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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGCTCATGGGAGTGCAGTAGGGCTTCCAACTGAGGATGACATGGGCAACAGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGGgtgaatttctcttcctgattttatttcttttatgaaatttttacatattataacctttatacacccaggatgtcccttcacaagtttgattcctttttga...

Basic information

species Vitis vinifera
transcript Vv08s0056g00200.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0056g00200.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os01g60190.2 (Oryza sativa), 5'ss of exon 2
AGGCTCATGGGAGTGCAGTAGGGCTTCCAACTGAGGATGACATGGGCAACAGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGGgtgaatttctcttcctgattttatttcttttatgaaatttttacatattataacctttatacacccaggatgtcccttcacaagtttgattcctttttga-----
|||||||||| |  || || || ||||| |  || ||||||||||||||||| ||||| || || ||||||||||||||||| ||||| | |||||| |||| |  |  | ||     ||||  ||| |||  |||            ||||   |  || ||| | | ||||    | |||||  || ||| || |        
AGGCTCATGGAACAGCTGTTGGTCTTCCTAGCGAAGATGACATGGGCAACAGCGAAGTGGGTCACAATGCTCTTGGTGCTGGTCGCATTTTTGCTCAGGGgtaagctgttgttg--agttttgattcatttgggaa-----------ctataggttggat-cactctgcatgttttgtgacaagcgtgtttcattctcactgtag

upper sequence: Vv08s0056g00200.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os05g40420.1 (Oryza sativa), 5'ss of exon 3
AGGCTCATGGGAGTGCAGTAGGGCTTCCAACTGAGGATGACATGGGCAACAGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGGgtgaatttctcttcctgattttatttcttttatgaaatttttacatattataacctttatacacccaggatgtcccttcacaagttt---gattcctttttga-
|||||||||| |  || || || || ||  |||| ||||||||||| |||||||| ||||| ||||| || ||||||||||| || || | |||||||||||  || | ||| |  | | |  ||| | |||  | | | | |    |||||| || |  |   |||  | ||   | |    ||||    |   ||| ||   
AGGCTCATGGAACAGCTGTTGGTCTCCCTTCTGATGATGACATGGGTAACAGTGAGGTTGGGCATAACGCACTTGGTGCTGGTCGGATTTTTGCTCAAGGgtacatgtttctcctggttctcttttttattagcacactgtca---gttataatctgtggatggccaaaaagtat-tgcgtttgtttctaaaggtcttattaca

upper sequence: Vv08s0056g00200.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G003385_T02 (Zea mays), 5'ss of exon 3
AGGCTCATGGGAGTGCAGTAGGGCTTCCAACTGAGGATGACATGGGCAACAGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGGgtgaatttctcttcctgattttatttcttttatgaaatttttacatattataacctttatacacccaggatgtcccttcacaagtttgattcctttttga--------
|||||||||| |  || || || || ||| |||| |||||||||||||||||||||||||| || ||||| ||||||||||| || || |  || |||||||   ||          ||||  ||  ||||   ||  | ||   | || ||||  | || | |   || |      |  ||  |     ||  | | ||        
AGGCTCATGGAACAGCTGTGGGTCTCCCATCTGATGATGACATGGGCAACAGTGAAGTTGGTCACAATGCACTTGGTGCTGGTCGGATTTTCGCCCAAGGgtatgttagat------atttagttatttttggaaatatgttttctgttgtaac--taatgcgctgtggtttcaatattgcatttgaacatcaatgtcgaaagctata

upper sequence: Vv08s0056g00200.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM5G833389_T02 (Zea mays), 5'ss of exon 3
AGGCTCATGGGAGTGCAGTAGGGCTTCCAACTGAGGATGACATGGGCAACAGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGGgtgaatttctcttcctgattttatttcttttatgaaatttttacatattataacctttatacacccaggatgtcccttcacaagtttgattcctttttga------
|||||||||| |  || || || || ||| |||| |||||||||||||||||||||||||| || ||||| ||||||||||| || || |  || |||||||  || |    |  | ||||| ||| ||  |   |  ||||   |  ||  |   | ||  ||    |||||   |||| |  ||  |||      |||      
AGGCTCATGGAACAGCTGTGGGCCTCCCATCTGATGATGACATGGGCAACAGTGAAGTTGGTCACAATGCACTTGGTGCTGGTCGAATTTTCGCCCAAGGgt--atgttagatgtttattttgttttttggaaatatgttttctgttgtaacaatgtgatgtact---gatgtggtttca-atattgcatttgaacatgatgccca

upper sequence: Vv08s0056g00200.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA18G45120.1 (Glycine max), 5'ss of exon 3
AGGCTCATGGGAGTGCAGTAGGGCTTCCAACTGAGGATGACATGGGCAACAGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGGgtgaattt---ctcttcctgattttatttcttttatgaaatttttacatattataacctttatacacccaggatgtcccttcacaagtttgattcctttttga--
 ||||||||| | ||| ||||| |||||||| || |||||||||||||| ||||||||||| || ||||| ||||| ||||| ||||||| |||||| |||| || |    ||   |    ||||   ||| ||  |     | |  || |||  ||||   ||     |   ||     || || |   |     ||  |||  
GGGCTCATGGTACTGCTGTAGGACTTCCAACAGAAGATGACATGGGCAATAGTGAAGTTGGTCACAATGCCCTTGGGGCTGGTCGCATATTTGCTCAGGGgtaaactaaaactagcctctctttttcatctatttggccccctgtgtatgttactacctaggtat---taaattgggg--tcgcagggccgtcaatttagtgata

upper sequence: Vv08s0056g00200.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA09G40690.1 (Glycine max), 5'ss of exon 2
AGGCTCATGGGAGTGCAGTAGGGCTTCCAACTGAGGATGACATGGGCAACAGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGGgtgaatttctcttcctgattttatttcttttatgaaatttttacatattataacctttatacacccaggatgtcccttcacaagt-ttgattcctttttga
 ||||||||| |  || ||||| |||||||| || ||||||||||| || ||||||||||| || ||||||||||| ||||| ||||||| |||||| |||| || |     |      | | |||| | |||            |  | | ||    |       |   |||     ||    | | ||||      |  
GGGCTCATGGTACCGCTGTAGGCCTTCCAACAGAAGATGACATGGGTAATAGTGAAGTTGGTCACAATGCTCTTGGGGCTGGTCGCATATTTGCTCAGGGgtaaactaaaactagcctctctttttcatctatttggccccatgcttatgttactaccaaggttttaaattgtggtcgcatggctgtcgatttagggata-

upper sequence: Vv08s0056g00200.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: PP1S145_164V6.2 (Physcomitrella patens), 5'ss of exon 3
AGGCTCATGGGAGTGCAGTAGGGCTTCCAACTGAGGATGACATGGGCAACAGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGGgtgaatttctcttcctgattttatttcttttatgaaatttttacatattataacctttatacacccaggatgtcccttcacaagtttgattcctttttga------
| || |||||   ||| |||||||| || || ||||| |||||||| |||||||| ||||||||||||||| | ||||| || ||||| | |   |||||||     | || | ||| | |  |   |   || |  ||  |    || ||       |||     |  ||| |  ||   ||   |   ||  | | |       
AAGCCCATGGAGCTGCGGTAGGGCTACCTACGGAGGAGGACATGGGTAACAGTGAGGTTGGCCATAATGCTTTGGGTGCAGGCCGCATTTTTAAGCAAGGgta----tgtcatgctggtctagtaaatcagat-atcttagtttccatcatgggtgcgatatcgagacaatggct-ttggtaatcgttgctcactgtaggctagtt

upper sequence: Vv08s0056g00200.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ14459 (Selaginella moellendorffii), 5'ss of exon 2
AGGCTCATGGGAGTGCAGTAGGGCTTCCAACTGAGGATGACATGGGCAACAGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGGgtgaatttctcttcctgatttt-atttcttttatgaaatttttacatattataacctttatacacccaggatgtcccttcacaagtttgattcctttttga
|||| |||||   ||| || || |||||||| |||||||||||||| || ||||| ||||| || |||||| | || || ||||| || | |||||||||||   ||      | |   | | |  | | | |     |||||   | ||   |  |                                            
AGGCGCATGGACCTGCCGTCGGCCTTCCAACCGAGGATGACATGGGAAATAGTGAGGTTGGTCACAATGCTTTGGGAGCGGGACGTATTTTTGCTCAAGGgtattttgtagagcttctctgtgagctttctcacagtgtttttgt-tcttcccatttcag-----------------------------------------

upper sequence: Vv08s0056g00200.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ26058 (Selaginella moellendorffii), 5'ss of exon 2
AGGCTCATGGGAGTGCAGTAGGGCTTCCAACTGAGGATGACATGGGCAACAGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGGgtgaatttctcttcctgattttatttcttttatgaaatttttacatattataacctttatacacccaggatgtcccttcacaagtttgattcctttttga
|||| |||||   ||| || || |||||||| |||||||||||||| || ||||| ||||| || |||||| | || || ||||| || | ||||||||||| | ||| |    ||  | |  |    ||| | | | ||||   | || |  || ||  |                                       
AGGCGCATGGACCTGCCGTCGGCCTTCCAACCGAGGATGACATGGGAAATAGTGAGGTTGGTCACAATGCTTTGGGAGCGGGACGTATTTTTGCTCAAGGgt-attttgtagagcttctctcgtgagctttctcacagtttt-tttgttcttcccatttcag--------------------------------------

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|110418028|gb|EC984140.1|EC984140
EST:     AGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATTTGCTCAAGG                         TGCAAAGCTTGTTGATTTTGCTCTGGACTCTGGGAAGATCTATGAGGGAGA
genomic: AGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGGgtgaatttct ... ctgaatgtagTGCAAAGCTTGTTGATTTTGCTCTGGACTCTGGGAAGATCTATGAGGGAGA
EST: gi|71858573|gb|DT007628.1|DT007628
EST:     AGTGGAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGG                         TGCAAAGCTTGTTGATTTTGCTCTGGACTCTGGGAAGATCTATGAGGGAGA
genomic: AGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGGgtgaatttct ... ctgaatgtagTGCAAAGCTTGTTGATTTTGCTCTGGACTCTGGGAAGATCTATGAGGGAGA
EST: gi|110732942|gb|EE108671.1|EE108671
EST:     AGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGG                         TGCAAAGCTTGTTGATTTTGCTCTGGACTCTGGGAAGATCTATGAGGGAGA
genomic: AGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGGgtgaatttct ... ctgaatgtagTGCAAAGCTTGTTGATTTTGCTCTGGACTCTGGGAAGATCTATGAGGGAGA
EST: gi|294965964|gb|GW839303.1|GW839303
EST:     AGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGG                         TGCAAAGCTTGTTGATTTTGCTTTGGACTCTGGGAAGATCTATGAGGGAGA
genomic: AGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGGgtgaatttct ... ctgaatgtagTGCAAAGCTTGTTGATTTTGCTCTGGACTCTGGGAAGATCTATGAGGGAGA
EST: gi|110731939|gb|EE106787.1|EE106787
EST:     AGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATTTGCTCAAGG                         TGCAAAGCTTGTTGATTTTGCTCTGGACTCTGGGAAGATCTACGAGGGAGA
genomic: AGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGGgtgaatttct ... ctgaatgtagTGCAAAGCTTGTTGATTTTGCTCTGGACTCTGGGAAGATCTATGAGGGAGA
EST: gi|71856163|gb|DT005218.1|DT005218
EST:     AGTTAAGTTGGCCATAATGCTCTGGGTGCTGGACGCATATTTGCTCAAGG                         TGCAAAGCTTGTTGATTTTGCTCTGGA
genomic: AGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGGgtgaatttct ... ctgaatgtagTGCAAAGCTTGTTGATTTTGCTCTGGA
EST: gi|110720962|gb|EE097416.1|EE097416
EST:     AGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGG                         TGCAAAGCTTGTTGATTTTGCTCTGGACTCTGGGAAGATCTATGAGGGAGA
genomic: AGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGGgtgaatttct ... ctgaatgtagTGCAAAGCTTGTTGATTTTGCTCTGGACTCTGGGAAGATCTATGAGGGAGA
EST: gi|161715825|gb|FC067428.1|FC067428
EST:     AGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATTTGCTCAAGG                         TGCAAAGCTTGTTGATTTTGCTCTGGACTCTGGGAAGATCTATGAGGGAGA
genomic: AGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGGgtgaatttct ... ctgaatgtagTGCAAAGCTTGTTGATTTTGCTCTGGACTCTGGGAAGATCTATGAGGGAGA
EST: gi|110718255|gb|EE094880.1|EE094880
EST:     AGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGG                         TGCAAAGCTTGTTGATTTTGCTCTGGACTCTGGGAAGATCTATGAGGGAGA
genomic: AGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGGgtgaatttct ... ctgaatgtagTGCAAAGCTTGTTGATTTTGCTCTGGACTCTGGGAAGATCTATGAGGGAGA
EST: gi|110721142|gb|EE097804.1|EE097804
EST:     AGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGG                         TGCAAAGCTTGTTGATTTTGCTCTGGACTCTGGGAAGATCTATGAGGGAGA
genomic: AGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGGgtgaatttct ... ctgaatgtagTGCAAAGCTTGTTGATTTTGCTCTGGACTCTGGGAAGATCTATGAGGGAGA
EST: gi|71855635|gb|DT004690.1|DT004690
EST:     AGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCGTATATGCTCAAGG                         TGCAAAGCTTGTTGATTTTGCTCTGGACTCTGGGAAGATCTGTGAGGGAGA
genomic: AGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGGgtgaatttct ... ctgaatgtagTGCAAAGCTTGTTGATTTTGCTCTGGACTCTGGGAAGATCTATGAGGGAGA
EST: gi|110723612|gb|EE101122.1|EE101122
EST:     AGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGG                         TGCAAAGCTTGTTGATTTTGCTCTGGACTCTGGGAAGATCTATGAGGGAGA
genomic: AGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGGgtgaatttct ... ctgaatgtagTGCAAAGCTTGTTGATTTTGCTCTGGACTCTGGGAAGATCTATGAGGGAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGCTCATGGGAGTGCAGTAGGGCTTCCAACTGAGGATGACATGGGCAACAGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGGgtgaatttctcttcctgattttatttcttttatgaaatttttacatattataacctttatacacccaggatgtcccttcacaagtttgattcctttttga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgaaa