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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCACATGTTTTTATACAAAAGCTATTAGGACGATATAGCTTTCTTGATGAACTATCAACTCTTGATCCTGAGCTCTACAGGAATCTTATGTATGTTAAGgtaaaccctcttgataaaagtacaggattttttattttatttttaatatcaggaaaaatataggaattttgaagtttaaaagcatttcattgtgtttttt...

Basic information

species Vitis vinifera
transcript Vv08s0007g04290.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g04290.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: LOC_Os03g47949.1 (Oryza sativa), 5'ss of exon 4
TTCACATGTTTTTATACAAAAGCTATTAGGACGATATAGCTTTCTTGATGAACTATCAACTCTTGATCCTGAGCTCTACAGGAATCTTATGTATGTTAAGgtaaaccctcttgataaaagtacaggatttt---ttattttatttttaatatcaggaaaaatataggaattttgaagtt--taaaagcatttcattgtgtttttt
||||| ||| ||| | || || ||  | || || ||||| ||| | ||||||||||||||||||||| ||||||| ||||| | ||| ||| |  | ||||||     | ||  |  ||| | | |||| |    || | |  || ||    ||  ||||| ||  ||||| | | | |  | |||| |     ||   |     
TTCACCTGTATTTGTGCAGAAACTTCTTGGGCGCTATAGTTTTTTGGATGAACTATCAACTCTTGATTCTGAGCTTTACAGAAGTCTAATGCAACTCAAGgtactgtttttttctttaagaaaaagattctgctgtaatcttgttctagacccaaaaaaaacatttgaattattatgctactgaaagtagcaatttacat-----

upper sequence: Vv08s0007g04290.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G461948_T01 (Zea mays), 5'ss of exon 8
TTCACATGTTTTTATACAAAAGCTATTAGGACGATATAGCTTTCTTGATGAACTATCAACTCTTGATCCTGAGCTCTACAGGAATCTTATGTATGTTAAGgtaaaccctcttgataaaagtacaggattttttattttatttttaatatcaggaaaaatataggaattttgaagtttaaaagcatttcattgtgtttttt
 ||||  || ||| | || || ||  | ||||| ||||  ||||| ||||||||||||||||||||||| ||||| || || ||||||||| |  | ||||||   |   ||  |     |     | |||      ||     ||  | |   |     ||  ||| ||     || |||  ||   |   ||  |   
CTCACCAGTATTTGTGCAGAAACTTCTTGGACGGTATAATTTTCTGGATGAACTATCAACTCTTGATCCCGAGCTTTATAGAAATCTTATGCAACTAAAGgtactacagattttttgctttggtttagtttcccagatacaagcaagttaaactactgcttaaaaatcttttctattgaaaagatcataagatgggtgga

upper sequence: Vv08s0007g04290.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA03G34650.1 (Glycine max), 5'ss of exon 9
TTCACATGTTTTTATACAAAAGCTATTAGGACGATATAGCTTTCTTGATGAACTATCAACTCTTGATCCTGAGCTCTACAGGAATCTTATGTATGTTAAGgtaaaccctcttgataaaagtacaggattttttattttatttttaatatcaggaaaaatataggaattt-tgaagtttaaaagcatttcattgtgtttttt---
 || ||||||||| | ||||||||||| |||||||||||||||||||||||| ||||||| |||||||| ||||| |||||||||||||||||||| |||||||||||  | || |||   |     ||||  || | ||| |||     |   |   |     ||||  | ||| || |   |  ||||   ||  |      
CTCCCATGTTTTTGTGCAAAAGCTATTGGGACGATATAGCTTTCTTGATGAATTATCAACACTTGATCCAGAGCTATACAGGAATCTTATGTATGTCAAGgtaaacccattagacaaatccatgttgttttccatctcattctta----taaatattttgccaaaattaatcaagattcaggactattcaaaatgactcgcatt

upper sequence: Vv08s0007g04290.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA19G37310.4 (Glycine max), 5'ss of exon 10
TTCACATGTTTTTATACAAAAGCTATTAGGACGATATAGCTTTCTTGATGAACTATCAACTCTTGATCCTGAGCTCTACAGGAATCTTATGTATGTTAAGgtaaaccctcttgataaaagtacaggattttttattttatttttaatatcaggaaaaatataggaattt-tgaagtttaaaagcatttcattgtgtttttt---
 || ||||| ||| ||||||||||||| |||||||||||||||||||||||| ||||||| |||||||| ||||| |||||||| ||||||||||| |||||||||||    || |||   |     ||||  || | ||| |||     |   |   |     ||||  | | | || |   |  ||||   ||  |      
CTCCCATGTCTTTGTACAAAAGCTATTGGGACGATATAGCTTTCTTGATGAATTATCAACACTTGATCCAGAGCTATACAGGAACCTTATGTATGTCAAGgtaaacccatgagacaaatccatgttgttttccatctcattctta----taaatattttgccaaaattaatcaggattcaggaccattcaaaatgactcgcatt

upper sequence: Vv08s0007g04290.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: AT3G53090.2 (Arabidopsis thaliana), 5'ss of exon 8
TTCACATGTTTTTATACAAAAGCTATTAGGACGATATAGCTTTCTTGATGAACTATCAACTCTTGATCCTGAGCTCTACAGGAATCTTATGTATGTTAAGgtaaaccctcttgataaaagtacagg----attttttattttatt-tttaatatcaggaaaaatataggaattttgaagtt-taaaagcatttcattgtgtttttt---
|||||| ||||| || || ||||| || || || ||||||||| ||||||||||||||   |||||||| |||||||||||||| || |||||||| ||||||||  |  |||       || |         |  ||| | |   || ||| |    | || |||   |     |   || | | | ||   | |||| | | |    
TTCACACGTTTTCATCCAGAAGCTTTTGGGGCGTTATAGCTTTATTGATGAACTATCAGGGCTTGATCCAGAGCTCTACAGGAACCTCATGTATGTCAAGgtaaaaaccgttgcaggtgatatatctgtcgcctcatatgtcaaaattcaatcttgtaataagtatcacaggaaagggtttctgagatcaagactttgtttatatgcag

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|110373009|gb|EC937214.1|EC937214
EST:     AACTATCAACTCTTGATCCTGAGCTCTACAGGAATCTTATGTATGTTAAG                         CATTATGATGGGGATGTGAAGGAACTCTCTCTGGATTTCACAGTTACAGAA
genomic: AACTATCAACTCTTGATCCTGAGCTCTACAGGAATCTTATGTATGTTAAGgtaaaccctc ... gtttctacagCATTATGATGGGGATGTGAAGGAACTCTCTCTGGATTTCACAGTTACAGAA
EST: gi|110380386|gb|EC945648.1|EC945648
EST:     AACTATCAACTCTTGATCCTGAGCTCTACAGGAATCTTATGTATGTTAAG                         CATTATGATGGGGATGTGAAGGAACTCTCTCTGGATTTCACAGTTACAGAA
genomic: AACTATCAACTCTTGATCCTGAGCTCTACAGGAATCTTATGTATGTTAAGgtaaaccctc ... gtttctacagCATTATGATGGGGATGTGAAGGAACTCTCTCTGGATTTCACAGTTACAGAA
EST: gi|110363275|gb|EC926852.1|EC926852
EST:     AACTATCAACTCTTGATCCTGAGCTCTACAGGAATCTTATGTATGTTAAG                         CATTATGATGGGGATGTGAAGGAACTCTCTCTGGATTTCACAGTTACAGAA
genomic: AACTATCAACTCTTGATCCTGAGCTCTACAGGAATCTTATGTATGTTAAGgtaaaccctc ... gtttctacagCATTATGATGGGGATGTGAAGGAACTCTCTCTGGATTTCACAGTTACAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCACATGTTTTTATACAAAAGCTATTAGGACGATATAGCTTTCTTGATGAACTATCAACTCTTGATCCTGAGCTCTACAGGAATCTTATGTATGTTAAGgtaaaccctcttgataaaagtacaggattttttattttatttttaatatcaggaaaaatataggaattttgaagtttaaaagcatttcattgtgtttttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaagca