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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaatcactaaaagcaatttcccttgtacttgctcttggatgaaaacattattcctcaatatgttcatcatcccttggtactttcatggatgcagATCAATACAAAGCAATCAATGATGAGGGAATGCCGCACCACCAAAGACCCTTCATGAAGGGTAAGCTTTACATCCATTTTGATGTGGAGTTCCCAGAGTC

Basic information

species Vitis vinifera
transcript Vv15s0021g02090.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0021g02090.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA03G27030.1 (Glycine max), 3'ss of exon 7
gtaaaaatcactaaaagcaatttcccttgtacttgctcttggatgaaaacattattcctcaatatgttcatcatcccttggtactttcatggatgcagATCAATACAAAGCAATCAATGATGAGGGAATGCCGCACCACCAAAGACCCTTCATGAAGGGTAAGCTTTACATCCATTTTGATGTGGAGTTCCCAGAGTC
|||| | | |  || |             |   ||   ||  ||   | || | |     | | | |   | ||   ||   | |||  |  |||||| |||||| |||||||| ||||||||||||||||| || ||| | || || ||||||||||||   ||||||||||| ||| |||| || |||||||| ||
gtaatacttaagaatattgggagtatgcatgactggaatttcattcgaccactctattcaattttatgatttatgaattttaattttgct--atgcagGTCAATATAAAGCAATAAATGATGAGGGAATGCCACAACACAATAGGCCATTCATGAAGGGTCGCCTTTACATCCAGTTTAATGTTGATTTCCCAGACTC

upper sequence: Vv15s0021g02090.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA07G14540.2 (Glycine max), 3'ss of exon 7
gtaaaaatcactaaaagcaatttcccttgtacttgctcttggatgaaaacattattcctcaatatgttcatcatcccttggtactttcatggatgcagATCAATACAAAGCAATCAATGATGAGGGAATGCCGCACCACCAAAGACCCTTCATGAAGGGTAAGCTTTACATCCATTTTGATGTGGAGTTCCCAGAGTC
|||| | | |  || |         |   ||  ||   ||  ||   | ||||  |  ||||| |  | ||       |  || |||     |||||| |||||| |||||| | ||||||||||||||||| || ||| | || || ||||||||||||   ||||||||||| ||| |||| || ||||| || ||
gtaatacttaagaatattgggagtacgcataactggaatttcatttgaccatt-ctattcaattttctgatttatgaattttaattttgct-atgcagGTCAATATAAAGCATTAAATGATGAGGGAATGCCACAACACAATAGGCCATTCATGAAGGGTCGCCTTTACATCCAATTTAATGTTGATTTCCCCGACTC

upper sequence: Vv15s0021g02090.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: EFJ30223 (Selaginella moellendorffii), 3'ss of exon 6
gtaaaaatcactaaaagcaatttcccttgtacttgctcttggatgaaaacattattcctcaatatgttcatcatcccttggtactttcatggatgcagATCAATACAAAGCAATCAATGATGAGGGAATGCCGCACCACCAAAGACCCTTCATGAAGGGTAAGCTTTACATCCATTTTGATGTGGAGTTCCCAGAGTC
              | |||| |  | | ||  | ||||||||             | ||| | | ||   ||  | ||     ||||||        |  |||| ||| || ||||| ||||| || ||||| |||||||| ||||||||||||||||| |  || |||||||| ||    || || ||||| |||||
------------gtatgcaaatcacttggtg-tagctcttgggc-----------ttctctaaacgtatgtctcctct-----ctttca--------gGCCAATTCAAGGCTATCAACGATGAAGGGATGCCTCACCACCAGAGACCCTTCATGAAGGGAACCCTGTACATCCACTTCTCGGTCGACTTCCCCGAGTC

upper sequence: Vv15s0021g02090.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: EFJ24912 (Selaginella moellendorffii), 3'ss of exon 6
gtaaaaatcactaaaagcaatttcccttgtacttgctcttggatgaaaacattattcctcaatatgttcatcatcccttggtactttcatggatgcagATCAATACAAAGCAATCAATGATGAGGGAATGCCGCACCACCAAAGACCCTTCATGAAGGGTAAGCTTTACATCCATTTTGATGTGGAGTTCCCAGAGTC
              | |||| |  | | ||  | |||||  |             | ||| | | ||   ||  | ||     ||||||        |  |||| ||| || ||||| ||||| |||||||| |||||||| ||||||||||||||||| |  || |||||||| ||    || || ||||| |||||
------------gtatgcaaatcacttagtg-tagctctcaggc-----------ttctctaaacgtatgtctcctct-----ctttca--------gGCCAATTCAAGGCTATCAACGATGAAGGAATGCCTCACCACCAGAGACCCTTCATGAAGGGAACCCTGTACATCCACTTCTCGGTCGACTTCCCCGAGTC

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|110716623|gb|EE091767.1|EE091767
EST:     TGGCAGGCAGCTTCTGATTAAATCAAACCCTGGCGAGATCATCAAACCAG                         ATCAATACAAAGCAATCAATGATGAGGGAATGCCGCACCACCAAAGACCCT
genomic: TGGCAGGCAGCTTCTGATTAAATCAAACCCTGGCGAGATCATCAAACCAGgtaaaaatca ... atggatgcagATCAATACAAAGCAATCAATGATGAGGGAATGCCGCACCACCAAAGACCCT
EST: gi|26264557|gb|CA815620.1|CA815620
EST:     TGGCAGGCAGCTTCTGATTAAATCAAACCCTGGCGAGATCATCAAACCAG                         ATCAATACAAAGCAATCAATGATGGGGGAATGCCGCACCACCAAAGACCCT
genomic: TGGCAGGCAGCTTCTGATTAAATCAAACCCTGGCGAGATCATCAAACCAGgtaaaaatca ... atggatgcagATCAATACAAAGCAATCAATGATGAGGGAATGCCGCACCACCAAAGACCCT
EST: gi|71857103|gb|DT006158.1|DT006158
EST:     TGGCAGGCAGCTTCTGATTAAATCAAACCCTGGCGAGATCATCAAACCAG                         ATCAATACAAAGCAATCAATGATGA
genomic: TGGCAGGCAGCTTCTGATTAAATCAAACCCTGGCGAGATCATCAAACCAGgtaaaaatca ... atggatgcagATCAATACAAAGCAATCAATGATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaaacattattcctcaatatgttcatcatcccttggtactttcatggatgcagATCAATACAAAGCAATCAATGATGAGGGAATGCCGCACCACCAAAGACCCTTCATGAAGGGTAAGCTTTACATCCATTTTGATGTGGAGTTCCCAGAGTC
                                        ctttcat  CT-rich tract
     acattatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaatcactaaaagcaatttcccttgtacttgctcttggatgaaaacattattcctcaatatgttcatcatcccttggtactttcatggatgcagATCAATACAAAGCAATCAATGATGAGGGAATGCCGCACCACCAAAGACCCTTCATGAAGGGTAAGCTTTACATCCATTTTGATGTGGAGTTCCCAGAGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG