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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacattctatatttctgttgggtcccctgattccgcagcatgcatgagtcatgtgaccgcacctgcaactgtactacacagcattatttttgtcttacagCTCAAAGGCTTCAGCTTGCTAATGTATACAAGGGAGAGGCTGAAAAGATCCTCCAAGTTAAGAAGGCAGAGGCTGAAGCTGAAGCCAAGTACCTAGGTGG

Basic information

species Vitis vinifera
transcript Vv16s0022g01690.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0022g01690.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os06g04460.1 (Oryza sativa), 3'ss of exon 4
tacattctatatttctgttgggtcccctgattccgcagcatgcatgagtcatgtgaccgcacctgcaactgtact-acacagc-attatttttgtcttacagCTCAAAGGCTTCAGCTTGCTAATGTATACAAGGGAGAGGCTGAAAAGATCCTCCAAGTTAAGAAGGCAGAGGCTGAAGCTGAAGCCAAGTACCTAGGTGG
 | ||| || |   |            |     ||    |||  | || ||  |         ||||  ||| || || || | ||||  ||  | | ||||| ||||||||||||||||| | ||| ||||| |||||||| || ||||| || |  || ||||| ||||| || || || || || ||  ||||    ||
-atattgtacaaaccacaccacaattatagcaacgtctgatgt-taagacaatttctgttttgtgcatgtgtgctcactcaactattaaattcttataacagCACAAAGGCTTCAGCTTGCAAGTGTCTACAAAGGAGAGGCGGAGAAGATTCTTCTGGTGAAGAAAGCAGAAGCAGAGGCAGAGGCAAAACACCTTTCCGG

upper sequence: Vv16s0022g01690.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G28170.1 (Glycine max), 3'ss of exon 4
tacattctatatttctgttgggtcccctgattccgcagcatgcatgagtcatgtgaccgcacctgcaactgtactacaca----gcattatttttgtcttacagCTCAAAGGCTTCAGCTTGCTAATGTATACAAGGGAGAGGCTGAAAAGATCCTCCAAGTTAAGAAGGCAGAGGCTGAAGCTGAAGCCAAGTACCTAGGTGG
      ||  ||| |       ||| |  ||  || | |||   || |||| |        |   ||  | |||||   |    | |||  |||| | |||||||||||||| | || ||||||| ||  ||||| ||||| ||||||||| |  | | |||||| || ||||||||||||||||||||||||||  | |||||
--ttccctccattccacccttctccaccaat--cgaaacattagtgggtcaagattatatgcaatcatatttactatttattgagaattgattttattttacagCTCAAAGGATGCAACTTGCTAGTGAGTACAAAGGAGAAGCTGAAAAGGTGTTGCTAGTTAAAAAAGCAGAGGCTGAAGCTGAAGCCAAGTATTTGGGTGG

upper sequence: Vv16s0022g01690.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA16G32990.1 (Glycine max), 3'ss of exon 4
tacattctatatttctgttgggtcccctgattccgcagcatgcatgagtcatg--tgaccgcacctgca---actgtactacacagcattatttttgtcttacagCTCAAAGGCTTCAGCTTGCTAATGTATACAAGGGAGAGGCTGAAAAGATCCTCCAAGTTAAGAAGGCAGAGGCTGAAGCTGAAGCCAAGTACCTAGGTGG
      ||  ||| |       ||| |  || |   | |||   || |||| |  ||   |||   | |   |||||  ||   || |||  |||| | |||||||||||||| | || ||||||| |   ||||| ||||| |||||||||||  | | |||||| || |||||||| |||||||||||||||||  | |||||
--ttccctccattccacccttttccaccaatcca--aacattagtgggtcaagactgtatgcaatcgtatttactgt-ttattgaggattgattttattttacagCTCAAAGGATGCAACTTGCTAGTCAGTACAAAGGAGAAGCTGAAAAGATTTTGCTAGTTAAAAAAGCAGAGGCCGAAGCTGAAGCCAAGTATTTGGGTGG

upper sequence: Vv16s0022g01690.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G51570.1 (Arabidopsis thaliana), 3'ss of exon 4
tacattctatatttctgttgggtcccctgattccgcagcatgcatgagtcatgtgaccgcacctgcaactgtactacacagcattatttttgtctta----cagCTCAAAGGCTTCAGCTTGCTAATGTATACAAGGGAGAGGCTGAAAAGATCCTCCAAGTTAAGAAGGCAGAGGCTGAAGCTGAAGCCAAGTACCTAGGTGG
|   ||  || ||||  |  |      ||       |   | ||   ||    ||||  ||  | ||| | | || | ||     ||| |   ||||    |||| |||||||| ||||| || | ||| ||||| ||||| || || ||||| |||||||| ||||  || || || ||||| |||||||||||| |||||||
tcagttagatgtttcgttaagagtttatgcgaagttaatttaca---gtttgttgacttcattt-caattttgcttctcaaatccattctctacttaaatgcagCACAAAGGCTCCAGCTCGCGAGTGTTTACAAAGGAGAAGCAGAGAAGATTCTCCAAGTGAAGAGAGCCGAAGCAGAAGCGGAAGCCAAGTACTTAGGTGG

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|34542871|gb|CF511103.1|CF511103
EST:     TATTATTCCTGATGCTTCTGTACGCAAGGCAATGAATGAGATAAATGCAG                         CTCAAAGGCTTCAGCTTGCTAATGTATACAAGGGAGAGGCTGAAAAGATCC
genomic: TATTATACCTGATGCTTCTGTACGCAAGGCAATGAATGAGATAAATGCAGgttttgacct ... tgtcttacagCTCAAAGGCTTCAGCTTGCTAATGTATACAAGGGAGAGGCTGAAAAGATCC
EST: gi|110393502|gb|EC958789.1|EC958789
EST:     TATTATACCTGATGCTTCTGTACGCAAGGCAATGAATGAGATAAATGCAG                         CTCAAAGGCTTCAGCTTGCTAATGTATACAAGGGAGAGGCTGAAAAGATCC
genomic: TATTATACCTGATGCTTCTGTACGCAAGGCAATGAATGAGATAAATGCAGgttttgacct ... tgtcttacagCTCAAAGGCTTCAGCTTGCTAATGTATACAAGGGAGAGGCTGAAAAGATCC
EST: gi|161716029|gb|FC065535.1|FC065535
EST:     TATTATACCTGATGCTTCTGTACGCAAGGCAATGAATGAGATAAATGCAG                         CTCAAAGGCTTCAGCTTGCTAATGTATACAAGGGAGAGGCTGAAAAGATCC
genomic: TATTATACCTGATGCTTCTGTACGCAAGGCAATGAATGAGATAAATGCAGgttttgacct ... tgtcttacagCTCAAAGGCTTCAGCTTGCTAATGTATACAAGGGAGAGGCTGAAAAGATCC
EST: gi|34542787|gb|CF511019.1|CF511019
EST:     TATTATACCTGATGCTTCTGTACGCAAGGCAATGAATGAGATAAATGCAG                         CTCAAAGGCTTCAGCTTGCTAATGTATACAAGGGAGAGGCTGAAAAGATCC
genomic: TATTATACCTGATGCTTCTGTACGCAAGGCAATGAATGAGATAAATGCAGgttttgacct ... tgtcttacagCTCAAAGGCTTCAGCTTGCTAATGTATACAAGGGAGAGGCTGAAAAGATCC
EST: gi|110366549|gb|EC930459.1|EC930459
EST:     TATTATACCTGATGCTTCTGTACGCAAGGCAATGAATGAGATAAATGCAG                         CTCAAAGGCTTCAGCTTGCTAATGTATACAAGGGAGAGGCTGAAAAGATCC
genomic: TATTATACCTGATGCTTCTGTACGCAAGGCAATGAATGAGATAAATGCAGgttttgacct ... tgtcttacagCTCAAAGGCTTCAGCTTGCTAATGTATACAAGGGAGAGGCTGAAAAGATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtcatgtgaccgcacctgcaactgtactacacagcattatttttgtcttacagCTCAAAGGCTTCAGCTTGCTAATGTATACAAGGGAGAGGCTGAAAAGATCCTCCAAGTTAAGAAGGCAGAGGCTGAAGCTGAAGCCAAGTACCTAGGTGG
                                         tttttgtctt  CT-rich tract
                                     attatttttgtctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacattctatatttctgttgggtcccctgattccgcagcatgcatgagtcatgtgaccgcacctgcaactgtactacacagcattatttttgtcttacagCTCAAAGGCTTCAGCTTGCTAATGTATACAAGGGAGAGGCTGAAAAGATCCTCCAAGTTAAGAAGGCAGAGGCTGAAGCTGAAGCCAAGTACCTAGGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - -tgttggg
- - - - - - - - - - - -cccctga
- - - - - - - - - - - - - - - - - - -gcatgca
- - - - - - - - - - - - - - - - - - - - - - - - -catgtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ccgcacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacagca