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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcagtgagatgggatccagttttggcatgtccagtttgatgtatcttcccctctgcctatcaatttaacctttttttgggattttgatgcagGTTACTGGGCACCCCCAATGAAGAGATGTGGCCAGGAGTGACGAAACTACCAAACTGGCATGAGTTCCCCCAGTGGAGCCCAAATCAGAATCCTAAGAAT

Basic information

species Vitis vinifera
transcript Vv18s0122g00550.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0122g00550.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os08g40170.1 (Oryza sativa), 3'ss of exon 4
-----------gttcagtga--gatgggatccagttttggcatgtccagtttgatgtatcttcccctctgcctatcaatttaacctttttttgggattttgatgcagGTTACTGGGCACCCCCAATGAAGAGATGTGGCCAGGAGTGACGAAACTACCAAACTGGCATGAGTTCCCCCAGTGGAGCCCAAATCAGAATCCTAAGAAT
           |||   | |   || |      ||  | || || |    |||| |  | |   | | |    ||     | |  | | ||     ||| | | |||||| ||||||||||| |||||  |  | |||||||||||||  || ||||| |||||||| |||| |||||||||||  ||     |     || |   |
gtactgtgcctgtttcctcatcaattgttctttgtgctcgc-tggcatacttgaggggtataatcgtgtattcatggtggtgatttatcttgattgtttggttccagGTTGCTGGGCACCCCAAATGAGCAAGTTTGGCCAGGAGTGAGCAAGCTACCTAACTGGCACGAGTACCCCCAGTGGAATCCCTCGAAAGTGTCTGATCTT
















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|34542681|gb|CF510913.1|CF510913
EST:     GCACTGTTTCCTGGGGATTCTGAACTGCAGCAGCTCCTTCATATTTTCAA                         GTTACTGGGCACCCCCAATGAAGAGATGTGGCCAGGAGTGACGAAACTACC
genomic: GCACTCTTTCCTGGGGATTCTGAACTGCAGCAGCTCCTTCATATTTTCAAgttcagtgag ... tttgatgcagGTTACTGGGCACCCCCAATGAAGAGATGTGGCCAGGAGTGACGAAACTACC
EST: gi|351055531|gb|FQ442327.1|FQ442327
EST:     GCACTGTTTCCTGGGGATTCTGAACTGCAGCAGCTCCTTCATATTTTCAA                         GTTACTGGGCACCCCCGATGAAGAGATGTGGCCAGGAGTGACGAAACTACC
genomic: GCACTCTTTCCTGGGGATTCTGAACTGCAGCAGCTCCTTCATATTTTCAAgttcagtgag ... tttgatgcagGTTACTGGGCACCCCCAATGAAGAGATGTGGCCAGGAGTGACGAAACTACC
EST: gi|110365343|gb|EC928182.1|EC928182
EST:     GCACTGTTTCCTGGGGATTCTGAACTGCAGCAGCTCCTTCATATTTTCAA                         GTTACTGGGCACCCCCAATGAAGAGATGTGGCCAGGAGTGACGAAACTACC
genomic: GCACTCTTTCCTGGGGATTCTGAACTGCAGCAGCTCCTTCATATTTTCAAgttcagtgag ... tttgatgcagGTTACTGGGCACCCCCAATGAAGAGATGTGGCCAGGAGTGACGAAACTACC
EST: gi|110376059|gb|EC941099.1|EC941099
EST:     GCACTGTTTCCTGGGGATTCTGAACTGCAGCAGCTCCTTCATATTTTCAA                         GTTACTGGGCACCCCCAATGAAGAGATGTGGCCAGGAGTGACGAAACTACC
genomic: GCACTCTTTCCTGGGGATTCTGAACTGCAGCAGCTCCTTCATATTTTCAAgttcagtgag ... tttgatgcagGTTACTGGGCACCCCCAATGAAGAGATGTGGCCAGGAGTGACGAAACTACC
EST: gi|110426132|gb|EC992529.1|EC992529
EST:     GCACTGTTTCCTGGGGATTCTGAACTGCAGCAGCTCCTTCATATTTTCAA                         GTTACTGGGCACCCCCAATGAAGAGATGTGGCCAGGAGTGACGAAACTACC
genomic: GCACTCTTTCCTGGGGATTCTGAACTGCAGCAGCTCCTTCATATTTTCAAgttcagtgag ... tttgatgcagGTTACTGGGCACCCCCAATGAAGAGATGTGGCCAGGAGTGACGAAACTACC
EST: gi|351039035|gb|FQ457710.1|FQ457710
EST:     GCACTGTTTCCTGGGGATTCTGAACTGCAGCAGCTCCTTCATATTTTCAA                         GTTACTGGGCACCCCCAATGAAGAGATGTGGCCAGGAGTGACGAAACTACC
genomic: GCACTCTTTCCTGGGGATTCTGAACTGCAGCAGCTCCTTCATATTTTCAAgttcagtgag ... tttgatgcagGTTACTGGGCACCCCCAATGAAGAGATGTGGCCAGGAGTGACGAAACTACC
EST: gi|110381644|gb|EC935009.1|EC935009
EST:     GCACTGTTTCCTGGGGATTCTGAACTGCAGCAGCTCCTTCATATTTTCAA                         GTTACTGGGCACCCCCAATGAAGAGATGTGGCCAGGAGTGACGAAACTACC
genomic: GCACTCTTTCCTGGGGATTCTGAACTGCAGCAGCTCCTTCATATTTTCAAgttcagtgag ... tttgatgcagGTTACTGGGCACCCCCAATGAAGAGATGTGGCCAGGAGTGACGAAACTACC
EST: gi|349827747|gb|FQ422615.1|FQ422615
EST:     GCACTGTTTCCTGGGGATTCTGAACTGCAGCAGCTCCTTCATATTTTCAA                         GTTACTGGGCACCCCCAATGAAGAGATGTGGCCAGGAGTGACGAAACTACC
genomic: GCACTCTTTCCTGGGGATTCTGAACTGCAGCAGCTCCTTCATATTTTCAAgttcagtgag ... tttgatgcagGTTACTGGGCACCCCCAATGAAGAGATGTGGCCAGGAGTGACGAAACTACC
EST: gi|34415970|gb|CF414724.1|CF414724
EST:     GCACTGTTTCCTGGGGATTCTGAACTGCAGCAGCTCCTTCATATTTTCAA                         GTTACTGGGCACCCCCAATGAAGAGATGTGGCCAGGAGTGACGAAACTACC
genomic: GCACTCTTTCCTGGGGATTCTGAACTGCAGCAGCTCCTTCATATTTTCAAgttcagtgag ... tttgatgcagGTTACTGGGCACCCCCAATGAAGAGATGTGGCCAGGAGTGACGAAACTACC
EST: gi|71870629|gb|DT019684.1|DT019684
EST:     GCACTGTTTCCTGGGGATTCTGAACTGCAGCAGCTCCTTCATATTTTCAA                         GTTACTGGGCACCCCCAATGAAGAGATGTGGCCAGGAGTGACGAAACTACC
genomic: GCACTCTTTCCTGGGGATTCTGAACTGCAGCAGCTCCTTCATATTTTCAAgttcagtgag ... tttgatgcagGTTACTGGGCACCCCCAATGAAGAGATGTGGCCAGGAGTGACGAAACTACC
EST: gi|33404794|gb|CF210421.1|CF210421
EST:     GCACTGTTTCCTGGGGATTCTGAACTGCAGCAGCTCCTTCATATTTTCAA                         GTTACTGGGCACCCCCAATGAAGAGATGTGGCCAGGAGTGACGAAACTACC
genomic: GCACTCTTTCCTGGGGATTCTGAACTGCAGCAGCTCCTTCATATTTTCAAgttcagtgag ... tttgatgcagGTTACTGGGCACCCCCAATGAAGAGATGTGGCCAGGAGTGACGAAACTACC
EST: gi|34542594|gb|CF510826.1|CF510826
EST:     GCACTGTTTCCTGGGGATTCTGAACTGCAGCAGCTCCTTCATATTTTCAA                         GTTACTGGGCACCCCCAATGAAGAGATGTGGCCAGGAGTGACGAAACTACC
genomic: GCACTCTTTCCTGGGGATTCTGAACTGCAGCAGCTCCTTCATATTTTCAAgttcagtgag ... tttgatgcagGTTACTGGGCACCCCCAATGAAGAGATGTGGCCAGGAGTGACGAAACTACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgtatcttcccctctgcctatcaatttaacctttttttgggattttgatgcagGTTACTGGGCACCCCCAATGAAGAGATGTGGCCAGGAGTGACGAAACTACCAAACTGGCATGAGTTCCCCCAGTGGAGCCCAAATCAGAATCCTAAGAAT
                        aatttaaccttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcagtgagatgggatccagttttggcatgtccagtttgatgtatcttcccctctgcctatcaatttaacctttttttgggattttgatgcagGTTACTGGGCACCCCCAATGAAGAGATGTGGCCAGGAGTGACGAAACTACCAAACTGGCATGAGTTCCCCCAGTGGAGCCCAAATCAGAATCCTAAGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG