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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAGgtactcttcattgtgggtgtgagttgtgtgactttatacatgcttttatttggtcacagtatcttttgcagatgccaatctgtaactagtttttatctgt...

Basic information

species Vitis vinifera
transcript Vv18s0001g12960.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g12960.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: LOC_Os08g26870.4 (Oryza sativa), 5'ss of exon 7
GTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAGgtac--tcttcattgtgggtgtgagttgtgtgactttatacatgcttttatttggtcacagtatcttttgcagatgccaatctgtaactagtttttatctgt
|| ||| |  | | ||| ||  |||  ||||| ||  |||||||||||||||| |||||||||||| | |||||||||   | ||   ||| |   |   |||      |||||   | ||   ||  |   |    |  |||  ||        |||| |  | || | |  ||| 
GTAGGTGACCATACAGAAAGTATCACCTTTGATCTAAGACCTTCAGATGCCATAAACATTGCTGTTCGCTGCAAGgtattattttgcctgttgaacttcattgctctcttttatgtctactgccatcagaggatgagagttttaccaagcagttctctg-attttgtctgtcgctg-

upper sequence: Vv18s0001g12960.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: LOC_Os08g26870.1 (Oryza sativa), 5'ss of exon 7
------------------GTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAGgtactcttca--ttgtgggtgtgagttgtgtgactttatacatgcttttatttggtcacagtatcttttgcagatgccaatctgtaactagtttttatctgt
                  || ||| |  | | ||| ||  |||  ||||| ||  |||||||||||||||| |||||||||||| | ||||||||| | ||     ||| |   |   |||      |||||   | ||   ||  |   |    |  |||  ||        |||| |  | || | |  ||| 
AAACTGCCTATACTGCAGGTAGGTGACCATACAGAAAGTATCACCTTTGATCTAAGACCTTCAGATGCCATAAACATTGCTGTTCGCTGCAAGgtattattttgcctgttgaacttcattgctctcttttatgtctactgccatcagaggatgagagttttaccaagcagttctctg-attttgtctgtcgctg-

upper sequence: Vv18s0001g12960.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G053531_T02 (Zea mays), 5'ss of exon 7
GTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAGgtactcttcat-tgtgggtgtgagttgtgtgactttatacatgcttttatttggtcacagtatcttttgcagatgccaatctgtaactagtttttatctgt-
||   | ||   | ||| | | |||  || || ||||| |||||||||||||| |||||||||||| | ||||||||| | |   | | ||    ||     ||  | ||| |   |   || |||   |     |   | ||| || |  | || |  |  |   || |       
GTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtattttctgtatatgtccttgctacatgctatttttttagtaaattgattc--ttgttattagtattgaaggtttctatgtccatatcacttgttcgaaca

upper sequence: Vv18s0001g12960.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G006468_T05 (Zea mays), 5'ss of exon 6
GTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAGgtactcttcattgtgggtgtgagttgtgtgactttatacatgcttttatttggtcacagtatcttttgcagatgccaatctgtaactagtttttatctgt-------
 | | | ||   | ||| ||| |||  || || ||||| |||||||||||||| |||||||||||| | |||||||||   ||   ||| | |||   |  ||  || |  || || ||| ||||         | | || | || ||   |   | ||     |  |||| |||       
ATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgta---tttgctgttgatgt---tcttgccacatgctaaat-cttctattactctgatttttattattcatattgaaggttttagtgcatgcttatttgtgggagca

upper sequence: Vv18s0001g12960.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G377595_T01 (Zea mays), 5'ss of exon 7
GTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAGgtactcttcat-tgtgggtgtgagttgtg-tgactttatacatgcttttatttg-gtcacagtatcttttgcagatgc-caatctgtaactagtttttatctgt
||   | ||   | ||| | |  ||  || || ||||| |||||||||||||| |||| ||||||| | ||||||||| | |   | | ||    ||     |  | | ||| |   |   || ||||  || |      ||  | || |||  |   ||||     |  |  | |   
GTCAATGATCCTACAGACAACACCACCTTCGATCTTCGGCCTTCAGATGCCATAAACACTGCTGTTCGTTGCAAGgtattttctgtatatgtccttgctacatactaatttttttagtaaattcatttttgttatctctactaatccatatgtacggactgtgg---gcgtgcaccca-

upper sequence: Vv18s0001g12960.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA17G37160.1 (Glycine max), 5'ss of exon 4
GTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAGgtactcttcattgtgggtgtgagttgtgtgactttatacatgcttttatttggtcacagtatcttttgcagatgccaatctgtaactagtttttatctgt----
|| || |||||   |||    || || ||||| ||||||||||||||||| || |||||||| || |||||||||||| | ||  ||       | || | | ||| |  ||   ||  |  ||    |  || | |||| |     ||   |   ||   | | ||||  |  |    
GTTGGAAATGAGGCAGAATATGTGAGCTTTGATCTTCGACCTTCAGATGCTATCAACATTGCAGTAAGATGCAAGgtaatatttgttaat----taaggtatttgaatacatcattggctgcatcatattgcattctcttattgctttgtttagtagttgttcgctttttcccctggtt

upper sequence: Vv18s0001g12960.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: AT1G19660.1 (Arabidopsis thaliana), 5'ss of exon 7
GTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAGgtactcttcattgtgggtgtgagttgtgtgactttatacatgcttttatttggtcacagtatcttttgcagatgccaatctgtaactagtttttatctgt----------------------------------------
|||||  || |    ||  | ||||| || || ||||| ||||| ||||| ||||| || ||||||||||||||||||   ||   |     | ||     |      || |  | |     | |    |||||   | | | ||   |   |||| ||||  | |   | ||                                          
GTGGGGGATAAGTCGGATTGTGTCAGCTTCGATCTTCGTCCTTCTGATGCAATTAATATAGCTGTTAGATGCAAGgtatagttatattaccatatgctcaattctttcttttctaggggcacagtca--cacagaggcctctccatgagatcatct-taaccggatacaaactacgtgatcactatgaaaaatggttttaatcctcactctttag

upper sequence: Vv18s0001g12960.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: AT1G75380.3 (Arabidopsis thaliana), 5'ss of exon 7
GTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAGgtact-cttcattgtgggtgtgagttgtgtgacttta-tacatgcttttatttggtcacagtatcttttgcagatgccaatctgtaactagtttttatctgt
||||||||||     ||| | ||||| ||||| ||| | ||||||||||| || || || |||||||||||||||||| | | |   | ||    | | |    |||  | | ||||    | | |||||     | |  || ||  |||  |  | ||||                
GTGGGTAATGCCTCGGAGTGTGTCAGCTTTGATCTTAGGCCTTCAGATGCAATCAATATAGCTGTTAGATGCAAGgtattacatagctatgttaattaatcagctgaggtaaatacaaatgtgtgtttggcggttgaaaattgtgttgat--cgttttgtag---------------

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|32245576|gb|CD711395.1|CD711395
EST:     GTTTTGACCTTCGACCTTCAGATGCCATTAACATTGNTGTTAGATGCAAG                         GTGCCAATACAAGTTAATAAGTATTTGGCATACAGCGATGGAATGAGAGTC
genomic: GTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAGgtactcttca ... tcctctgcagGTGCCAATACAAGTTAATAAGTATTTGGCATACAGCGATGGAATGAGAGTC
EST: gi|27578891|gb|CB001586.1|CB001586
EST:     TTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGNCA-G                         GTGCCAATACAAGTTAATAAGTATTTGGCATACAGCGATGGA
genomic: TTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATG-CAAGgtactcttca ... tcctctgcagGTGCCAATACAAGTTAATAAGTATTTGGCATACAGCGATGGA
EST: gi|45770383|gb|CN006235.1|CN006235
EST:     GTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAG                         GTGCCAATACAAGTTAATAAGTATTTGGCATACAGCGATGGAATGAGAGTC
genomic: GTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAGgtactcttca ... tcctctgcagGTGCCAATACAAGTTAATAAGTATTTGGCATACAGCGATGGAATGAGAGTC
EST: gi|27580870|gb|CB003565.1|CB003565
EST:     GTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAG                         GTGCCAATACAAGTTAATAAGTATTTGGCATACAGCGATGGAATGAGAGTC
genomic: GTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAGgtactcttca ... tcctctgcagGTGCCAATACAAGTTAATAAGTATTTGGCATACAGCGATGGAATGAGAGTC
EST: gi|22007151|gb|BQ792185.1|BQ792185
EST:     GTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAG                         GTGCCAATACAAGTTAATAAGTATTTGGCATACAGCGATGGAATGAGAGTC
genomic: GTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAGgtactcttca ... tcctctgcagGTGCCAATACAAGTTAATAAGTATTTGGCATACAGCGATGGAATGAGAGTC
EST: gi|26261297|gb|CA812360.1|CA812360
EST:     GTTTTGACCTTCGACCTTCAGATGCCATT-A-ATTGCTGTTAGATGCAAG                         GTGCCAATACAAGTTAATAAGTATTTGGCATACAGCGATGGAATGAGAGTC
genomic: GTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAGgtactcttca ... tcctctgcagGTGCCAATACAAGTTAATAAGTATTTGGCATACAGCGATGGAATGAGAGTC
EST: gi|46919387|gb|CN548716.1|CN548716
EST:     GTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAG                         GTGCCAATACAAGTTAATAAGTATTTGGCATACAGCGATGGAATGAGAGTC
genomic: GTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAGgtactcttca ... tcctctgcagGTGCCAATACAAGTTAATAAGTATTTGGCATACAGCGATGGAATGAGAGTC
EST: gi|32246108|gb|CD711927.1|CD711927
EST:     TTCAGATGCCATTAACATTGCTGTTAGATGCAAG                         GTGCCAATACAAGTTAATAAGTATTTGGCATACAGCGATGGAATGAGAGTC
genomic: TTCAGATGCCATTAACATTGCTGTTAGATGCAAGgtactcttca ... tcctctgcagGTGCCAATACAAGTTAATAAGTATTTGGCATACAGCGATGGAATGAGAGTC
EST: gi|26260812|gb|CA811875.1|CA811875
EST:     GTTTTGACCTTCGACCTTCAGATGCCATTAA--TTGCTGTTAGATGCAAG                         GTGCCAATACAAGTTAATAAGTATTTGGCATACAGCGATGGAATGAGAGTC
genomic: GTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAGgtactcttca ... tcctctgcagGTGCCAATACAAGTTAATAAGTATTTGGCATACAGCGATGGAATGAGAGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAGgtactcttcattgtgggtgtgagttgtgtgactttatacatgcttttatttggtcacagtatcttttgcagatgccaatctgtaactagtttttatctgt

- - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT