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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAACCAGGACAGAAGGATATCTTCTACATCACGGGTAACAGCAAGGAGCAATTGGAGAAGTCTCCATTCCTTGAGAGGCTTACAAAGAAGAATTATGAGgtatgattggaaaagataactacttgcttttcaaccgtccttgattagtctggtcttattcttttcctaaggtactatccttggtttttaacaacttgttttctttctgaatcattctattgcag

Basic information

species Vitis vinifera
transcript Vv18s0001g14500.t01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 5'ss of exon 13
GAAACCAGGACAGAAGGATATCTTCTACATCACGGGTAACAGCAAGGAGCAATTGGAGAAGTCTCCATTCCTTGAGAGGCTTACAAAGAAGAATTATGAGgtatgattggaaaagataactacttgcttttcaaccgtccttgattagtctggtcttattcttttcctaaggtactatccttggtttttaacaacttgttttctttctgaatcattctattgcag
||| ||||| |||||||| ||||| ||||| || || | ||||||||| ||||| ||||| || || |||||||||||||| || || ||||| || ||||| || |    | ||    |   ||  |     | | |   | ||   |    | || || ||||   ||   | | |  |   |  ||  |  ||| |                          
GAAGCCAGGGCAGAAGGACATCTTTTACATTACCGGAAGCAGCAAGGAACAATTAGAGAAATCACCGTTCCTTGAGAGGCTAACCAAAAAGAACTACGAGgtgtgttaccgagaggcctcatttttttacagtatcttatgtcatgcattctatgttttttttttttgaaaagaatgtattctatggttt-ctccttatgg------------------------

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GRMZM2G141931_T02 (Zea mays), 5'ss of exon 13
GAAACCAGGACAGAAGGATATCTTCTACATCACGGGTAACAGCAAGGAGCAATTGGAGAAGTCTCCATTCCTTGAGAGGCTTACAAAGAAGAATTATGAGgtatgattggaaaagataactacttgcttttcaaccgtccttgattagtctgg--tcttattcttttccta-aggtactatccttggtttttaacaacttgttttctttctgaatcattctattgcag
|||  |||| ||||| || ||||||||||||||||| | |||||| |||||  ||||||||||||||||||| |||||||| || |||||||| || |||||||  |      |     ||  | | || || ||   | ||     |||||   |||         | |   || | || |  ||    || |    || |||| ||| || |              
GAAGTCAGGGCAGAAAGACATCTTCTACATCACGGGAAGCAGCAAAGAGCAGCTGGAGAAGTCTCCATTCCTCGAGAGGCTAACCAAGAAGAACTACGAGgtatttt------atgctgctggtggtttatccacttccattatagtgtctgagatctggaatacagcttgtgggaagtaacgctgtcgcttga----tttttttgtttgtgcag-------------

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GRMZM2G399073_T02 (Zea mays), 5'ss of exon 15
GAAACCAGGACAGAAGGATATCTTCTACATCACGGGTAACAGCAAGGAGCAATTGGAGAAGTCTCCATTCCTTGAGAGGCTTACAAAGAAGAATTATGAGgtatgattggaaaagataactacttgcttttcaaccgtccttgattagtctggtctt--attcttttcctaaggtactatccttggtttttaacaacttgttttctttctgaatcattctattgcag
||| ||||| ||||| || ||||||||| ||||||| | |||||| || ||  ||||||||||||| ||||| |||||||| || |||||||| || |||||||   || |        || || | || || ||  || ||     ||  |||||   || |   |    | |||| | |  ||   ||       ||||||| |||     |  |  | ||||||
GAAGCCAGGGCAGAAAGACATCTTCTACCTCACGGGAAGCAGCAAAGATCAGCTGGAGAAGTCTCCGTTCCTGGAGAGGCTAACCAAGAAGAACTACGAGgtatatatgtatg------ctgctggtttatccactttcattacagtgtggggtctggaatacagcttgagaagtaccaacgctgcgctt----gttttgttttgtttt---gttttgtttttgcag

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA17G37820.1 (Glycine max), 5'ss of exon 13
-GAAACCAGGACAGAAGGATATCTTCTACATCACGGGTAACAGCAAGGAGCAATTGGAGAAGTCTCCATTCCTTGAGAGGCTTACAAAGAAGAATTATGAGgtatgattggaaaag-------ataactacttgcttttcaaccg---tccttgattagtctggtcttattcttttcctaaggtactatc-cttggt-ttttaacaacttgttttctttctgaatcattctattgcag
 |||| | || |||||||||||||| ||||| || || | |||||| || ||| |||| || ||||||||||||||| ||||||  ||||| |||| ||||||   |||  ||  |        | | || ||||| |   |      ||  | |  |   | | |||  | || | || |||    ||   ||  | | ||   | | | ||||||||   | |   |  |      
TGAAAGCTGGGCAGAAGGATATCTTTTACATAACTGGAACCAGCAAAGAACAACTGGAAAACTCTCCATTCCTTGAGCGGCTTAAGAAGAAAAATTTTGAggtgcaatttaaattgtttgatttttattatttgctctattattttgttctctaaaaacattagcctttctattctgctgaggggtgatgatttaatgtcttctaagcgtattttcttttcaatttcctaca------

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA14G40320.1 (Glycine max), 5'ss of exon 13
GAAACCAGGACAGAAGGATATCTTCTACATCACGGGTAACAGCAAGGAGCAATTGGAGAAGTCTCCATTCCTTGAGAGGCTTACAAAGAAGAATTATGAGgtatgattggaaaag----------ataac-----tacttgcttt-tcaaccgtcct--tgattagtctggtcttattcttttcctaaggtactatc-cttggtttttaacaacttgttttctttctgaatcattctattgcag
|||| | || |||||||||||||| ||||| || || | |||||| || ||| |||| || ||||| ||||||||| ||||||  ||||| |||| |||||||  |||  ||  |          || ||     || ||||| | | |   || ||  | |  |   | |||||  | || | || ||  |  ||   ||  | | |   || |   |||  || |||||  | |||  |   
GAAAACTGGGCAGAAGGATATCTTTTACATAACTGGAACCAGCAAAGAACAACTGGAAAACTCTCCCTTCCTTGAGCGGCTTAAGAAGAAAAATTTTGAGgtacaatttaaattgtttgatttttattacaagtatatttgctctattatttgttcttttaaaaacatttgtctttctattctgctgagagatgatgatttaatgtcttctaaatgtattttcttttgaatt-tgctacag---

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|28970695|gb|CB349728.1|CB349728
EST:     ATTGGGAGAAGTCTCCATTCCTTGAGAGGCTTACAAAGAAGAATTATGAG                         GTTATTTTCTTTACTGACCCAGTGGATGAGTACCTGATGCAATACCTGATG
genomic: ATT-GGAGAAGTCTCCATTCCTTGAGAGGCTTACAAAGAAGAATTATGAGgtatgattgg ... tctattgcagGTTATTTTCTTTACTGACCCAGTGGATGAGTACCTGATGCAATACCTGATG
EST: gi|33410302|gb|CF215929.1|CF215929
EST:     AATTGGAGAAGTCTCCATTCCTCGAGAGGCTTACAAAGAAGAATTATGAG                         GTTATTTTCTTTACTGACCCAGTGGATGAGTACCTGATGCAATACCTGATG
genomic: AATTGGAGAAGTCTCCATTCCTTGAGAGGCTTACAAAGAAGAATTATGAGgtatgattgg ... tctattgcagGTTATTTTCTTTACTGACCCAGTGGATGAGTACCTGATGCAATACCTGATG
EST: gi|161715138|gb|FC064271.1|FC064271
EST:     AATTGGAGAAGTCTCCATTCCTTGAGAGGCTTACAAAGAAGAATTATGAG                         GTTATTTTCTTTACTGACCCAGTGGATGAGTACCTGATGCAATACCTGATG
genomic: AATTGGAGAAGTCTCCATTCCTTGAGAGGCTTACAAAGAAGAATTATGAGgtatgattgg ... tctattgcagGTTATTTTCTTTACTGACCCAGTGGATGAGTACCTGATGCAATACCTGATG
EST: gi|22008983|gb|BQ794017.1|BQ794017
EST:     AATTGGAGAAGTCTCCATTCCTTGAGAGGCTTACAAAGAAGAATTATGAG                         GTTATTTTCTTTACTGACCCAGTGGATGAGTACCTGATGCAATACCTGATG
genomic: AATTGGAGAAGTCTCCATTCCTTGAGAGGCTTACAAAGAAGAATTATGAGgtatgattgg ... tctattgcagGTTATTTTCTTTACTGACCCAGTGGATGAGTACCTGATGCAATACCTGATG
EST: gi|110719823|gb|EE095290.1|EE095290
EST:     AATTGGAGAAGTCTCCATTCCTTGAGAGGCTTACAAAGAAGAATTATGAG                         GTTATTTTCTTTACTGACCCAGTGGATGAGTACCTGATGCAATACCTGATG
genomic: AATTGGAGAAGTCTCCATTCCTTGAGAGGCTTACAAAGAAGAATTATGAGgtatgattgg ... tctattgcagGTTATTTTCTTTACTGACCCAGTGGATGAGTACCTGATGCAATACCTGATG
EST: gi|294966850|gb|GW839725.1|GW839725
EST:     GGCTTACAAAGAAGAATTATGAG                         GTTATTTTCTTTACTGACCCAGTGGATGAGTACCTGATGCAATACCTGATG
genomic: GGCTTACAAAGAAGAATTATGAGgtatgattgg ... tctattgcagGTTATTTTCTTTACTGACCCAGTGGATGAGTACCTGATGCAATACCTGATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAACCAGGACAGAAGGATATCTTCTACATCACGGGTAACAGCAAGGAGCAATTGGAGAAGTCTCCATTCCTTGAGAGGCTTACAAAGAAGAATTATGAGgtatgattggaaaagataactacttgcttttcaaccgtccttgattagtctggtcttattcttttcctaaggtactatccttggtttttaacaacttgttttctttctgaatcattctattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG