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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTATATTTCGGTTGGGCTGGATTATCAAAACAGGGTGTCTACAAGATGGTGATGAGCATTGGCTGGAATCCATATTTCAACAACACCGAGAAAACTATAgtgagtgcaacttggactgtaaaggtggaccttccaaatattttttctctctgtttttctaaatctcatttacaattttag

Basic information

species Vitis vinifera
transcript Vv00s0181g00130.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0181g00130.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: LOC_Os10g32730.1 (Oryza sativa), 5'ss of exon 9
AGTATATTTCGGTTGGGCTGGATTATCAAAACAGGGTGTCTACAAGATGGTGATGAGCATTGGCTGGAATCCATATTTCAACAACACCGAGAAAACTATAgtgagtgcaacttggactgtaaaggtggaccttccaaatattttttctctctgtttttctaaatctcatttacaattttag
 ||||| || || ||||||||| | ||||  |  ||| | |  |||||||| ||||||||||||||||| || |||||  | ||||| ||||| ||||| |||||||   ||       |     |  |  ||    |  |   |    |   || |||||||   ||||    |      
GGTATACTTTGGCTGGGCTGGACTTTCAACGCGAGGTATATTTAAGATGGTCATGAGCATTGGCTGGAACCCTTATTTTGATAACACGGAGAAGACTATTgtgagtgtttctcaatacatcccctttcatgtttagtacttcagtatattagtttattctaaaagacattggtcacag---

upper sequence: Vv00s0181g00130.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G027115_T02 (Zea mays), 5'ss of exon 9
AGTATATTTCGGTTGGGCTGGATTATCAAAACAGGGTGTCTACAAGATGGTGATGAGCATTGGCTGGAATCCATATTTCAACAACACCGAGAAAACTATAgtgagtgcaacttggactgtaaaggtggaccttccaaatattttttctctctgtttttctaaatctcatttacaattttag---------
 ||||| || || ||||| ||| | ||||  |  ||| | || |||||||| ||||||||||||||||| ||||||||| |||| |||||||| ||  ||||| |||   ||   ||   | | |    || | ||   ||| ||   ||     ||     |  |  ||   ||    |          
GGTATACTTTGGCTGGGCAGGACTTTCAACGCGTGGTATATATAAGATGGTTATGAGCATTGGCTGGAACCCATATTTCGACAATACCGAGAAGACAGTAgtgggtgtt-ctctcacaccacatgcattccatgcagccattcttctactactacttctactactttgttctaaacgccatccactgtag

upper sequence: Vv00s0181g00130.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA08G06330.1 (Glycine max), 5'ss of exon 3
AGTATATTTCGGTTGGGCTGGATTATCAAAACAGGGTGTCTACAAGATGGTGATGAGCATTGGCTGGAATCCATATTTCAACAACACCGAGAAAACTATAgtgagtgcaacttggactgtaaaggtggaccttccaaatat---tttttctctctgtttttctaaatctcatttacaattttag-----
||| ||||| | |||||||||||| |||      ||||| |  || ||||||||||||||||| |||||||| |||||||||||||  ||||| |||||||| ||||    ||  |||| | |       | |||| ||||   |  ||  || ||  ||| |  ||    | | |  ||||       
AGTTTATTTTGATTGGGCTGGATTGTCAGCCAGAGGTGTTTTTAAAATGGTGATGAGCATTGGTTGGAATCCTTATTTCAACAACAAAGAGAAGACTATAgtaagtg----ttttactgcaca-------cctccagatataactacttgcctgtgaatttttgtattatctatgcctttttgttgtag

upper sequence: Vv00s0181g00130.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA07G30970.1 (Glycine max), 5'ss of exon 8
AGTATATTTCGGTTGGGCTGGATTATCAAAACAGGGTGTCTACAAGATGGTGATGAGCATTGGCTGGAATCCATATTTCAACAACACCGAGAAAACTATAgtgagtgcaacttggactgtaaaggtggaccttccaaatattttttctctctgtttttctaaatctcatttacaattttag-----
 || ||||| |||||||||||||| ||   |   ||||| |  || ||||||||||||||||| ||||||||||||||||||||||  || ||  ||||||| |||||    |  | | || |  |  | ||    |  | | |||  || ||  |||  | ||    | | |  ||||       
TGTTTATTTTGGTTGGGCTGGATTGTCGGCAAGAGGTGTTTTTAAAATGGTGATGAGCATTGGTTGGAATCCATATTTCAACAACAAAGAAAAGGCTATAgtaagtgc----tttattatatacctccagct----ataactatttacctatgaattttcatattatctatgcctttttgtttcag

upper sequence: Vv00s0181g00130.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: AT4G21470.1 (Arabidopsis thaliana), 5'ss of exon 8
AGTATATTTCGGTTGGGCTGGATTATCAAAACAGGGTGTCTACAAGATGGTGATGAGCATTGGCTGGAATCCATATTTCAACAACACCGAGAAAACTATAgtgagtgcaacttggactgtaaaggtggaccttccaaatattttttctctctgtttttctaaatctcatt-tacaattttag
||| || || |||||||| || ||  ||||    |||||||  || ||||| ||||||||||| |||||||| |||||||| ||||  ||||||||||| |||||| ||  |   |   | ||     |   |      | |  ||   ||| |   | ||  | |  || || |       
AGTGTACTTTGGTTGGGCAGGCTTGGCAAAGAGAGGTGTCTTTAAAATGGTCATGAGCATTGGTTGGAATCCTTATTTCAATAACAAGGAGAAAACTATTgtgagttca--taaaaagttcaaacaaaattcttactccagtggttgcttctttaactttagcttttgttatatag------

upper sequence: Vv00s0181g00130.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: PP1S79_94V6.1 (Physcomitrella patens), 5'ss of exon 8
AGTATATTTCGGTTGGGCTGGATTATCAAAACAGGGTGTCTACAAGATGGTGATGAGCATTGGCTGGAATCCATATTTCAACAACACCGAGAAAACTATAgtgagtgcaacttggactgtaaa-ggtggaccttccaaatattttttctctctgtttttctaaatctcatttacaattttag----------------------------------------------
  | ||  | || |||||||| ||  | ||   ||||||||||||||||||||||||| |||| ||||| || || ||| ||||||  |||||  |  | ||||||     ||    ||||   |    ||  ||   |||| | | | |   ||     || |  ||||| | | | |                                                 
GATCTACATTGGCTGGGCTGGCTTGGCCAATAGGGGTGTCTACAAGATGGTGATGAGCGTTGGATGGAACCCCTACTTCGACAACAAAGAGAAGGCAGTGgtgagt----ttttatgtgtatttgacacactgtcgtgatatatgtgcac---gtagccgtagagatcattcatactatcgaccaatttgataaactctccccatgctgttttatttgtaacatatag

upper sequence: Vv00s0181g00130.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: EFJ22483 (Selaginella moellendorffii), 5'ss of exon 8
AGTATATTTCGGTTGGGCTGGATTATCAAAACAGGGTGTCTACAAGATGGTGATGAGCATTGGCTGGAATCCATATTTCAACAACACCGAGAAAACTATAgtgagtgcaacttggac---tgtaaaggtggaccttccaaatattttttctctctgtttttctaaatctcatttacaattttag
  | ||| | || |||||  |  | ||  |  |||| || |  ||||||||||||||| | |||||||||||||||||| ||||  | || |||||  | || ||||||| ||  ||   ||| | |   ||   || |  |  |  | ||                                 
GATTTATCTAGGCTGGGCGAGGCTTTCGGACAAGGGAGTGTTTAAGATGGTGATGAGCGTCGGCTGGAATCCATATTTCGACAATGCAGAAAAAACAGTGgtaagtgcaagttttacgtttgttaggaaagaagctc-agttgctgctactacag-----------------------------

upper sequence: Vv00s0181g00130.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: EFJ11705 (Selaginella moellendorffii), 5'ss of exon 8
AGTATATTTCGGTTGGGCTGGATTATCAAAACAGGGTGTCTACAAGATGGTGATGAGCATTGGCTGGAATCCATATTTCAACAACACCGAGAAAACTATAgtgagtgcaacttggac---tgtaaaggtggaccttccaaatattttttctctctgtttttctaaatctcatttacaattttag
  | ||| | || |||||  |  | ||  |  |||| || |  ||||||||||||||| | |||||||||||||||||| ||||  | ||||||||  | || ||||||| ||  ||   ||| | |  | | ||  ||  |  |  | ||                                 
GATTTATCTAGGCTGGGCGAGGCTTTCGGACAAGGGAGTGTTTAAGATGGTGATGAGCGTCGGCTGGAATCCATATTTCGACAATGCAGAGAAAACAGTGgtaagtgcaagttttacgtttgttaggaagaagct--cagttgctgctactacag-----------------------------

upper sequence: Vv00s0181g00130.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: EFJ19251 (Selaginella moellendorffii), 5'ss of exon 8
AGTATATTTCGGTTGGGCTGGATTATCAAAACAGGGTGTCTACAAGATGGTGATGAGCATTGGCTGGAATCCATATTTCAACAACACCGAGAAAACTA-TAgtga-gtgcaacttggac---tgtaaaggtggaccttccaaatattttttctctctgtttttctaaatctcatttacaattttag
      | | || |||||  |  | ||  |  |||| || |  ||||||||||||||| | |||||||||||||||||| ||||  | || ||||  | | || | |||||| ||  ||   ||| | |  |||   || |  |  |  | ||                                 
------TCTAGGCTGGGCGAGGCTTTCGGACAAGGGAGTGTTTAAGATGGTGATGAGCGTCGGCTGGAATCCATATTTCGACAATGCAGAAAAAAACAGTGGTAAAgtgcaagttttacgtttgttaggaaggaagctc-aggtgctgctactacag-----------------------------

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|122688581|gb|EC921621.1|EC921621
EST:     TGATGAGCATTGGCTGGAATCCATATTTCAACAACACTGAGAAAACTATA                         GAGCCATGGCTGCTTCACGAATTTGATGAGGATTTCTATGGCGAGGAATTA
genomic: TGATGAGCATTGGCTGGAATCCATATTTCAACAACACCGAGAAAACTATAgtgagtgcaa ... acaattttagGAGCCATGGCTGCTTCATGAATTTGATGAGGATTTCTATGGCGAGGAATTA
EST: gi|122688643|gb|EC920309.1|EC920309
EST:     TGATGAGCATTGGCTGGAATCCATATTTCAACAACACTGAGAAAACTATA                         GAGCCATGGCTGCTTCACGAATTTGATGAGGATTTCTATGGCGAGGAATTA
genomic: TGATGAGCATTGGCTGGAATCCATATTTCAACAACACCGAGAAAACTATAgtgagtgcaa ... acaattttagGAGCCATGGCTGCTTCATGAATTTGATGAGGATTTCTATGGCGAGGAATTA
EST: gi|122688583|gb|EC921683.1|EC921683
EST:     TGATGAGCATTGGCTGGAATCCATATTTCAACAACACTGAGAAAACTATA                         GAGCCATGGCTGCTTCACGAATTTGATGAGGATTTCTATGGCGAGGAATTA
genomic: TGATGAGCATTGGCTGGAATCCATATTTCAACAACACCGAGAAAACTATAgtgagtgcaa ... acaattttagGAGCCATGGCTGCTTCATGAATTTGATGAGGATTTCTATGGCGAGGAATTA
EST: gi|122688609|gb|EC923003.1|EC923003
EST:     TGATGAGCATTGGCTGGAATCCATATTTCAACAACACTGAGAAAACTATA                         GAGCCATGGCTGCTTCACGAATTTGATGAGGATTTCTATGGCGAGGAATTA
genomic: TGATGAGCATTGGCTGGAATCCATATTTCAACAACACCGAGAAAACTATAgtgagtgcaa ... acaattttagGAGCCATGGCTGCTTCATGAATTTGATGAGGATTTCTATGGCGAGGAATTA
EST: gi|122688550|gb|EC920300.1|EC920300
EST:     TGATGAGCATTGGCTGGAATCCATATTTCAACAACACTGAGAAAACTATA                         GAGCCATGGCTGCTTCACGAATTTGATGAGGATTTCTATGGCGAGGAATTA
genomic: TGATGAGCATTGGCTGGAATCCATATTTCAACAACACCGAGAAAACTATAgtgagtgcaa ... acaattttagGAGCCATGGCTGCTTCATGAATTTGATGAGGATTTCTATGGCGAGGAATTA
EST: gi|122688646|gb|EC920398.1|EC920398
EST:     TGATGAGCATTGGCTGGAATCCATATTTCAACAACACTGAGAAAACTATA                         GAGCCATGGCTGCTTCACGAATTTGATGAGGATTTCTATGGCGAGGAATTA
genomic: TGATGAGCATTGGCTGGAATCCATATTTCAACAACACCGAGAAAACTATAgtgagtgcaa ... acaattttagGAGCCATGGCTGCTTCATGAATTTGATGAGGATTTCTATGGCGAGGAATTA
EST: gi|122688569|gb|EC921114.1|EC921114
EST:     TGATGAGCATTGGCTGGAATCCATATTTCAACAACACTGAGAAAACTATA                         GAGCCATGGCTGCTTCACGAATTTGATGAGGATTTCTATGGCGAGGAATTA
genomic: TGATGAGCATTGGCTGGAATCCATATTTCAACAACACCGAGAAAACTATAgtgagtgcaa ... acaattttagGAGCCATGGCTGCTTCATGAATTTGATGAGGATTTCTATGGCGAGGAATTA
EST: gi|122688616|gb|EC923325.1|EC923325
EST:     TGATGAGCATTGGCTGGAATCCATATTTCAACAACACTGAGAAAACTATA                         GAGCCATGGCTGCTTCACGAATTTGATGAGGATTTCTATGGCGAGGAATTA
genomic: TGATGAGCATTGGCTGGAATCCATATTTCAACAACACCGAGAAAACTATAgtgagtgcaa ... acaattttagGAGCCATGGCTGCTTCATGAATTTGATGAGGATTTCTATGGCGAGGAATTA
EST: gi|122688561|gb|EC920714.1|EC920714
EST:     TGATGAGCATTGGCTGGAATCCATATTTCAACAACACTGAGAAAACTATA                         GAGCCATGGCTGCTTCACGAATTTGATGAGGATTTCTATGGCGAGGAATTA
genomic: TGATGAGCATTGGCTGGAATCCATATTTCAACAACACCGAGAAAACTATAgtgagtgcaa ... acaattttagGAGCCATGGCTGCTTCATGAATTTGATGAGGATTTCTATGGCGAGGAATTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTATATTTCGGTTGGGCTGGATTATCAAAACAGGGTGTCTACAAGATGGTGATGAGCATTGGCTGGAATCCATATTTCAACAACACCGAGAAAACTATAgtgagtgcaacttggactgtaaaggtggaccttccaaatattttttctctctgtttttctaaatctcatttacaattttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA