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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGAGGGAAATTCTGGTTATGGTCGTGGCGATTACTTTCTTGTTGGTCACGACTTCCCTGGCTACATGGATGCTCAGGCAAGAGTGGATGAAGCCTACAAgtaagaaactaacgctctcctaatctttaaatataacaacgctctgtacatcagattttactttatattaaaaggaagcaaggaaaggaaagctataaag...

Basic information

species Vitis vinifera
transcript Vv06s0004g06020.t01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g06020.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GRMZM2G085577_T01 (Zea mays), 5'ss of exon 14
TAGAGGGAAATTCTGGTTATGGTCGTGGCGATTACTTTCTTGTTGGTCACGACTTCCCTGGCTACATGGATGCTCAGGCAAGAGTGGATGAAGCCTACAAgtaagaa-actaacgctctcctaatctttaaatataacaacgctctgtacatcagattttactttata-ttaaaaggaagcaaggaaaggaaagctataaag
| || || |||||||| | ||| ||||| ||||| || ||||||||  | ||||||||  ||||||| ||||| ||||   | ||||||| |||||||||||||||| ||||||  | |  |  | ||| | ||     ||   |      |  || |    ||| || ||  |   ||  ||     |      ||| |  
TTGAAGGGAATTCTGGATTTGGGCGTGGTGATTATTTCCTTGTTGGCTATGACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacactaacaatatttt--tttttcattaagctcacctgcaagctcttggactgctgtttgtaattttacccaaaaaatcggtgccttcatattagt

upper sequence: Vv06s0004g06020.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA18G07480.1 (Glycine max), 5'ss of exon 14
TAGAGGGAAATTCTGGTTATGGTCGTGGCGATTACTTTCTTGTTGGTCACGACTTCCCTGGCTACATGGATGCTCAGGCAAGAGTGGATGAAGCCTACAAgtaagaaactaacgctctcctaatctttaaatataacaacgctctgtacatcagattttactttatattaaaaggaagcaaggaaaggaaagctataaag-----------
| || ||||||||||||||||||||||| ||||||||||| |||||||| ||||||||  ||||||||||| |||| |||| ||| |||||||  ||   ||||||  ||||  |||          ||   ||    ||| | |      |     ||  ||   || ||||  || |       | | || || | |            
TGGAAGGAAATTCTGGTTATGGTCGTGGTGATTACTTTCTAGTTGGTCATGACTTCCCAAGCTACATGGATACTCAAGCAAAAGTTGATGAAGTGTATCGgtaaga--ctaaatctcg---------taggcattttcacgttttactttcctctacttgtttgtcatcaaaataaaaccctttttgtatagttacataagtatacagcca

upper sequence: Vv06s0004g06020.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA08G45210.1 (Glycine max), 5'ss of exon 15
TAGAGGGAAATTCTGGTTATGGTCGTGGCGATTACTTTCTTGTTGGTCACGACTTCCCTGGCTACATGGATGCTCAGGCAAGAGTGGATGAAGCCTACAAgtaagaaactaac-----gctctcctaatctttaaatataacaacgctctgtacatcagattttactttatattaaaaggaagcaaggaaaggaaagctataaag
| || ||||||||||||||||| ||||| ||||||||||| |||||||| ||||| ||  ||||||||||| ||||||||| ||| |||||||| |||  ||||||  | | |     |   |  | |  ||||| | |       || | | |    ||| | |   | | ||   |       |  |    | | |||     
TGGAAGGAAATTCTGGTTATGGCCGTGGTGATTACTTTCTAGTTGGTCATGACTTTCCAAGCTACATGGATACTCAGGCAAAAGTTGATGAAGCATACCGgtaagagtcaatcttgtagacgttttcacgtttaagtttcctcttcctgtttgccgttgatataaaactctttttgcaaagttacattagtacacaacta-----

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|110701189|gb|EE078511.1|EE078511
EST:     GACTTCCCTGGCTACATGGATGCTCAGGCAAGGGTGGATGAAGCCTACAA                         GGATAGGAAAAGATGGCTAAAGATGTCTATATTGAGCACTGCTGGGAGTGG
genomic: GACTTCCCTGGCTACATGGATGCTCAGGCAAGAGTGGATGAAGCCTACAAgtaagaaact ... ttgcctgcagGGATAGGAAAAGATGGCTAAAGATGTCTATATTGAGCACTGCTGGGAGTGG
EST: gi|110703465|gb|EE080336.1|EE080336
EST:     GACTTCCCTGGCTACATGGATGCTCAGGCAAGGGTGGATGAAGCCTACAA                         GGATAGGAAAAGATGGCTAAAGATGTCTATATTGAGCACTGCTGGGAGTGG
genomic: GACTTCCCTGGCTACATGGATGCTCAGGCAAGAGTGGATGAAGCCTACAAgtaagaaact ... ttgcctgcagGGATAGGAAAAGATGGCTAAAGATGTCTATATTGAGCACTGCTGGGAGTGG
EST: gi|46910305|gb|CN545680.1|CN545680
EST:     GACTTCCCTGGCTACATGGATGCTCAGGCAAGGGTGGATGGAGCCTACAA                         GGATAGGAAAAGACGGCTAAAGATGTCTATATTGAGCACTGCTGGGAGTGG
genomic: GACTTCCCTGGCTACATGGATGCTCAGGCAAGAGTGGATGAAGCCTACAAgtaagaaact ... ttgcctgcagGGATAGGAAAAGATGGCTAAAGATGTCTATATTGAGCACTGCTGGGAGTGG
EST: gi|110384669|gb|EC949123.1|EC949123
EST:     GACTTCCCTGGCTACATGGATGCTCAGGCAAGAGTGGATGAAGCCTACAA                         GGATAGGAAAAGATGGCTAAAGATGTCTATATTGAGCACTGCTGGGAGTGG
genomic: GACTTCCCTGGCTACATGGATGCTCAGGCAAGAGTGGATGAAGCCTACAAgtaagaaact ... ttgcctgcagGGATAGGAAAAGATGGCTAAAGATGTCTATATTGAGCACTGCTGGGAGTGG
EST: gi|110390714|gb|EC955638.1|EC955638
EST:     GACTTCCCTGGCTACATGGATGCTCAGGCAAGGGTGGATGAAGCCTACAA                         GGATAGGAAAAGATGGCTAAAGATGTCTATATTGAGCACTGCTGGGAGTGG
genomic: GACTTCCCTGGCTACATGGATGCTCAGGCAAGAGTGGATGAAGCCTACAAgtaagaaact ... ttgcctgcagGGATAGGAAAAGATGGCTAAAGATGTCTATATTGAGCACTGCTGGGAGTGG
EST: gi|28960619|gb|CB340317.1|CB340317
EST:     GACTTCCCTGGCTACATGGATGCTCAGGCAAGGGTGGATGAAGCCTACAA                         GGATAGGAAAAGATGGCTAAAGATGTCTATATTGAGCACTGCTGGGAGTGG
genomic: GACTTCCCTGGCTACATGGATGCTCAGGCAAGAGTGGATGAAGCCTACAAgtaagaaact ... ttgcctgcagGGATAGGAAAAGATGGCTAAAGATGTCTATATTGAGCACTGCTGGGAGTGG
EST: gi|18458867|gb|BM437145.1|BM437145
EST:     GTGGATGAAGCCTACAA                         GGATAGGAAAAGATGGCTAAAGATGTCTATATTGAGCACTGCTGGGAGTGG
genomic: GTGGATGAAGCCTACAAgtaagaaact ... ttgcctgcagGGATAGGAAAAGATGGCTAAAGATGTCTATATTGAGCACTGCTGGGAGTGG
EST: gi|37190441|gb|CF609790.1|CF609790
EST:     GACTTCCCTGGCTACATGGATGCTCAGGCAAGGGTGGATGAAGCCTACAA                         GGATAGGAAAAGATGGCTAAAGATGTCTATATTGAGCACTGCTGGGAGTGG
genomic: GACTTCCCTGGCTACATGGATGCTCAGGCAAGAGTGGATGAAGCCTACAAgtaagaaact ... ttgcctgcagGGATAGGAAAAGATGGCTAAAGATGTCTATATTGAGCACTGCTGGGAGTGG
EST: gi|30135822|gb|CB921160.1|CB921160
EST:     GACTTCCCTGGCTACATGGATGCTCAGGCAAGGGTGGATGAAGCCTACNA                         GGATAGGANAAGATGGCNTAA-GATGTCTATATTGAGCACTGCTGGGAGTG
genomic: GACTTCCCTGGCTACATGGATGCTCAGGCAAGAGTGGATGAAGCCTACAAgtaagaaact ... ttgcctgcagGGATAGGAAAAGATGGC-TAAAGATGTCTATATTGAGCACTGCTGGGAGTG
EST: gi|28960453|gb|CB340229.1|CB340229
EST:     GACTTCCCTGGCTACATGGATGCTCAGGCAAGGGTGGATGAAGCCTACAA                         GGATAGGAAAAGATGGCTAAAGATGTCTATATTGAGCACTGCTGGGAGTGG
genomic: GACTTCCCTGGCTACATGGATGCTCAGGCAAGAGTGGATGAAGCCTACAAgtaagaaact ... ttgcctgcagGGATAGGAAAAGATGGCTAAAGATGTCTATATTGAGCACTGCTGGGAGTGG
EST: gi|110379272|gb|EC944457.1|EC944457
EST:     GACTTCCCTGGCTACATGGATGCTCAGGCAAGAGTGGATGAAGCCTACAA                         GGATAGGAAAAGATGGCTAAAGATGTCTATATTGAGCACTGCTGGGAGTGG
genomic: GACTTCCCTGGCTACATGGATGCTCAGGCAAGAGTGGATGAAGCCTACAAgtaagaaact ... ttgcctgcagGGATAGGAAAAGATGGCTAAAGATGTCTATATTGAGCACTGCTGGGAGTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGAGGGAAATTCTGGTTATGGTCGTGGCGATTACTTTCTTGTTGGTCACGACTTCCCTGGCTACATGGATGCTCAGGCAAGAGTGGATGAAGCCTACAAgtaagaaactaacgctctcctaatctttaaatataacaacgctctgtacatcagattttactttatattaaaaggaagcaaggaaaggaaagctataaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataacaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaggaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggaaag