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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAATTTTGCGCAAAAGAAGAGCAGGAAAACTTCCTGGTGACACTACTTCTGTCTTAAAAGCTTGGTGGCAATCACATTCTAAGTGGCCATACCCTACAgtaagtattggcttctttgtcttaataatatgaactcttatgtcttacgaagatttccaattgtcactttaagctcaagtcaattatatttttcctaatg...

Basic information

species Vitis vinifera
transcript Vv04s0008g06130.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g06130.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: PP1S154_83V6.1 (Physcomitrella patens), 5'ss of exon 8
AGAAATTTTGCGCAAAAGAAGAGCAGGAAAACTTCCTGGTGACACTACTTCTGTCTTAAAAGCTTGGTGGCAATCACATTCTAAGTGGCCATACCCTACAgtaagtattggcttctttg----tcttaataatatgaactc--ttatgtcttacgaagatttccaattgtcacttta-agctcaagtcaattatatttttcctaatg------------------------------------------------
 || ||  | |||||| |  | || ||||| || ||||  |  |||||  | ||||| || |||||||||||| ||||||| ||||||||||| || || |||   |     |  |  |     || ||  |  |  |  |  | |||  ||| |      | ||   || | || | |  || | | |  ||||| | |     |                                                 
GGAGATCCTACGCAAACGGCGTGCTGGAAAGCTGCCTGAGGGAACTACAACAGTCTTGAAGGCTTGGTGGCAAGCACATTCAAAGTGGCCATATCCCACGgtatcaaaaaattcatcaggaatcctgaactacgtatatccattcatgctttatgttctagttca--cgtaatttcagaattccatttatatatatatatatacgtattggtgacatgctgatttttccacctctgttttgcactcctcaaccag
















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|71887415|gb|DT036470.1|DT036470
EST:     CTGTCTTAAAAGCTTGGTGGCAATCACATTCTAAGTGGCCATACCCTACA                         GAGGAGGACAAGGCAAAGCTGGTACAAGAAACAGGCTTGCAACTAAAGCAG
genomic: CTGTCTTAAAAGCTTGGTGGCAATCACATTCTAAGTGGCCATACCCTACAgtaagtattg ... atcttcttagGAGGAGGACAAGGCAAAGTTGGTACAAGAAACAGGCTTGCAACTAAAGCAG
EST: gi|71883895|gb|DT032950.1|DT032950
EST:     CTGTCTTAAAAGCTTGGTGGCAATCACATTCTAAGTGGCCATACCCTACA                         GAGGAGGACAAGGCAAAGCTGGTACAAGAAACAGGCTTGCAACTAAAGCAG
genomic: CTGTCTTAAAAGCTTGGTGGCAATCACATTCTAAGTGGCCATACCCTACAgtaagtattg ... atcttcttagGAGGAGGACAAGGCAAAGTTGGTACAAGAAACAGGCTTGCAACTAAAGCAG
EST: gi|71886598|gb|DT035653.1|DT035653
EST:     CTGTCTTAAAAGCTTGGTGGCAATCACATTCTAAGTGGCCATACCCTACA                         GAGGAGGACAAGGCAAAGCTGGTACAAGAAACAGGCTTGCAACTAAAGCAG
genomic: CTGTCTTAAAAGCTTGGTGGCAATCACATTCTAAGTGGCCATACCCTACAgtaagtattg ... atcttcttagGAGGAGGACAAGGCAAAGTTGGTACAAGAAACAGGCTTGCAACTAAAGCAG
EST: gi|352764559|gb|FQ472916.1|FQ472916
EST:     TCACATTCTAAGTGGCCATACCCTACA                         GAGGGGGACAAGGCAAAGTTGGTACAAGAAACAGGCTTGCAACTAAAGCAG
genomic: TCACATTCTAAGTGGCCATACCCTACAgtaagtattg ... atcttcttagGAGGAGGACAAGGCAAAGTTGGTACAAGAAACAGGCTTGCAACTAAAGCAG
EST: gi|352781649|gb|FQ468947.1|FQ468947
EST:     TCTAAGTGGCCATTCCCTACA                         GAGGAGGACAAGGCAAAGTTGGTACAAGAAACAGGCTTGCAAATAAAGCAG
genomic: TCTAAGTGGCCATACCCTACAgtaagtattg ... atcttcttagGAGGAGGACAAGGCAAAGTTGGTACAAGAAACAGGCTTGCAACTAAAGCAG
EST: gi|352772548|gb|FQ472023.1|FQ472023
EST:     CAATCACATTCTAGGTGGCCATACCCTACA                         GAGGAGGACAAGGCAAAGTTGGTACAGGAAACAGGCTTGCAACTAAAGCAG
genomic: CAATCACATTCTAAGTGGCCATACCCTACAgtaagtattg ... atcttcttagGAGGAGGACAAGGCAAAGTTGGTACAAGAAACAGGCTTGCAACTAAAGCAG
EST: gi|30325535|gb|CD008797.1|CD008797
EST:     CTGTCTTAAAAGCTTGGTGGCAATCACATTCTAAGTGGCCATACCCTACA                         GAGGAGGACAAGGCAAAGTTGGTACAAGAAACAGGCTTGCAACTAAAGCAG
genomic: CTGTCTTAAAAGCTTGGTGGCAATCACATTCTAAGTGGCCATACCCTACAgtaagtattg ... atcttcttagGAGGAGGACAAGGCAAAGTTGGTACAAGAAACAGGCTTGCAACTAAAGCAG
EST: gi|71856605|gb|DT005660.1|DT005660
EST:     CTGTCTTAAAAGCTTGGTGGCAATCACATTCTAAGTGGCCATACCCTACA                         GAGGAGGACAAGGCAAAGCTGGTACAAGAAACAGGCTTGCAACTAAAGCAG
genomic: CTGTCTTAAAAGCTTGGTGGCAATCACATTCTAAGTGGCCATACCCTACAgtaagtattg ... atcttcttagGAGGAGGACAAGGCAAAGTTGGTACAAGAAACAGGCTTGCAACTAAAGCAG
EST: gi|30324320|gb|CD007582.1|CD007582
EST:     CTGTCTTAAAAGCTTGGTGGCAATCACATTCTAAGTGGCCATACCCTACA                         GAGGAGGACAAGGCAAAGTTGGTACAAGAAACAGGCTTGCAACTAAAGCAG
genomic: CTGTCTTAAAAGCTTGGTGGCAATCACATTCTAAGTGGCCATACCCTACAgtaagtattg ... atcttcttagGAGGAGGACAAGGCAAAGTTGGTACAAGAAACAGGCTTGCAACTAAAGCAG
EST: gi|110386833|gb|EC951462.1|EC951462
EST:     CTGTCTTAAAAGCTTGGTGGCAATCACATTCTAAGTGGCCATACCCTACA                         GAGGAGGACAAGGCAAAGTTGGTACAAGAAACAGGCTTGCAACTAAAGCAG
genomic: CTGTCTTAAAAGCTTGGTGGCAATCACATTCTAAGTGGCCATACCCTACAgtaagtattg ... atcttcttagGAGGAGGACAAGGCAAAGTTGGTACAAGAAACAGGCTTGCAACTAAAGCAG
EST: gi|32272512|gb|CD721671.1|CD721671
EST:     CTGTCTTAAAAGCTTGGTGGCAATCACATTCTAAGTGGCCATACCCTACA                         GAGGAGGACAAGGCAAAGTTGGTACAAGAAACAGGCTTGCAACTAAAGCAG
genomic: CTGTCTTAAAAGCTTGGTGGCAATCACATTCTAAGTGGCCATACCCTACAgtaagtattg ... atcttcttagGAGGAGGACAAGGCAAAGTTGGTACAAGAAACAGGCTTGCAACTAAAGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAATTTTGCGCAAAAGAAGAGCAGGAAAACTTCCTGGTGACACTACTTCTGTCTTAAAAGCTTGGTGGCAATCACATTCTAAGTGGCCATACCCTACAgtaagtattggcttctttgtcttaataatatgaactcttatgtcttacgaagatttccaattgtcactttaagctcaagtcaattatatttttcctaatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acgaaga