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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctcgatcttttagtgaattatagccatatgtatttagatgaaaatgactgaattctccagcatgcaattttaatcaggtctacattatactcctgcagGTCCTCAACTTAGAAGCTATGGACAAAACCAGGCATTGGAAAATTGTGGGCTGCAGCGCAATCACGGGTGAAGGGCTTCTTGAGGGATTTGATTGGTTGG

Basic information

species Vitis vinifera
transcript Vv04s0023g01820.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g01820.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G154890_T03 (Zea mays), 3'ss of exon 5
-----tgctcgatcttttagtgaattatagccatatgtatttagatgaaaatgactgaattctccagcatgcaattttaatcaggtctacattatactcctgcagGTCCTCAACTTAGAAGCTATGGACAAAACCAGGCATTGGAAAATTGTGGGCTGCAGCGCAATCACGGGTGAAGGGCTTCTTGAGGGATTTGATTGGTTGG
     || | |  ||   | || |  ||  |   |  |    |  ||||   |  |     ||    || |  |     |       | |||     |  | ||||| || ||  | ||||  ||||||| || |||||| ||||| |||||||||||||||||   |||||| || |||||||| ||||| || || ||| |||
tattttgtttgtgctgcgaatgcagaat--ctgcagttccccatctgaattagtttatggccttttccacggcaggccgactcaccttccatc---ttttttcagGTTCTGAATCTGGAAGTGATGGACAGAAGCAGGCACTGGAAGATTGTGGGCTGCAGCGCTTACACGGGAGAGGGGCTTCTCGAGGGCTTCGACTGGCTGG

upper sequence: Vv04s0023g01820.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA01G38270.1 (Glycine max), 3'ss of exon 4
tgctcgatcttttagtgaattatagccatatgtatttagatga-aaatgactgaattctccagcatgcaattttaatcaggtctacattatactcc-----tgcagGTCCTCAACTTAGAAGCTATGGACAAAACCAGGCATTGGAAAATTGTGGGCTGCAGCGCAATCACGGGTGAAGGGCTTCTTGAGGGATTTGATTGGTTGG
      |  ||| |  |  |   | ||  |     | | |  | || | |||  | |  | |   |       |  | || | |    | | ||||     ||||||| || ||||| ||||| ||||| ||| |  |||||||| | || || ||||| ||||||  ||| ||||| || || ||||||||||||||||||||||
------aattttaaacgggtccaatcccaagaacctgaaaccacaagtaactccagttacaattgtttctaagttgttagatttcttatgtgctccaacaatgcagGTGCTGAACTTGGAAGCCATGGATAAATCTCGGCATTGGCAGATAGTTGGCTGTAGCGCATACACTGGTGAGGGTCTGCTTGAGGGATTTGATTGGTTGG

upper sequence: Vv04s0023g01820.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G07330.1 (Glycine max), 3'ss of exon 4
tgctcgatcttttagtgaattatagccatatgtatttaga--tgaaaatgact-gaatt-ctccagcatgcaattttaatcaggtctacattatactcc-----tgcagGTCCTCAACTTAGAAGCTATGGACAAAACCAGGCATTGGAAAATTGTGGGCTGCAGCGCAATCACGGGTGAAGGGCTTCTTGAGGGATTTGATTGGTTGG
         |||||     ||  |  |  | | |  |  |     || | ||| || || | |  |  |  || ||   | |||| || | ||| ||||     ||||||| || ||||| ||||| ||||| ||| |  |||||||| | || || ||||| || |||  ||| ||||| || || ||||||||||||||||||||||
-------atttttaaactgttccaatcccaagaacctgaaaccacaagtaacttgagttacacttgtttctaagtt--gttaggtttataatatgctccaaccatgcagGTGCTGAACTTGGAAGCCATGGATAAATCTCGGCATTGGCAGATAGTTGGCTGTAGTGCATACACTGGTGAGGGTCTGCTTGAGGGATTTGATTGGTTGG

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|77585513|gb|DV221842.1|DV221842
EST:     CAAATAAGCAAGATATAAATGGAGCTCTTACACCAGCAGAAATAGCTAAG                         GTCCTCAACTTAGAAGCTATGGACAAAACCAGGCATTGGAAAATTGTGGGC
genomic: CAAATAAGCAAGATATAAATGGAGCTCTTACACCAGCAGAAATAGCTAAGgtaagggtgc ... actcctgcagGTCCTCAACTTAGAAGCTATGGACAAAACCAGGCATTGGAAAATTGTGGGC
EST: gi|110705966|gb|EE083420.1|EE083420
EST:     CAAATAAGCAAGATATAAATGGAGCTCTTACACCAGCAGAAATAGCTAAG                         GTCCTCAACTTAGAAGCTATGGACAAAACCAGGCATTGGAAAATTGTGGGC
genomic: CAAATAAGCAAGATATAAATGGAGCTCTTACACCAGCAGAAATAGCTAAGgtaagggtgc ... actcctgcagGTCCTCAACTTAGAAGCTATGGACAAAACCAGGCATTGGAAAATTGTGGGC
EST: gi|27586914|gb|CB009609.1|CB009609
EST:     CAAATAAGCAAGATATAAATGGAGCTCTTACACCAGCAGAAATAGCTAAG                         GTCCTCAACTTAGAAGCTATGGACAAAACCAGGCATTGGAAAATTGTGGGC
genomic: CAAATAAGCAAGATATAAATGGAGCTCTTACACCAGCAGAAATAGCTAAGgtaagggtgc ... actcctgcagGTCCTCAACTTAGAAGCTATGGACAAAACCAGGCATTGGAAAATTGTGGGC
EST: gi|110389868|gb|EC954740.1|EC954740
EST:     CAAATAAGCAAGATATAAATGGAGCTCTTACACCAGCAGAAATAGCTAAG                         GTCCTCAACTTAGAAGCTATGGACAAAACCAGGCATTGGAAAATTGTGGGC
genomic: CAAATAAGCAAGATATAAATGGAGCTCTTACACCAGCAGAAATAGCTAAGgtaagggtgc ... actcctgcagGTCCTCAACTTAGAAGCTATGGACAAAACCAGGCATTGGAAAATTGTGGGC
EST: gi|71877049|gb|DT026104.1|DT026104
EST:     CAAATAAGCAAGATATAAATGGAGCTCTTACACCAGCAGAAATAGCTAAG                         GTCCTCAACTTAGAAGCTATGGACAAAACCAGGCATTGGAAAATTGTGGGC
genomic: CAAATAAGCAAGATATAAATGGAGCTCTTACACCAGCAGAAATAGCTAAGgtaagggtgc ... actcctgcagGTCCTCAACTTAGAAGCTATGGACAAAACCAGGCATTGGAAAATTGTGGGC
EST: gi|77588566|gb|DV223498.1|DV223498
EST:     CAAATAAGCAAGATATAAATGGAGCTCTTACACCAGCAGAAATAGCTAAG                         GTCCTCAACTTAGAAGCTATGGACAAAACCAGGCATTGGAAAATTGTGGGC
genomic: CAAATAAGCAAGATATAAATGGAGCTCTTACACCAGCAGAAATAGCTAAGgtaagggtgc ... actcctgcagGTCCTCAACTTAGAAGCTATGGACAAAACCAGGCATTGGAAAATTGTGGGC
EST: gi|77582928|gb|DV220463.1|DV220463
EST:     CAAATAAGCAAGATATAAATGGAGCTCTTACACCAGCAGAAATAGCTAAG                         GTCCTCAACTTAGAAGCTATGGACAAAACCAGGCATTGGAAAATTGTGGGC
genomic: CAAATAAGCAAGATATAAATGGAGCTCTTACACCAGCAGAAATAGCTAAGgtaagggtgc ... actcctgcagGTCCTCAACTTAGAAGCTATGGACAAAACCAGGCATTGGAAAATTGTGGGC
EST: gi|30330574|gb|CD013836.1|CD013836
EST:     CAAATAAGCAAGATATAAATGGAGCTCTTACACCAGCAGAAATAGCTAAG                         GTCCTCAACTTAGAAGCTATGGACAAAACCAGGCATTGGAAAATTGTGGGC
genomic: CAAATAAGCAAGATATAAATGGAGCTCTTACACCAGCAGAAATAGCTAAGgtaagggtgc ... actcctgcagGTCCTCAACTTAGAAGCTATGGACAAAACCAGGCATTGGAAAATTGTGGGC
EST: gi|110705632|gb|EE082702.1|EE082702
EST:     CAAATAAGCAAGATATAAATGGAGCTCTTACACCAGCAGAAATAGCTAAG                         GTCCTCAACTTAGAAGCTATGGACAAAACCAGGCATTGGAAAATTGTGGGC
genomic: CAAATAAGCAAGATATAAATGGAGCTCTTACACCAGCAGAAATAGCTAAGgtaagggtgc ... actcctgcagGTCCTCAACTTAGAAGCTATGGACAAAACCAGGCATTGGAAAATTGTGGGC
EST: gi|110688789|gb|EE067741.1|EE067741
EST:     CAAATAAGCAAGATATAAATGGAGCTCTTACACCAGCAGAAATAGCTAAG                         GTCCTCAACTTAGAAGCTATGGACAAAACCAGGCATTGGAAAATTGTGGGC
genomic: CAAATAAGCAAGATATAAATGGAGCTCTTACACCAGCAGAAATAGCTAAGgtaagggtgc ... actcctgcagGTCCTCAACTTAGAAGCTATGGACAAAACCAGGCATTGGAAAATTGTGGGC
EST: gi|37189475|gb|CF608824.1|CF608824
EST:     CAAATAAGCAAGATATAAATGGAGCTCTTACACCAGCAGAAATAGCTNAG                         GTCCTCAACTTAGTAGCTATGGACAAAACCAGGCATTGGA
genomic: CAAATAAGCAAGATATAAATGGAGCTCTTACACCAGCAGAAATAGCTAAGgtaagggtgc ... actcctgcagGTCCTCAACTTAGAAGCTATGGACAAAACCAGGCATTGGA
EST: gi|71875381|gb|DT024436.1|DT024436
EST:     CAAATAAGCAAGATATAAATGGAGCTCTTACACCAGCAGAAATAGCTAAG                         GTCCTCAACTTAGAAGCTATGGACAAAACCAGGCATTGGAAAATTGTGGGC
genomic: CAAATAAGCAAGATATAAATGGAGCTCTTACACCAGCAGAAATAGCTAAGgtaagggtgc ... actcctgcagGTCCTCAACTTAGAAGCTATGGACAAAACCAGGCATTGGAAAATTGTGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgactgaattctccagcatgcaattttaatcaggtctacattatactcctgcagGTCCTCAACTTAGAAGCTATGGACAAAACCAGGCATTGGAAAATTGTGGGCTGCAGCGCAATCACGGGTGAAGGGCTTCTTGAGGGATTTGATTGGTTGG
                        ttttaat  putative branch site (score: 3)
                                            tactcct  putative PPT
                      aattttaatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctcgatcttttagtgaattatagccatatgtatttagatgaaaatgactgaattctccagcatgcaattttaatcaggtctacattatactcctgcagGTCCTCAACTTAGAAGCTATGGACAAAACCAGGCATTGGAAAATTGTGGGCTGCAGCGCAATCACGGGTGAAGGGCTTCTTGAGGGATTTGATTGGTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - -ccatatg
- - - - - - - - - - - - - - - - - - - - - aaaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgca