctttataacagGGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAAACTTTGCTTGCAAGGGCAGTAGCTCATCATACTGACTGTACTTTCATCAGGGTTTCTGGTTCTG
    ||  | ||  ||| ||    |         || |   | | | |    |   ||    |  | |  ||| ||| |  ||||| ||||| || ||||| || || || ||||| || || ||| | ||| | || || |||||||| |||||||| || ||||||||||| ||||||||||
gtttgttttcttttttgaagaccatcttaaccttttgaactttacatgtaggtggaaaagacggatcttgtttgttttt--cagGGTGTCCTTCTTTATGGACCTCCGGGCACAGGAAAGACATTGTTGGCACGTGCGGTTGCTCATCACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTG

upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 4
-------gtagttttag----ttgtagtattttgctggagcttaagtatcata---agct-tttattaatttgatt--ttgatttctt-----tataacagGGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAAACTTTGCTTGCAAGGGCAGTAGCTCATCATACTGACTGTACTTTCATCAGGGTTTCTGGTTCTG
        |  |||| |    |||    ||||||      | | || | || |    | | ||||||  | || ||  |   | ||||      || |||||| |||||||| |||||||||||||||||||| ||||| ||| | || |||||||| |||||||||||||||||||| ||||||||||| ||||||||||
gtagtttctcattttggggtgttgctaaattttgtcattccatcagcagcacacttggttgtttatttttctgtttgctgagtctcttgaacacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGTAAAACATTGTTGGCTAGGGCAGTGGCTCATCATACTGACTGTACATTCATCAGGGTGTCTGGTTCTG

upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G24000.1 (Glycine max), 3'ss of exon 4
-------gtagttttag-----ttgtagtattttgctggagcttaagtatcataagctttt-attaatttgatt--ttgatttctt-----tataacagGGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAAACTTTGCTTGCAAGGGCAGTAGCTCATCATACTGACTGTACTTTCATCAGGGTTTCTGGTTCTG
        |  |||| |     |||    ||||||      | | || |   |  | | || |||  | || ||  |  || ||||      || |||||| |||||||| |||||||||||||||||||| ||||| ||| | || |||||||| |||||||||||||||||||| ||||||||||| ||||||||||
gtagtgtctgattttggggttgttgctaaattttgtcattccatcagcacacttggttgttgatttttctgtttgctgaatctcttgatcacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGGGCAGTGGCTCATCATACTGACTGTACATTCATCAGGGTGTCTGGTTCTG

upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 4
gta-gttttagttgtagtattttgctggagcttaagtatcataagcttttattaatttgatt--ttgatttctttataacagGGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAAACTTTGCTTGCAAGGGCAGTAGCTCATCATACTGACTGTACTTTCATCAGGGTTTCTGGTTCTG
|||   || | ||  |    ||  ||  |   | |   |  ||||    | |  |  |||||  ||       |  |   |||| ||  || |||| || |||||||| || ||||| ||  |  | ||  |||| || || ||||| |||||||||||||||||||| |||||||||||||
gtacacttgaatttcaaagcttatctatattgtgacgctgctaagtggatttcgaactgattgcttctccctctcttttaagGGTGTGTTGTTGTACGGTCCACCTGGAACTGGGAAGACACTATTGGCTCGGGCTGTGGCACATCACACTGACTGTACTTTCATCAGAGTTTCTGGTTCTG

upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 4
gta-gttttagttgtag---tattttgctggagcttaagtatcataagcttttattaatttgattttgatttctttata---acagGGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAAACTTTGCTTGCAAGGGCAGTAGCTCATCATACTGACTGTACTTTCATCAGGGTTTCTGGTTCTG
|||   || | |  ||    |  ||  |   |   | |  ||  ||||  |  ||||     | | | || ||| | |      |||| ||  || | || || |||||||| || ||||| ||  |  | ||  |||| || || ||||| ||||||||||||||||| || ||||||||||| |
gtacacttgaatcttaaaccttcttctccatattgtgatgatgctaag--tggattagacgtaatctcatctctctgtctttctagGGTGTGTTGTTATACGGTCCACCTGGAACTGGGAAGACACTATTGGCTCGGGCTGTTGCACATCACACTGACTGTACTTTCATAAGAGTTTCTGGTTCCG

upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ04162 (Selaginella moellendorffii), 3'ss of exon 3
gtagttttagttgtagtattttgctggagcttaagtatcataagcttttattaatttgattttgatttctttataacagGGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAAACTTTGCTTGCAAGGGCAGTAGCTCATCATACTGACTGTACTTTCATCAGGGTTTCTGGTTCTG
            |||  ||||||||          |  | |  | |   |  | | |  | |||  ||||      |||||||| || |||||||| || ||||| || || || |||||||| ||  |||| || ||||| |||||||||||||| ||||| || ||||| || || |
------------gtaaaattttgctaacaaaagtttggcttttggtaccagca-tctattcttgtcttctgctgtgcagGGAGTGCTACTGTATGGCCCTCCTGGAACTGGAAAGACTTTGCTGGCTCGGGCCGTGGCTCACCATACTGACTGTACATTCATAAGAGTTTCAGGGTCCG

upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ20576 (Selaginella moellendorffii), 3'ss of exon 4
gtagttttagttgtagtattttgctggagcttaagtatcataagcttttattaatttgattttgatttctttataacagGGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAAACTTTGCTTGCAAGGGCAGTAGCTCATCATACTGACTGTACTTTCATCAGGGTTTCTGGTTCTG
            |||  |||||||| |        |  | |  | |   |  | | |  | ||   ||||      |||||||| || |||||||| || ||||| || || ||||||||||| ||  |||| || ||||| |||||||||||||| ||||| || ||||| || || |
------------gtaaaattttgctagcaaaagtttggcttttggtaccagca-tctattcttatcttctgctgtgcagGGAGTGCTACTGTATGGCCCTCCTGGAACTGGAAAAACTTTGCTGGCTCGGGCCGTGGCTCACCATACTGACTGTACATTCATAAGAGTTTCAGGGTCCG

upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ28638 (Selaginella moellendorffii), 3'ss of exon 4
gtagttttagttgtagtattttgctggagcttaagtatcataagcttttattaatttgattttgatttctttataacagGGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAAACTTTGCTTGCAAGGGCAGTAGCTCATCATACTGACTGTACTTTCATCAGGGTTTCTGGTTCTG
            |||  ||||||||          |  | |  | |   |  | | |  | |||  ||||      |||||||| || |||||||| || ||||| || || ||||||||||| ||  |||| || ||||| ||||| |||||||| ||||| || ||||| || || |
------------gtaaaattttgctaacaaaagtttggcttttggtaccagca-tctattcttgtcttctgctgcgcagGGAGTGCTACTGTATGGTCCTCCTGGAACTGGAAAAACTTTGCTGGCTCGGGCCGTGGCTCACCATACGGACTGTACATTCATAAGAGTTTCGGGGTCCG

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|110393121|gb|EC958077.1|EC958077
EST:     CAATTAAACACCCTGAACTGTTTGAGAGTCTTGGAATAGCTCAACCAAAG                         GGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAAACTTTGCTTGCAAGG
genomic: CAATTAAACACCCTGAACTGTTTGAGAGTCTTGGAATAGCTCAACCAAAGgtagttttag ... tttataacagGGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAAACTTTGCTTGCAAGG
EST: gi|110698891|gb|EE076909.1|EE076909
EST:     CAATTAAACACCCTGAACTGTTTGAGAGTCTTGGAATAGCTCAACCAAAG                         GGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAAACTTTGCTTGCAAGG
genomic: CAATTAAACACCCTGAACTGTTTGAGAGTCTTGGAATAGCTCAACCAAAGgtagttttag ... tttataacagGGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAAACTTTGCTTGCAAGG
EST: gi|156737153|gb|EV241267.1|EV241267
EST:     CAATTAAACACCCTGAACTGTTTGAGAGTCTTGGAATAGCTCAACCAAAG                         GGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAAACTTTGCTTGCAAGG
genomic: CAATTAAACACCCTGAACTGTTTGAGAGTCTTGGAATAGCTCAACCAAAGgtagttttag ... tttataacagGGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAAACTTTGCTTGCAAGG
EST: gi|110713901|gb|EE090225.1|EE090225
EST:     CAATTAAACACCCTGAACTGTTTGAGAGTCTTGGAATAGCTCAACCAAAG                         GGAGTCCTGCTGTATGGGCCACCTGGTACAGGGGAAAACTT-GCTTGCAAG
genomic: CAATTAAACACCCTGAACTGTTTGAGAGTCTTGGAATAGCTCAACCAAAGgtagttttag ... tttataacagGGAGTCCTGCTGTATGGGCCACCTGGTACAGGG-AAAACTTTGCTTGCAAG
EST: gi|26256905|gb|CA807968.1|CA807968
EST:     CAATTAAACACCCTGAACTGTTTGAGAGTCTTGGAATAGCTCAACCAAAG                         GGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAAACTTTGCTTGCAAGG
genomic: CAATTAAACACCCTGAACTGTTTGAGAGTCTTGGAATAGCTCAACCAAAGgtagttttag ... tttataacagGGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAAACTTTGCTTGCAAGG
EST: gi|110699382|gb|EE076332.1|EE076332
EST:     CAATTAAACACCCTGAACTGTTTGAGAGTCTTGGAATAGCTCAACCAAAG                         GGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAAACTTTGCTTGCAAGG
genomic: CAATTAAACACCCTGAACTGTTTGAGAGTCTTGGAATAGCTCAACCAAAGgtagttttag ... tttataacagGGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAAACTTTGCTTGCAAGG
EST: gi|110733070|gb|EE108911.1|EE108911
EST:     CAATTAAACACCCTGAACTGTTTGAGAGTCTTGGAATAGCTCAACCAAAG                         GGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAAACTTTGCTTGCAAGG
genomic: CAATTAAACACCCTGAACTGTTTGAGAGTCTTGGAATAGCTCAACCAAAGgtagttttag ... tttataacagGGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAAACTTTGCTTGCAAGG
EST: gi|110707762|gb|EE084531.1|EE084531
EST:     CAATTAAACACCCTGAACTGTTTGAGAGTCTTGGAATANCTCAACCAAAG                         GGAGTCCTGCTGTATGGGCCACCTGGTACAGGAAAAACTTTGCTTTGCAAG
genomic: CAATTAAACACCCTGAACTGTTTGAGAGTCTTGGAATAGCTCAACCAAAGgtagttttag ... tttataacagGGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAAACTTTGCTT-GCAAG
EST: gi|294964426|gb|GW838229.1|GW838229
EST:     CAATTAAACACCCTGAACTGTTTGAGAGTCTTGGAATAGCTCAACCAAAG                         GGAGTCCTGCTGTATGGGCCTCCTGGTACAGGGAAA
genomic: CAATTAAACACCCTGAACTGTTTGAGAGTCTTGGAATAGCTCAACCAAAGgtagttttag ... tttataacagGGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAA
EST: gi|30322287|gb|CD005549.1|CD005549
EST:     CAATTAAACACCCTGAACTGTTTGAGAGTCTTGGAATAGCTCAACCAAAG                         GGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAAACTTTGCTTGCAAGG
genomic: CAATTAAACACCCTGAACTGTTTGAGAGTCTTGGAATAGCTCAACCAAAGgtagttttag ... tttataacagGGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAAACTTTGCTTGCAAGG
EST: gi|161713411|gb|FC063391.1|FC063391
EST:     CAATTAAACACCCTGAACTGTTTGAGAGTCTTGGAATAGCTCAACCAAAG                         GGAGTCCTGCTGTATG
genomic: CAATTAAACACCCTGAACTGTTTGAGAGTCTTGGAATAGCTCAACCAAAGgtagttttag ... tttataacagGGAGTCCTGCTGTATG
EST: gi|161716828|gb|FC068100.1|FC068100
EST:     CAATTAAACACCCTGAACTGTTTGAGAGTCTTGGAATAGCTCAACCAAAG                         GGAGTCCTGCTGTATGGGCCACCTGGTACAGGG
genomic: CAATTAAACACCCTGAACTGTTTGAGAGTCTTGGAATAGCTCAACCAAAGgtagttttag ... tttataacagGGAGTCCTGCTGTATGGGCCACCTGGTACAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggagcttaagtatcataagcttttattaatttgattttgatttctttataacagGGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAAACTTTGCTTGCAAGGGCAGTAGCTCATCATACTGACTGTACTTTCATCAGGGTTTCTGGTTCTG
                                         tttctttat  CT-rich tract
               ataagcttttattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagttttagttgtagtattttgctggagcttaagtatcataagcttttattaatttgattttgatttctttataacagGGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAAACTTTGCTTGCAAGGGCAGTAGCTCATCATACTGACTGTACTTTCATCAGGGTTTCTGGTTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA