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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTCAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAGgtataatatataatgtcatgcttgatctatcaaaaaatatataatgccatgcttgtattctgatgaaaaaacttaattggcttatgttaatagcttaactgtctcatttacttaaaatttttctttttcctccctctctctctctcaactctggcctgttcaaataatcag

Basic information

species Vitis vinifera
transcript Vv18s0117g00150.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0117g00150.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os08g23120.1 (Oryza sativa), 5'ss of exon 4
GTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTCAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAGgtataatatataatgtcatgcttgatctatcaaaaaatatataatgccatgcttgtattctgatgaaaaaacttaattggcttatgttaatagcttaactgtctcatttacttaaaatttttctttttcctccctctctctctctcaactctggcctgttcaaataatcag
||||| ||||| ||||| |||||||| ||  |||  |     || |||||||| || ||||| |||||||||||||||||||||||| |  | |  |||||||| | || || | |  || |||    | ||   | ||  | ||   ||     |||| | || |  | ||| ||   | | |||   |||  || || |                                                                      
GTTGAAATTAAGAGAACTATTCCAAAGGGTGCTGCCCCCCTAAAAGATTTCAAGACGAAGAAAATATTTGTTGGTGGATTACCATCTGCTTTGAAAGAAGgtattacatgta-tatattgtttgcctaaccatggactagctcatattat-----tatttt-ataagtatactgaacatgttgatgc-gataatttgacag----------------------------------------------------------------------

upper sequence: Vv18s0117g00150.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G152526_T01 (Zea mays), 5'ss of exon 4
GTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTCAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAGgtataatatataatgtcatgcttgatctatcaaaaaatatataatgccatgcttgtattctgatgaaaaaacttaattggcttatgttaatagc-ttaactgtctcatttacttaaaatttttctttttcctccctctctctctctcaactctggcctgttcaaataatcag
||||| ||||| ||||| || || || ||  ||| ||  | ||| |||||||| || |||||||| ||||||||||||||||| ||  |  | |  ||||||||| |           || ||  |       | | |    |||||  |  || | | |||   |  ||| | |||| | |  | | | | |  || || |                                                                      
GTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTCAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAGgtatatt---------tgtgtttccttggctgcatagtggcaaatgcgcttttt-tgtcctgcatagtaaattgaatttgttggtataatttgaattgacag----------------------------------------------------------------------
















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|33407717|gb|CF213344.1|CF213344
EST:     CAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAG                         ATGAGTTCAAGGATTTCTTCTCCAAGTATGGGAAGGTGGAGGAGCACCAGA
genomic: CAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAGgtataatata ... aaataatcagATGAGTTCAAGGATTTCTTCTCCAAGTATGGGAAGGTGGAGGAGCACCAGA
EST: gi|110712411|gb|EE090004.1|EE090004
EST:     CAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAG                         ATGAGTTCAAGGATTTCTTCTCCAAGTATGGGAAGGTGGAGGAGCACCAGA
genomic: CAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAGgtataatata ... aaataatcagATGAGTTCAAGGATTTCTTCTCCAAGTATGGGAAGGTGGAGGAGCACCAGA
EST: gi|110719186|gb|EE096875.1|EE096875
EST:     CAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAG                         ATGAGTTCAAGGATTTCTTCTCCAAGTATGGGAAGGTGGAGGAGCACCAGA
genomic: CAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAGgtataatata ... aaataatcagATGAGTTCAAGGATTTCTTCTCCAAGTATGGGAAGGTGGAGGAGCACCAGA
EST: gi|71873142|gb|DT022197.1|DT022197
EST:     CAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAG                         ATGAGTTCAAGGATTTCTTCTCCAAGTATGGGAAGGTGGAGGAGCACCAGA
genomic: CAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAGgtataatata ... aaataatcagATGAGTTCAAGGATTTCTTCTCCAAGTATGGGAAGGTGGAGGAGCACCAGA
EST: gi|161721778|gb|FC071127.1|FC071127
EST:     CAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAG                         ATGAGTTCAAGGATTTCTTCTCCAAGTATGGGAAGGTGGAGGAGCACCAGA
genomic: CAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAGgtataatata ... aaataatcagATGAGTTCAAGGATTTCTTCTCCAAGTATGGGAAGGTGGAGGAGCACCAGA
EST: gi|37188093|gb|CF607444.1|CF607444
EST:     CAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAG                         ATGAGTTCAAGGATTTCTTCTCCAAGTATGGGAAGGTGGAGGAGCACCAGA
genomic: CAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAGgtataatata ... aaataatcagATGAGTTCAAGGATTTCTTCTCCAAGTATGGGAAGGTGGAGGAGCACCAGA
EST: gi|351030617|gb|FQ437043.1|FQ437043
EST:     CAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAG                         ATGAGTTCAAGGATTTCTTCTCCAAGTATGGGAAGGTGGAGGAGCACCAGA
genomic: CAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAGgtataatata ... aaataatcagATGAGTTCAAGGATTTCTTCTCCAAGTATGGGAAGGTGGAGGAGCACCAGA
EST: gi|351027170|gb|FQ440038.1|FQ440038
EST:     CAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAG                         ATGAGTTCAAGGATTTCTTCTCCAAGTATGGGAAGGTGGAGGAGCACCAGA
genomic: CAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAGgtataatata ... aaataatcagATGAGTTCAAGGATTTCTTCTCCAAGTATGGGAAGGTGGAGGAGCACCAGA
EST: gi|110710940|gb|EE087573.1|EE087573
EST:     CAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAG                         ATGAGTTCAAGGATTTCTTCTCCAAGTATGGGAAGGTGGAGGAGCACCAGA
genomic: CAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAGgtataatata ... aaataatcagATGAGTTCAAGGATTTCTTCTCCAAGTATGGGAAGGTGGAGGAGCACCAGA
EST: gi|351014903|gb|FQ438103.1|FQ438103
EST:     CAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAG                         ATGAGTTCAAGGATTTCTTCTCCAAGTATGGGAAGGTGGAGGAGCACCAGA
genomic: CAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAGgtataatata ... aaataatcagATGAGTTCAAGGATTTCTTCTCCAAGTATGGGAAGGTGGAGGAGCACCAGA
EST: gi|351045405|gb|FQ447670.1|FQ447670
EST:     CAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAG                         ATGAGTTCAAGGATTTCTTCTCCAAGTATGGGAAGGTGGAGGAGCACCAGA
genomic: CAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAGgtataatata ... aaataatcagATGAGTTCAAGGATTTCTTCTCCAAGTATGGGAAGGTGGAGGAGCACCAGA
EST: gi|351039455|gb|FQ461322.1|FQ461322
EST:     CAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAG                         ATGAGTTCAAGGATTTCTTCTCCAAGTATGGGAAGGTGGAGGAGCACCAGA
genomic: CAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAGgtataatata ... aaataatcagATGAGTTCAAGGATTTCTTCTCCAAGTATGGGAAGGTGGAGGAGCACCAGA
EST: gi|110707058|gb|EE083127.1|EE083127
EST:     CAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAG                         ATGAGTTCAAGGATTTCTTCTCCAAGTATGGGAAGGTGGAGGAGCACCAGA
genomic: CAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAGgtataatata ... aaataatcagATGAGTTCAAGGATTTCTTCTCCAAGTATGGGAAGGTGGAGGAGCACCAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTCAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAGgtataatatataatgtcatgcttgatctatcaaaaaatatataatgccatgcttgtattctgatgaaaaaacttaattggcttatgttaatagcttaactgtctcatttacttaaaatttttctttttcctccctctctctctctcaactctggcctgttcaaataatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG