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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGTGTACTACTGTCAAATGTGGTGCATCACTAGTTTTTGCTTCCATAGGAGCCGGGATTGGTGCCACCCTTTTCCGTCCTTCAGCCGGCCAGTGGATTGgtaagtacatctcctcctccaagactacctgataaagctttttgtggaatctctgtaagtttgctaattttatagaatgtagaaaggaaaagatctctgatatgtaaaatttccaatactaaaatgtacttttcctgcag

Basic information

species Vitis vinifera
transcript Vv19s0015g00180.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0015g00180.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA16G26380.1 (Glycine max), 5'ss of exon 6
-ACGTGTACTACTGTCAAATGTGGTGCATCACTAGTTTTTGCTTCCATAGGAGCCGGGATTGGTGCCACCCTTTTCCGTCCTTCAGCCGGCCAGTGGATTGgtaagtacatctcctcctccaagactacctgataaagctttttgtggaatctctgtaagtttgctaattttatagaatgtagaaaggaaaagatctctgatatgtaaaatttccaatactaaaatgtacttttcctgcag
  | | | |||| || | ||||  | ||||  || ||||||| ||||||||||| || |||||||| |||||| | ||||| ||   |||||||||| ||||||||    |   |  | |    |     | | ||   || |||   | |   ||  | |||  | |||| |   |  ||   || |||    |   |   |                                      
TTCAT-TGCTACAGTTAGATGTACTTCATCTTTAATTTTTGCCTCCATAGGAGCAGGAATTGGTGCAACCCTTATTCGTCCATCGCTCGGCCAGTGGGTTGgtaagattgtaaacaacacattcagagaattacaaga-ttgttgcatattacttg--aattttgtgatttaaggtatcgtgtgaatgaactttttcatagcac-------------------------------------
















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|110375093|gb|EC940050.1|EC940050
EST:     AGCCGGGATTGGTGCCACCCTTTTCCGTCCTTCAGCCGGCCAGTGGATTG                         GCTGTGCTGCTGGGGACTTGGCTGGGCCCATTATTGTATCAGTTTGCTTTG
genomic: AGCCGGGATTGGTGCCACCCTTTTCCGTCCTTCAGCCGGCCAGTGGATTGgtaagtacat ... tttcctgcagGCTGTGCTGCTGGGGACTTGGCTGGGCCCATTATTGTATCAGTTTGCTTTG
EST: gi|110414980|gb|EC980847.1|EC980847
EST:     AGCCGGGATTGGTGCCACCCTTTTCCGTCCTTCAGCCGGCCAGTGGATTG                         GCTGTGCTGCTGGGGACTTGGCTGGGCCCATTATTGTATCAGTTTGCTTTG
genomic: AGCCGGGATTGGTGCCACCCTTTTCCGTCCTTCAGCCGGCCAGTGGATTGgtaagtacat ... tttcctgcagGCTGTGCTGCTGGGGACTTGGCTGGGCCCATTATTGTATCAGTTTGCTTTG
EST: gi|352791152|gb|FQ477479.1|FQ477479
EST:     AGCCGGGATTGGTGCCACCCTTTTCCGTCCTTCAGCCGGCCAGTGGATTG                         GCTGTGCTGCTGGGGACTTGGCTGGGCCCATTATTGTATCAGTTTGCTTTG
genomic: AGCCGGGATTGGTGCCACCCTTTTCCGTCCTTCAGCCGGCCAGTGGATTGgtaagtacat ... tttcctgcagGCTGTGCTGCTGGGGACTTGGCTGGGCCCATTATTGTATCAGTTTGCTTTG
EST: gi|110362995|gb|EC926560.1|EC926560
EST:     AGCCGGGATTGGTGCCACCCTTTTCCGTCCTTCAGCCGGCCAGTGGATTG                         GCTGTGCTGCTGGGGACTTGGCTGGGCCCATTATTGTATCAGTTTGCTTTG
genomic: AGCCGGGATTGGTGCCACCCTTTTCCGTCCTTCAGCCGGCCAGTGGATTGgtaagtacat ... tttcctgcagGCTGTGCTGCTGGGGACTTGGCTGGGCCCATTATTGTATCAGTTTGCTTTG
EST: gi|34361692|gb|CF403277.1|CF403277
EST:     AGCCGGGATTGGTGCCACCCTTTTCCGTCCTTCAACCGGCCAGTGGATTG                         GCTGTGCTGCTGGGGACTTGGCTGGGCCCATTATTGTATCAGTTTGCTTTG
genomic: AGCCGGGATTGGTGCCACCCTTTTCCGTCCTTCAGCCGGCCAGTGGATTGgtaagtacat ... tttcctgcagGCTGTGCTGCTGGGGACTTGGCTGGGCCCATTATTGTATCAGTTTGCTTTG
EST: gi|110422941|gb|EC989275.1|EC989275
EST:     AGCCGGGATTGGTGCCACCCTTTTCCGTCCTTCAGCCGGCCAGTGGATTG                         GCTGTGCTGCTGGGGACTTGGCTGGGCCCATTATTGTATCAGTTTGCTTTG
genomic: AGCCGGGATTGGTGCCACCCTTTTCCGTCCTTCAGCCGGCCAGTGGATTGgtaagtacat ... tttcctgcagGCTGTGCTGCTGGGGACTTGGCTGGGCCCATTATTGTATCAGTTTGCTTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACGTGTACTACTGTCAAATGTGGTGCATCACTAGTTTTTGCTTCCATAGGAGCCGGGATTGGTGCCACCCTTTTCCGTCCTTCAGCCGGCCAGTGGATTGgtaagtacatctcctcctccaagactacctgataaagctttttgtggaatctctgtaagtttgctaattttatagaatgtagaaaggaaaagatctctgatatgtaaaatttccaatactaaaatgtacttttcctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA