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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATAAAGAATCCAAAGCTTGTTCCTGGTGGGGGTGCTACAGAGTTAACTGTTTCAGCTACCCTAAAACAGAAAAGTTCATCTGTTGAAGGCATTGAAAAGgtaaattttgcttctttctcatgtatcaaatttgatgtggtttttccatttgaatttttcaagataaatattggttgataatcaccaaggttttatgaaattgtttagttattgcactgcagttttctgatgctttatgcaattttccctatttgtaattttctgctcgtttgtgaaacag

Basic information

species Vitis vinifera
transcript Vv17s0000g08170.t01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g08170.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA16G33380.1 (Glycine max), 5'ss of exon 11
GATAAAGAATCCAAAGCTTGTTCCTGGTGGGGGTGCTACAGAGTTAACTGTTTCAGCTACCCTAAAACAGAAAAGTTCATCTGTTGAAGGCATTGAAAAGgtaaattttgcttctttctcatgtatcaaatttgatgtggtttttccatttgaatttttcaagataaatattggttgataatcaccaaggttttatgaaattgtttagttattgcactgcagttttctgatgctttatgcaattttccctatttgtaattttctgctcgtttgtgaaacag
 ||||| |||||||| ||||||||||| || |||||||||||||| || || |||||| || | |||||||| ||||||||| |||| ||||| || ||||| |   | | ||||     ||| | ||       |     ||||  |||||    |||   |||  ||  | |||    ||| |      |    | |   |||||   | ||     || ||   || || |   ||  |                                       
TATAAAAAATCCAAAACTTGTTCCTGGAGGTGGTGCTACAGAGTTGACAGTGTCAGCTGCCTTGAAACAGAAGAGTTCATCTATTGAGGGCATAGAGAAGgtgagcgtagtttct-----atgaaccagtagcagtactacttttt-atttggtggttt---gatggattctagtt--ctatctcttg---tccgagtagcagttta--cactgattctcacttaagtgttgttgactgacag--------------------------------------

upper sequence: Vv17s0000g08170.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA20G35760.1 (Glycine max), 5'ss of exon 8
GATAAAGAATCCAAAGCTTGTTCCTGGTGGGGGTGCTACAGAGTTAACTGTTTCAGCTACCCTAAAACAGAAAAGTTCATCTGTTGAAGGCATTGAAAAGgtaaattttgcttctttctcatgtatcaaatttgatgtggtttttccatttgaatttttcaagataaatattggttgataatcaccaaggttttatgaaattgtt-tagttattgcactgcagttttctgatgctttatgcaattttccctatttgtaattttctgctcgtttgtgaaacag
 ||||| ||| |||| ||||||||||| || |||||||| ||||| ||| | ||||| || || || ||||| |||||||||||| |||| ||  | ||||| | | |       | |||||       | ||    |  |  ||| |||    | |      |  |   |   |||||  |||      ||| |||    |||| | |||  || || |                                                              
AATAAAAAATTCAAAACTTGTTCCTGGAGGAGGTGCTACTGAGTTGACTATATCAGCAACACTGAAGCAGAAGAGTTCATCTGTTCAAGGTATACAGAAGgtgagtgtaa-----tactcattgtctgtactttgcctactagttctattattgtctcatggcagtagcttacattgattctcat-----tttcatgttcatgttcttgttgatgaacag--------------------------------------------------------------

upper sequence: Vv17s0000g08170.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA09G28650.2 (Glycine max), 5'ss of exon 11
GATAAAGAATCCAAAGCTTGTTCCTGGTGGGGGTGCTACAGAGTTAACTGTTTCAGCTACCCTAAAACAGAAAAGTTCATCTGTTGAAGGCATTGAAAAGgtaaattttgcttctttctcatgtatcaaatttgatgtggtttttccatttgaatttttcaagataaatattggttgataatcaccaaggttttatgaaattgtttagttattgcactgcagttttctgatgctttatgcaattttccctatttgtaattttctgctcgtttgtgaaacag
 ||||| ||||| || ||||||||||| || |||||||||||||| || || || ||| || | ||||| || ||||||||| |||| ||||| || ||||| |   | | ||   |   |    |   | | | |||  |  ||    | ||   ||  |     |    | || |  | |  |  || ||  |   ||||  ||| |||    | ||  |||  ||||                                                   
TATAAAAAATCCTAAACTTGTTCCTGGAGGCGGTGCTACAGAGTTGACGGTGTCGGCTGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAGgtgagcgtagttttactga-accagtagcagtagctgtactacttttgatgga---ttctagttctatctcttgtcgggagtagc--agtttacactgaatt-cttactta--agattgttgttgactgacag------------------------------------------------

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|352764587|gb|FQ472944.1|FQ472944
EST:     TTTCAGCTACCCTAAAACAGAAAAGTTCATCTGTTGAAGGCATTGAAAAG                         TGGCCTTATGAAGCTGCTGCTATAGCTTTTGAGGCTATTCCACGTACTTTG
genomic: TTTCAGCTACCCTAAAACAGAAAAGTTCATCTGTTGAAGGCATTGAAAAGgtaaattttg ... tgtgaaacagTGGCCTTATGAAGCTGCTGCTATAGCTTTTGAGGCTATTCCACGTACTTTG
EST: gi|32269227|gb|CD718386.1|CD718386
EST:     TTTCAGCTACCCTAAAACAGAAAAGTTCATCTGTTGAAGGCATTGAAAAG                         TGGCCTTATGAAGCTGCTGCAATAGCTTTTGAGGCTATTCCACGTACTTTG
genomic: TTTCAGCTACCCTAAAACAGAAAAGTTCATCTGTTGAAGGCATTGAAAAGgtaaattttg ... tgtgaaacagTGGCCTTATGAAGCTGCTGCTATAGCTTTTGAGGCTATTCCACGTACTTTG
EST: gi|30325800|gb|CD009062.1|CD009062
EST:     TTTCAGCTACCCTAAAACAGAAAAGTTCATCTGTTGAAGGCATTGAAAAG                         TGGCCTTATGAAGCTGCTGCAATAGCTTTTGAGGCTATTCCACGTACTTTG
genomic: TTTCAGCTACCCTAAAACAGAAAAGTTCATCTGTTGAAGGCATTGAAAAGgtaaattttg ... tgtgaaacagTGGCCTTATGAAGCTGCTGCTATAGCTTTTGAGGCTATTCCACGTACTTTG
EST: gi|110365989|gb|EC929587.1|EC929587
EST:     TTTCAGCTACCCTAAAACAGAAAAGTTCATCTGTTGAAGGCATTGAAAAG                         TGGCCTTATGAAGCTGCTGCAATAGCTTTTGAGGCTATTCCACGTACTTTG
genomic: TTTCAGCTACCCTAAAACAGAAAAGTTCATCTGTTGAAGGCATTGAAAAGgtaaattttg ... tgtgaaacagTGGCCTTATGAAGCTGCTGCTATAGCTTTTGAGGCTATTCCACGTACTTTG
EST: gi|30324113|gb|CD007375.1|CD007375
EST:     TTTCAGCTACCCTAAAACAGAAAAGTTCATCTGTTGAAGGCATTGAAAAG                         TGGCCTTATGAAGCTGCTGCAATAGCTTTTGAGGCTATTCCACGTACTTTG
genomic: TTTCAGCTACCCTAAAACAGAAAAGTTCATCTGTTGAAGGCATTGAAAAGgtaaattttg ... tgtgaaacagTGGCCTTATGAAGCTGCTGCTATAGCTTTTGAGGCTATTCCACGTACTTTG
EST: gi|161716671|gb|FC065567.1|FC065567
EST:     TTTCAGCTACCCTAAAACAGAAAAGTTCATCTGTTGAAGGCATTGAAAAG                         TGGCCTTATGAAGCTGCTGCAATAGCTTTTGAGGCTATTCCACGTACTTTG
genomic: TTTCAGCTACCCTAAAACAGAAAAGTTCATCTGTTGAAGGCATTGAAAAGgtaaattttg ... tgtgaaacagTGGCCTTATGAAGCTGCTGCTATAGCTTTTGAGGCTATTCCACGTACTTTG
EST: gi|32248018|gb|CD713837.1|CD713837
EST:     TTTCAGCTACCCTAAAACAGAAAAGTTCATCTGTTGAAGGCATTGAAAAG                         TGGCCTTATGAAGCTGCTGCAATAGCTTTTGAGGCTATTCCACGTACTTTG
genomic: TTTCAGCTACCCTAAAACAGAAAAGTTCATCTGTTGAAGGCATTGAAAAGgtaaattttg ... tgtgaaacagTGGCCTTATGAAGCTGCTGCTATAGCTTTTGAGGCTATTCCACGTACTTTG
EST: gi|110392915|gb|EC957538.1|EC957538
EST:     TTTCAGCTACCCTAAAACAGAAAAGTTCATCTGTTGAAGGCATTGAAAAG                         TGGCCTTATGAAGCTGCTGCAATAGCTTTTGAGGCTATTCCACGTACTTTG
genomic: TTTCAGCTACCCTAAAACAGAAAAGTTCATCTGTTGAAGGCATTGAAAAGgtaaattttg ... tgtgaaacagTGGCCTTATGAAGCTGCTGCTATAGCTTTTGAGGCTATTCCACGTACTTTG
EST: gi|32247862|gb|CD713681.1|CD713681
EST:     TTTCAGCTACCCTAAAACAGAAAAGTTCATCTGTTGAAGGCATTGAAAAG                         TGGCCTTATGAAGCTGCTGCAATAGCTTTTGAGGCTATTCCACGTACTTTG
genomic: TTTCAGCTACCCTAAAACAGAAAAGTTCATCTGTTGAAGGCATTGAAAAGgtaaattttg ... tgtgaaacagTGGCCTTATGAAGCTGCTGCTATAGCTTTTGAGGCTATTCCACGTACTTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATAAAGAATCCAAAGCTTGTTCCTGGTGGGGGTGCTACAGAGTTAACTGTTTCAGCTACCCTAAAACAGAAAAGTTCATCTGTTGAAGGCATTGAAAAGgtaaattttgcttctttctcatgtatcaaatttgatgtggtttttccatttgaatttttcaagataaatattggttgataatcaccaaggttttatgaaattgtttagttattgcactgcagttttctgatgctttatgcaattttccctatttgtaattttctgctcgtttgtgaaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG