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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATGgtattttcatacatcatttaacataaatttttttgatgctgtaatccaattcttcatctgagtcatgtgtttgaacataatagcctttccatgctcctaa...

Basic information

species Vitis vinifera
transcript Vv00s0225g00090.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0225g00090.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: LOC_Os04g40040.1 (Oryza sativa), 5'ss of exon 12
GTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATGgtat---tttcatacatcatttaacataaat-ttttttgatgctgtaatccaattcttcatctgagtcatgtgtttgaacataatagcctttccatgctcctaa---------------------------------------------
|||||| |||||  | || || || ||  | ||||| ||||||||||||||||||||||| | ||| || || | ||||||||||      |  |   |  ||||  | |||    || |  ||  |   | ||  ||| |   |  |        ||    |   |   |  | |  | |  ||                                              
GTATGTGTTTGGGCTCACCCATATCCCAAGGCTGGAGGACTGGCCTGTCATGCCAGTGGAACGCATCGGCTTCATGCTCATGgtaaagacctttttttttttttagaacaaagaccttctcttgtagcctttcatatctcctctttggcagacgacttctctagtttccaccgttctggtttttacagtatcagctcaaagcctgtttgtgtcttgtttaattcttttcag

upper sequence: Vv00s0225g00090.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA18G20800.1 (Glycine max), 5'ss of exon 11
GTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATGgtattttcatacatcatttaacataaatttttttgatgctgtaatccaattcttcatctgagtcatgtgtttgaacataatagcctttcca--tgctcctaa
||| ||||||||||||||||||||||||||  |||||||||||||||| ||||| ||||| | ||||||||| | ||| |||||||   ||| || |||| |  ||  |   || |      | | | ||| |     ||  | | |     || |    ||||  |     |  || |   ||
GTACGTATTTGGAGTGACACACATTCCTCGATTGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATGgtatgc-cattcaccatt-agtatttaccattctctctgcgaatttcaaatgagattcgtactaacacacttcactcgaataaacaagagaaatgttaacaa

upper sequence: Vv00s0225g00090.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA08G38990.1 (Glycine max), 5'ss of exon 11
GTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATGgtattttcatacatcatttaacataaatttttttgatgctgtaatccaattcttcatctgagtcatgtgtttgaacataatagcctt---tccatgctcctaa---
||| |||||||||||||||||||||||| |  |||||||||||||||| ||||| ||||| | ||||||||| | ||| |||||||  | || || |||| |   |     |||   |  || |    | ||| ||||  ||||     |  |  ||||   |   ||    |  |   |  | |   
GTACGTATTTGGAGTGACACACATTCCTAGATTGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATGgtatgct-attcaccatt-agtttgtgcctttaccactctttg---cgatt-ttcaaatgagattcatactgaaacacttttcactcaaatgtacaatattgaaga

upper sequence: Vv00s0225g00090.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA02G04360.1 (Glycine max), 5'ss of exon 11
GTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATGgtattttcatacatcatttaacataaatttttttgatgctgtaatccaattcttcatctgagtcatgtgtttgaacataatagcctttccatgctcctaa--
||| || |||||  | ||||||||||| ||  ||||||||||||| || ||||||||||| | |||||| |||| ||| ||||||||  ||  ||  | ||| | ||  |  ||   || || |      |    |    ||||     | ||  |  |  ||| | |    | | |  | |  
GTACGTGTTTGGTATAACACACATTCCCCGATTGGAAGACTGGCCAGTTATGCCAGTGGAACGCATTGGCTTTATGCTTATGgtattc-cactcaa-agttagcgtatttcattgccattctttctgtgcaaaaatagagtgagattcatattgaactactataacatgcttagggttatcaca

upper sequence: Vv00s0225g00090.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: PP1S9_129V6.2 (Physcomitrella patens), 5'ss of exon 6
GTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATGgtattttcatacatcattta----------acataaatttttttgatgctgtaatccaattcttcatctgagtcatgtgtttgaacataatagcctttccatgctcctaa-----------------------------------------------
||||||||||||||| || ||||| ||| | |||||||| ||||| || ||||| |||||||||||||| || ||  |  ||||   |  |    |  | ||          |  || | |  ||  |   |   | ||| |  |   | |  ||    |  ||| | | | ||| |||    | || || |                                               
GTATGTATTTGGAGTCACTCACATACCTAGACTGGAAGATTGGCCAGTTATGCCTGTGGAGCACATTGGATTCAGTTTGGTGgttagtgtacctcttgtctatatacccgaaagctagagtccttgaaaaattctacccattggtctgtttctgttgaat-cttggata-agtagtcttaa-gtacttctgaagccgtgcactaacatagaaaaattgactggttttgatctggtacag

upper sequence: Vv00s0225g00090.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: PP1S26_107V6.1 (Physcomitrella patens), 5'ss of exon 10
GTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATGgtattttcata--catcattt---aacataaatttttttgatgctgtaatcca---attcttca-------tctgagtcatgtg----tttgaacataat-agcctttccatgctcctaa-------------------------------------------------------------------------------
|||||| ||||| ||||| ||| | ||||| || ||||| |||||||||||||| ||||||||| |||| || |  ||  |||||||    ||  |  |  ||     | |||||    ||||| | | |  |     |||||| |       ||| |||  ||||    || ||   || | | ||  | |  | |  | |                                                                               
GTATGTCTTTGGTGTGACGCACGTCCCTCGTCTTGAAGATTGGCCTGTCATGCCTGTGGAGCACGTTGGCTTCAAACTTCTGgtattcctctaacctgcgcttcgaggcttaaatacagttgattcagcatcctctacattcttaaatacagttcttagttctgtgattcttcgagtttactcatccagttcgggttattcagtgcatgctgatcactaaaattatccatagctcacagcgttatgtcttgtactgacttgatggtattgacgtgttgcag

upper sequence: Vv00s0225g00090.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: PP1S178_54V6.1 (Physcomitrella patens), 5'ss of exon 13
GTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATGgtattttcatacatcattt---aacataaatttttttgatgctgtaatccaattcttcatctgagtcatgtgtttgaacataatagcctttccatgctcctaa--------------------------------------------
||||||||||||||| || ||||||||| | || ||||||||||| || ||||| |||||||||||||| || ||  | |||||   |   |   || | |   ||| |     | |    |||   | |   |   | | | |    | ||| ||| || |   |    |   ||||||||                                               
GTATGTATTTGGAGTTACTCACATTCCTAGACTTGAAGACTGGCCAGTAATGCCTGTGGAGCACATTGGATTCAGTTTGATGgtgagtatgtctgtcgtgtttaaaccttgcactatgcactgcaacagtaagaccttgcttattgaac-tgtttttaaagaatcttagatacacatgctccattcatctgaaacagtggtataatatggttgcgttgttttgatacag

upper sequence: Vv00s0225g00090.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: EFJ13052 (Selaginella moellendorffii), 5'ss of exon 10
GTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATGgtattttcatacatcatttaacataaatttttttgatgctgtaatccaattcttcatctgagtcatgtgtttgaacataatagcctttccatgctcctaa
||| |||||||||||||||||||| ||| | || || || ||||| || ||||||||||||| ||| || || |  |||| ||||         ||| |  | |     ||  | ||  || |  | | | |  |  ||  |  ||  |                                 
GTACGTATTTGGAGTGACACACATACCTAGGCTCGAGGATTGGCCCGTGATGCCAGTGGAGCGCATCGGATTCACACTCACGgta------ggaatcctcgatcgc---ttgctatggcgccgctaacgagtgatcgat--ggatcgcgcag------------------------------

upper sequence: Vv00s0225g00090.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: EFJ14061 (Selaginella moellendorffii), 5'ss of exon 10
GTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATGgtattttcatacatcatttaacataaatttttttgatgctgtaatccaattcttcatctgagtcatgtgtttgaacataatagcctttccatgctcctaa
||| |||||||||||||||||||| ||| | || || || ||||| || ||||||||||||| ||| || || |  |||| ||||         ||| |  | |     ||  | ||  || |  | | | |  |  ||  |  |   |                                 
GTACGTATTTGGAGTGACACACATACCTAGGCTCGAGGATTGGCCCGTGATGCCAGTGGAGCGCATCGGATTCACACTCACGgta------ggaatcctcgatcgc---ttgctatggcgccgctaacgagtgatcgat--ggattgcgcag------------------------------

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|110429682|gb|EC996183.1|EC996183
EST:     TGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATG                         CCTCATGGGTTCTTTAACTGCTCACCAGCGGTGGATGTCCCTCCCAGCACA
genomic: TGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATGgtattttcat ... tgtggcacagCCTCATGGGTTCTTTAACTGCTCACCAGCGGTGGATGTCCCTCCCAGCACA
EST: gi|83275167|gb|DV939263.1|DV939263
EST:     TGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATG                         CCTCATGGGTTCTTTAACTGCTCACCAGCGGTGGATGTCCCTCCCAGCACA
genomic: TGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATGgtattttcat ... tgtggcacagCCTCATGGGTTCTTTAACTGCTCACCAGCGGTGGATGTCCCTCCCAGCACA
EST: gi|71874908|gb|DT023963.1|DT023963
EST:     TGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATG                         CCTCATGGGTTCTTTAACTGCTCACCAGCGGTGGATGTCCCTCCCAGCACA
genomic: TGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATGgtattttcat ... tgtggcacagCCTCATGGGTTCTTTAACTGCTCACCAGCGGTGGATGTCCCTCCCAGCACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATGgtattttcatacatcatttaacataaatttttttgatgctgtaatccaattcttcatctgagtcatgtgtttgaacataatagcctttccatgctcctaa

- - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctttcc