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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTTCGAGCTCATGTTCCAAGAATGACTTTGGATGAGCTGTTTGAACAAAAGGGTGATGTTGCTCAAACCGTCTTGGAGGAGCTTGAGAAGgtaatttgatgctgttacagatgattgaatggttaatagtgatatgccaagttttatggaaagatgcatattaaattgacctatattttggttcattcaa...

Basic information

species Vitis vinifera
transcript Vv16s0022g01690.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0022g01690.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA16G32990.1 (Glycine max), 5'ss of exon 3
TGGTTCGAGCTCATGTTCCAAGAATGACTTTGGATGAGCTGTTTGAACAAAAGGGTGATGTTGCTCAAACCGTCTTGGAGGAGCTTGAGAAGgtaatttgatgctgttacagatgattgaatggttaatagtgatatgccaagttttatggaaagatgcatattaaattgacctatattttggttcattcaa---
||  ||| |||  |||||| |||||||  ||||| ||||||||||| || |||||||| |||||  || | ||||||||||| ||||| ||||||  ||  | || |||    | | | | |   |   | |  |     || | |    ||||  || | |  |  ||    |   || | |||||   ||   
TGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAGgtatcttacttcttttatt--taagtaagtt-ctggcattcttgaattaaatatgtaagaaaagtgaagagaagcttagtattagttgttgttcacaaaatat

upper sequence: Vv16s0022g01690.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA09G28170.1 (Glycine max), 5'ss of exon 3
TGGTTCGAGCTCATGTTCCAAGAATGACTTTGGATGAGCTGTTTGAACAAAAGGGTGATGTTGCTCAAACCGTCTTGGAGGAGCTTGAGAAGgtaatttgatgctgttacagatgattgaatggttaatagtgat--atgccaagttttatggaaagatgcatattaaattgacctatattttggttcattcaa
||  ||| |||  |||||| |||||||  |||||||| || ||||| || |||||||| |||||  || | ||||||||||| ||||| ||||||| |  |   |  |  |  |  | |  |  || ||    |   | |  ||||||  | |        |||| |||||     || |  |  |  |   | 
TGACTCGTGCTATTGTTCCTAGAATGAACTTGGATGAACTCTTTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAGgtaact--acttttatttaagttctggcgttctttatgaaaagtgaagagaagtttagttgttcacaaaatatcaaattatttcatttccttttaaaactat
















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|34542871|gb|CF511103.1|CF511103
EST:     GGAGCTTGAGAAG                         GTGATGGGAGCTTACGGATATAACATAGAGCACATACTGATGGTTGATATT
genomic: GGAGCTTGAGAAGgtaatttgat ... catggatcagGTGATGGGAGCTTACGGATATAACATAGAGCACATACTGATGGTTGATATT
EST: gi|110393502|gb|EC958789.1|EC958789
EST:     TTGAACAAAAGGGTGATGTTGCTCAAACCGTCTTGGAGGAGCTTGAGAAG                         GTGATGGGAGCTTACGGATATAACATAGAGCACATACTGATGGTTGATATT
genomic: TTGAACAAAAGGGTGATGTTGCTCAAACCGTCTTGGAGGAGCTTGAGAAGgtaatttgat ... catggatcagGTGATGGGAGCTTACGGATATAACATAGAGCACATACTGATGGTTGATATT
EST: gi|161716029|gb|FC065535.1|FC065535
EST:     TTGAACAAAAGGGTGATGTTGCTCAAACCGTCTTGGAGGAGCTTGAGAAG                         GTGATGGGAGCTTACGGATATAACATAGAGCACATACTGATGGTTGATATT
genomic: TTGAACAAAAGGGTGATGTTGCTCAAACCGTCTTGGAGGAGCTTGAGAAGgtaatttgat ... catggatcagGTGATGGGAGCTTACGGATATAACATAGAGCACATACTGATGGTTGATATT
EST: gi|34542787|gb|CF511019.1|CF511019
EST:     TCTTGGAGGAGCTTGAGAAG                         GTGATGGGAGCTTACGGATAT-AGATCAGAGCACATACTGATGGTTGATAT
genomic: TCTTGGAGGAGCTTGAGAAGgtaatttgat ... catggatcagGTGATGGGAGCTTACGGATATAACAT-AGAGCACATACTGATGGTTGATAT
EST: gi|110366549|gb|EC930459.1|EC930459
EST:     GGAGCTTGAGAAG                         GTGATGGGAGCTTACGGATATAAACATAGAGCACATACTGATGGTTGATAT
genomic: GGAGCTTGAGAAGgtaatttgat ... catggatcagGTGATGGGAGCTTACGGATAT-AACATAGAGCACATACTGATGGTTGATAT

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTTCGAGCTCATGTTCCAAGAATGACTTTGGATGAGCTGTTTGAACAAAAGGGTGATGTTGCTCAAACCGTCTTGGAGGAGCTTGAGAAGgtaatttgatgctgttacagatgattgaatggttaatagtgatatgccaagttttatggaaagatgcatattaaattgacctatattttggttcattcaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaattga