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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACCATATCTATCGATGAGATGGCTGGTGGCTCATTCACAATATCCAATGGTGGTGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAGgtaagaagcttcatagaccattcttctatcctgttaggataattttaggatttcttactgttcacatatttcttttgaattgtctaatgaattgtgaaac...

Basic information

species Vitis vinifera
transcript Vv10s0116g01480.t01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0116g01480.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: GRMZM2G079538_T01 (Zea mays), 5'ss of exon 11
CACCATATCTATCGATGAGATGGCTGGTGGCTCATTCACAATATCCAATGGTGGTGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAGgtaagaagcttcatagaccattcttctatcctgttaggataattttaggatttcttactgttcacatatttcttttgaattgtctaatgaattgtgaaac
  |  | || || ||||| ||||| |||||  ||||||| || ||||| ||||||||||||||||||||  | || || || |||||||||||||| |||||||   ||| ||     ||||  ||  |      |  | ||||||      | |   |||| |   || |    ||   | | |  |||||||      
GGCGCTCTCAATTGATGACATGGCAGGTGGAACATTCACCATCTCCAACGGTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaact-gctgca-----catttatcagt---agcaacacaattttgtatcatgtagatgtttattgatctgaaatgtgatctatg-tgaattgcag---

upper sequence: Vv10s0116g01480.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: GRMZM5G807639_T01 (Zea mays), 5'ss of exon 1
CACCATATCTATCGATGAGATGGCTGGTGGCTCATTCACAATATCCAATGGTGGTGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAGgtaagaagcttcatagaccattcttctatcctgttaggataattttaggatttcttactgttcacatatttcttttgaattgtcta-atgaattgtgaaac
  |  | || || ||||| ||||| || ||  ||||||| || ||||||||||||||||||||||||||  | || || || ||||||||||| || ||||||    |||      || |  | | ||||  |||   | |  |||      |     |||| | ||   |||     ||  ||||  |||| ||      
GGCGCTCTCGATTGATGACATGGCAGGAGGAACATTCACTATCTCCAATGGTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgta----gct------actaaacatttatca-gttgcaacacatttgtagcatgcagatgtttatattgatctgaaacatgatctatgtgaaatgcag---

upper sequence: Vv10s0116g01480.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: AT5G55070.1 (Arabidopsis thaliana), 5'ss of exon 14
CACCATATCTATCGATGAGATGGCTGGTGGCTCATTCACAATATCCAATGGTGGTGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAGgtaagaagcttcatagaccattcttctatcctgttaggataattttaggatttcttactgttcacatatttcttttg--aattgtctaatgaattgtgaaac
 |||||||| |||||||||||||| || || ||||||||| |||| |||||||||||||||||||| ||  | || || || |||||||||||||| |||||  ||  |        | || ||   | ||  | |    ||      | | | ||  ||||    | || ||  ||  |||      || |   ||     
AACCATATCAATCGATGAGATGGCAGGAGGATCATTCACAGTATCAAATGGTGGTGTCTATGGAAGTCTTATAAGCACTCCTATCATCAACCCTCCTCAGgttcgattcgatccttgcaatactaaaaaccaatcaaagaaa------ggtgtttttttgtttgtttgttactaatgcaaataaatctatcatacgtag---

upper sequence: Vv10s0116g01480.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: AT4G26910.3 (Arabidopsis thaliana), 5'ss of exon 9
CACCATATCTATCGATGAGATGGCTGGTGGCTCATTCACAATATCCAATGGTGGTGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAGgtaagaagcttcatagaccattcttcta---tcctgttaggataattttaggatttcttactgttcacatatttcttttgaattgtctaatgaattgtgaaac
 |||||||| || |||||||||||||| || ||||||||  | || ||||| |||||||||||||| ||  | || || || ||||| || ||||| |||||   ||  || ||   ||||    |      || || || |  |  ||    ||| |||    | || | |   |||  |                      
AACCATATCCATAGATGAGATGGCTGGCGGATCATTCACCGTTTCAAATGGCGGTGTCTATGGAAGTCTCATAAGCACTCCGATCATTAATCCTCCTCAGgtttaaa--tttatttcccatctcaccgggtcccagtcagaaccacgttt---tttgttaacagtaacctgtggttttgcag---------------------

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|110374185|gb|EC938784.1|EC938784
EST:     GTGGCGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAG                         TCAGCTATCTTGGGAATGCACTCGATAGTGAACCGTCCAATGGTTGTTGGG
genomic: GTGGTGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAGgtaagaagct ... atgtttacagTCAGCTATCTTGGGAATGCACTCAATAGTGAACCGTCCAATGGTTGTTGGG
EST: gi|30129251|gb|CB914590.1|CB914590
EST:     CAATCATCAACCCTCCCCAG                         TCAGCTATCTTGGGAATGCACTCGATAGTGAACCGTCCAATGGTTGTTGGG
genomic: CAATCATCAACCCTCCCCAGgtaagaagct ... atgtttacagTCAGCTATCTTGGGAATGCACTCAATAGTGAACCGTCCAATGGTTGTTGGG
EST: gi|110358011|gb|EC921922.1|EC921922
EST:     GTGGCGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAG                         TCAGCTATCTTGGGAATGCACTCGATAGTGAACCGTCCAATGGTTGTTGGG
genomic: GTGGTGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAGgtaagaagct ... atgtttacagTCAGCTATCTTGGGAATGCACTCAATAGTGAACCGTCCAATGGTTGTTGGG
EST: gi|71865965|gb|DT015020.1|DT015020
EST:     CATCAACCCTCCCCAG                         TCAGCTATCTTGGGAATGCACTCGATAGTGAACCGTCCAATGGTTGTTGGG
genomic: CATCAACCCTCCCCAGgtaagaagct ... atgtttacagTCAGCTATCTTGGGAATGCACTCAATAGTGAACCGTCCAATGGTTGTTGGG
EST: gi|22013541|gb|BQ798575.1|BQ798575
EST:     GTGGTGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAG                         TCAGCTATCTTGGGAATGCACTCAATAGTGAACCGTCCAATGGTTGTTGGG
genomic: GTGGTGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAGgtaagaagct ... atgtttacagTCAGCTATCTTGGGAATGCACTCAATAGTGAACCGTCCAATGGTTGTTGGG
EST: gi|110358726|gb|EC923155.1|EC923155
EST:     GTGGCGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAG                         TCAGCTATCTTGGGAATGCACTCGATAGTGAACCGTCCAATGGTTGTTGGG
genomic: GTGGTGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAGgtaagaagct ... atgtttacagTCAGCTATCTTGGGAATGCACTCAATAGTGAACCGTCCAATGGTTGTTGGG
EST: gi|110362847|gb|EC926404.1|EC926404
EST:     GTGGCGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAG                         TCAGCTATCTTGGGAATGCACTCGATAGTGAACCGTCCAATGGTTGTTGGG
genomic: GTGGTGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAGgtaagaagct ... atgtttacagTCAGCTATCTTGGGAATGCACTCAATAGTGAACCGTCCAATGGTTGTTGGG
EST: gi|294964448|gb|GW838251.1|GW838251
EST:     GTGGTGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAG                         TCAGCTATCTTGGGGATGCACTCGATAGTGAACCGTCCAATGGTTGTAGGG
genomic: GTGGTGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAGgtaagaagct ... atgtttacagTCAGCTATCTTGGGAATGCACTCAATAGTGAACCGTCCAATGGTTGTTGGG
EST: gi|33410472|gb|CF216099.1|CF216099
EST:     GTGGTGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAG                         TCAGCTATCTTGGGAATGCACTCGATAGTGAACCGTCCAATGGTTGTTGGG
genomic: GTGGTGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAGgtaagaagct ... atgtttacagTCAGCTATCTTGGGAATGCACTCAATAGTGAACCGTCCAATGGTTGTTGGG
EST: gi|83275590|gb|DV939598.1|DV939598
EST:     GAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAG                         TCAGCTATCTTGGGAATGCACTCGATAGTGAACCGTCCAAAGGTTGTTGGG
genomic: GAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAGgtaagaagct ... atgtttacagTCAGCTATCTTGGGAATGCACTCAATAGTGAACCGTCCAATGGTTGTTGGG
EST: gi|33407761|gb|CF213388.1|CF213388
EST:     GTGGTGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAG                         TCAGCTATCTTGGGAATGCACTCGATAGTGAACCGTCCAATGGTTGTTGGG
genomic: GTGGTGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAGgtaagaagct ... atgtttacagTCAGCTATCTTGGGAATGCACTCAATAGTGAACCGTCCAATGGTTGTTGGG
EST: gi|110415386|gb|EC981291.1|EC981291
EST:     GTGGTGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAG                         TCAGCTATCTTGGGAATGCACTCGATAGTGAACCGTCCAATGGTTGTTTGG
genomic: GTGGTGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAGgtaagaagct ... atgtttacagTCAGCTATCTTGGGAATGCACTCAATAGTGAACCGTCCAATGGTTGTTGGG
EST: gi|22009921|gb|BQ794955.1|BQ794955
EST:     GTGGTGTCTATGNAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAG                         TCAGCTATCTTGGGAATGCACTCGATAGTGAACCGTCCAATGGTTGTTGGG
genomic: GTGGTGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAGgtaagaagct ... atgtttacagTCAGCTATCTTGGGAATGCACTCAATAGTGAACCGTCCAATGGTTGTTGGG
EST: gi|34362782|gb|CF404367.1|CF404367
EST:     GTCTATGGAAGCCTGTTGAGTGCCCCAATCATCAACCCTCCCCAG                         TCAGCTATCTTGGGAATGCCCTCGATAGTGAACCGTCCAATGGTTGTTGGG
genomic: GTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAGgtaagaagct ... atgtttacagTCAGCTATCTTGGGAATGCACTCAATAGTGAACCGTCCAATGGTTGTTGGG
EST: gi|161714785|gb|FC063933.1|FC063933
EST:     GTGGCGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAG                         TCAGCTATCTTGGGAATGCACTCGATAGTGAACCGTCCAATGGTTGTTGGG
genomic: GTGGTGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAGgtaagaagct ... atgtttacagTCAGCTATCTTGGGAATGCACTCAATAGTGAACCGTCCAATGGTTGTTGGG
EST: gi|110718184|gb|EE094729.1|EE094729
EST:     GTGGTGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAG                         TCAGCTATCTTGGGAATGCACTCGATAGTGAACCGTCCAATGGTTGTTGGG
genomic: GTGGTGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAGgtaagaagct ... atgtttacagTCAGCTATCTTGGGAATGCACTCAATAGTGAACCGTCCAATGGTTGTTGGG
EST: gi|110699660|gb|EE076855.1|EE076855
EST:     GTGGTGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAG                         TCAGCTATCTTGGGAATGCACTCGATAGTGAACCGTCCAATGGTTGTTGGG
genomic: GTGGTGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAGgtaagaagct ... atgtttacagTCAGCTATCTTGGGAATGCACTCAATAGTGAACCGTCCAATGGTTGTTGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACCATATCTATCGATGAGATGGCTGGTGGCTCATTCACAATATCCAATGGTGGTGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAGgtaagaagcttcatagaccattcttctatcctgttaggataattttaggatttcttactgttcacatatttcttttgaattgtctaatgaattgtgaaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aggataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgaaa