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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattttagcatggtataataattgtggaaggataggttgttaggattacgataaaattttaaatatatcaagttctgagcaatccatatgttctttatagACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTCAACATTGCTCTGGATGATGTGTCCATTACAAGCCTTACTTTTGGGAGGG

Basic information

species Vitis vinifera
transcript Vv19s0085g00730.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0085g00730.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os03g60000.1 (Oryza sativa), 3'ss of exon 3
-------------------------------------tattttagcatggtata--ataattgtggaagga-taggttgttaggat-tacgataaaattttaaatatatcaagttctgagcaatccatatgttctttat-------agACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTCAACATTGCTCTGGATGATGTGTCCATTACAAGCCTTACTTTTGGGAGGG
                                     ||| ||  ||||||||   ||  | ||  |||   ||   |  |||||| |    |  ||   | ||||||  | | | |  || |   ||   | ||||||       || |||| || ||||| ||  | ||| |  ||||||| |||||   ||| ||||||||||||||||||||||||||||| ||||| || |  ||||| |  |
gtactgtcatcatatctatctgtgtttaaatatctaatatgtttccatggtatgctatgctagtttaagagctaatatagtaggatatttagtttaagagttaatatagtaggatatatgctaataattactcctttatccaacacagGCTGTGAGCAGGGAGATTAGGAAGATCCTGACAGAGAGGGCTAGCAACTTCAACATTGCTCTGGATGATGTGTCCATCACAAGTCTCAGCTTTGGAAAAG

upper sequence: Vv19s0085g00730.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os03g62490.1 (Oryza sativa), 3'ss of exon 3
----------------------------------------------------tattttagcatggtataataattg-tggaaggataggttgttaggattacgataaaatttta-aatatatcaagttctgagcaatccatatgttctttatagACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTCAACATTGCTCTGGATGATGTGTCCATTACAAGCCTTACTTTTGGGAGGG
                                                    |||  ||   | || ||| |  |  |  |    || | | ||  | ||| ||   ||| |   |  ||||   ||  | |  | ||| | | | |   | || |||| || ||||| ||  | ||| |  ||||||| |||||   ||| ||||||||||||||||||||||||||||| ||||| || |  ||||| |  |
gtactgtcttatcatatctatctgtgtttaaatatctaatatgtttccatggtatgctatgctagtttaagagctaatatagtagtatgatatttagtttaagagctaatatagtaggatatatggtaataattattcctt-tatccaacacagGCTGTGAGCAGGGAGATTAGGAAGATCCTGACAGAGAGGGCTAGCAACTTCAACATTGCTCTGGATGATGTGTCCATCACAAGTCTCAGCTTTGGAAAAG

upper sequence: Vv19s0085g00730.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AC217358.3_FGT005 (Zea mays), 3'ss of exon 3
------------tattttagcatggtataataattgtggaaggataggttgttaggattacgataaaattttaaatatatcaagttctgagcaatccatatg--ttctttatagACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTCAACATTGCTCTGGATGATGTGTCCATTACAAGCCTTACTTTTGGGAGGG
              | |   || | | |      | |   |   |   ||| |||||||  ||| | |||    |||| | ||    | |   || |||  |  | |  |  || |||| || ||||| ||  | ||| |  |||| || |||||   ||| ||||| ||||||||||||||||||||||| |||||||| |  ||||| |  |
gtaccattcatgcgtctagacacgatgttccccatataacaac-tgtcttgctaggattg-gatgagatta-ggatatgttaacagttcattcatgcattcgattccgatgcagGCTGTGAGCAGGGAGATTAGGAAGATTCTGACTGAGAGGGCCAACAACTTCAATATTGCTCTGGATGATGTGTCCATCACAAGCCTCAGCTTTGGAAAAG

upper sequence: Vv19s0085g00730.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G30410.1 (Glycine max), 3'ss of exon 5
--tattttagcatggtataataattgtggaaggataggttgttaggat-tacgataaaattttaaatatatcaagttctgagcaatccatatgttctttatagACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTCAACATTGCTCTGGATGATGTGTCCATTACAAGCCTTACTTTTGGGAGGG
  || ||        | |  |  |  |   || ||   ||  ||| |   | || |   | || || |  | ||  | | |     || ||   ||||| ||| |||||||| ||||||| || ||| | ||||| |||||||| || || ||||| ||||| || ||||||||||| ||||| || || |||||||| | ||
attagttccatgcaatgttttcttatttcgagtattcatttctagcacacaggagagtgtgtttaa-acttaaacatttaacttgaccttaa--tctttgtagGCTGTTAGTCGGGAAATCCGGAAGATTTTGACTGAAAGGGCTGCTAACTTCAATATTGCCCTTGATGATGTGTCAATTACTAGTCTGACTTTTGGCAAGG

upper sequence: Vv19s0085g00730.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G36940.1 (Glycine max), 3'ss of exon 4
--tattttagcatggtataataattgtggaaggataggttgttaggattacgataaaattttaaatatatcaagttctgagcaatccatatgttctttatagACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTCAACATTGCTCTGGATGATGTGTCCATTACAAGCCTTACTTTTGGGAGGG
  || ||        | |  |  |  |   || ||   ||  ||| |  ||  || | |||     |  | ||    | | |    | | |  ||||| ||| |||||||| ||||||| || ||| |  |||| |||||||| || || ||||| ||||| || ||||||||||| ||||| || || |||||||| | ||
attagttccatgcaatgttttcttatttcgagtattcatttctagcac-acagtagagtttgtttgaacttaaacatttaacttgacct-taatctttgtagGCTGTTAGTCGGGAAATCCGGAAGATTCTGACTGAAAGGGCTGCTAACTTCAATATTGCCCTTGATGATGTGTCAATTACTAGTCTGACTTTTGGCAAGG

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|110360428|gb|EC923520.1|EC923520
EST:     AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGAGAG                         ACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTC
genomic: AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGAGAGgtaggtctga ... ttctttatagACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTC
EST: gi|110417983|gb|EC984089.1|EC984089
EST:     AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGAGAG                         ACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTC
genomic: AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGAGAGgtaggtctga ... ttctttatagACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTC
EST: gi|110733003|gb|EE108782.1|EE108782
EST:     AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGAGAG                         ACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTC
genomic: AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGAGAGgtaggtctga ... ttctttatagACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTC
EST: gi|71867260|gb|DT016315.1|DT016315
EST:     AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGAGAG                         ACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTC
genomic: AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGAGAGgtaggtctga ... ttctttatagACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTC
EST: gi|110696854|gb|EE073329.1|EE073329
EST:     AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGAGAG                         ACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTC
genomic: AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGAGAGgtaggtctga ... ttctttatagACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTC
EST: gi|71870697|gb|DT019752.1|DT019752
EST:     AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGAGAG                         ACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTC
genomic: AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGAGAGgtaggtctga ... ttctttatagACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTC
EST: gi|30126574|gb|CB911913.1|CB911913
EST:     AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGAGAG                         ACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTC
genomic: AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGAGAGgtaggtctga ... ttctttatagACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTC
EST: gi|110379537|gb|EC944738.1|EC944738
EST:     AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGAGAG                         ACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTC
genomic: AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGAGAGgtaggtctga ... ttctttatagACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTC
EST: gi|110688172|gb|EE066420.1|EE066420
EST:     AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGAGAG                         ACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTC
genomic: AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGAGAGgtaggtctga ... ttctttatagACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTC
EST: gi|161712704|gb|FC062276.1|FC062276
EST:     AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGAGAG                         ACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTC
genomic: AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGAGAGgtaggtctga ... ttctttatagACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTC
EST: gi|77588331|gb|DV223379.1|DV223379
EST:     AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGAGAG                         ACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTC
genomic: AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGAGAGgtaggtctga ... ttctttatagACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTC
EST: gi|110687081|gb|EE064178.1|EE064178
EST:     AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGAGAG                         ACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTC
genomic: AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGAGAGgtaggtctga ... ttctttatagACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTC
EST: gi|110731197|gb|EE109145.1|EE109145
EST:     AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGAGAG                         ACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTC
genomic: AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGAGAGgtaggtctga ... ttctttatagACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTC
EST: gi|161716392|gb|FC068402.1|FC068402
EST:     AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGAGAG                         ACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTC
genomic: AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGAGAGgtaggtctga ... ttctttatagACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTC
EST: gi|110708369|gb|EE085834.1|EE085834
EST:     AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGAGAG                         ACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTC
genomic: AAGCTGTGGTTGCACAGTATAATGCTAGCCAGCTTATTACTCAGAGAGAGgtaggtctga ... ttctttatagACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacgataaaattttaaatatatcaagttctgagcaatccatatgttctttatagACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTCAACATTGCTCTGGATGATGTGTCCATTACAAGCCTTACTTTTGGGAGGG
                                           tgttcttt  CT-rich tract
     ataaaattttaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattttagcatggtataataattgtggaaggataggttgttaggattacgataaaattttaaatatatcaagttctgagcaatccatatgttctttatagACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTCAACATTGCTCTGGATGATGTGTCCATTACAAGCCTTACTTTTGGGAGGG

- - - -gcatggt
- - - - - - - - - - -ttgtgga
- - - - - - - - - - - - - - - - - - - - - - - - -gataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatcca