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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGAAGAAAGGGCCTTGGACTCCTGAAGAAGATCAGAAGCTGGTCAGCTACGTTCAGAAACATGGCCATGGAAGCTGGAGAGCTCTCCCTAAGCTTGCAGgtctatgttaattaattggatccctctccctgtctctcattttttcagtacttcaccatttcatcatttcccttttactcctgcag

Basic information

species Vitis vinifera
transcript Vv18s0001g05670.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g05670.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os06g11780.1 (Oryza sativa), 5'ss of exon 1
CTGAAGAAAGGGCCTTGGACTCCTGAAGAAGATCAGAAGCTGGTCAGCTACGTTCAGAAACATGGCCATGGAAGCTGGAGAGCTCTCCCTAAGCTTGCAGgtctatgttaattaattggatccctctccctgtctctcattttttcagtacttc--accatttcatcatttccctt--ttactcctgcag
|| ||||| || || |||||||||||||||||| |||||||  | |||||| |||||||||||||||||| |||||||||||   | ||| | ||||| |||   |     |   |        ||| ||       ||| | ||||||   |   |        | | |||| |   ||  |  |||||
CTCAAGAAGGGCCCCTGGACTCCTGAAGAAGATGAGAAGCTCATGAGCTACATTCAGAAACATGGCCATGCAAGCTGGAGAGTCTTACCTGAACTTGCTGgtgcttacacctctctcatgcatgtcttcc-acagaacatgtattcagtttcttgtatagaagtcttacttccgtatattgtttttgcag

upper sequence: Vv18s0001g05670.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os02g51799.1 (Oryza sativa), 5'ss of exon 1
CTGAAGAAAGGGCCTTGGACTCCTGAAGAAGATCAGAAGCTGGTCAGCTACGTTCAGAAACATGGCCATGGAAGCTGGAGAGCTCTCCCTAAGCTTGCAGgtctatgttaattaat--tggatccctctccctgtctctcatttttt---cagtact--tcaccatttcatcatttcccttttactcctgcag-----------------------------
|| ||||| || || |||||  | || |||||| |||||||  |    ||| | |||||  | |||||||| ||||||||||| || ||||||||||||||| | |||  ||  |    ||||  |  | | |  || | || || |    || |    ||   ||      ||  | |  |  |    ||                               
CTCAAGAAGGGCCCCTGGACCACGGAGGAAGATGAGAAGCTCATGGAGTACATCCAGAAGAACGGCCATGGCAGCTGGAGAGCGCTGCCTAAGCTTGCAGgtatgtgtacatgcacaacggatggcg-tacgtagctttgatcttgtagctagcatcgatccaaatgcagctatagctcgatggccatggcgttgagttttccttttttttacatgttgcag

upper sequence: Vv18s0001g05670.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA02G13770.1 (Glycine max), 5'ss of exon 1
CTGAAGAAAGGGCCTTGGACTCCTGAAGAAGATCAGAAGCTGGTCAGCTACGTTCAGAAACATGGCCATGGAAGCTGGAGAGCTCTCCCTAAGCTTGCAGgtctatgttaattaattg--gatccctctccctgtctctcattttttcagtactt-caccatttcatcatttcccttttactcctgcag------------
 |||||||||| |||||||| |||||||||||||| |||||  |     || ||||||||||||| |||| ||||||||||||||| || || || ||||||     ||  ||| |||  || ||   ||          ||   |    || ||  |  | ||||| || ||   |||| |   |               
TTGAAGAAAGGCCCTTGGACACCTGAAGAAGATCAAAAGCTTATTGATCACATTCAGAAACATGGTCATGCAAGCTGGAGAGCTCTTCCAAAACTAGCAGgtactatttttttatttgtagaaccaaatcgaatataaatatccatcagatatttataataattcat-atatcttatttaattacgtgagctagagtatta

upper sequence: Vv18s0001g05670.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA01G09280.1 (Glycine max), 5'ss of exon 1
CTGAAGAAAGGGCCTTGGACTCCTGAAGAAGATCAGAAGCTGGTCAGCTACGTTCAGAAACATGGCCATGGAAGCTGGAGAGCTCTCCCTAAGCTTGCAGgtctatgttaattaattggatccctctccct-gtctctcattttttcagtacttcaccatttcatcatttcccttttactcctgcag------------------------
 |||||||||| |||||||| |||||||||||||| |||||  |   | || |||| ||| |||| |||| ||||||||| ||||| || || |||||||||     |  ||| |||| ||     |  |  |  ||||||  ||  | || ||   ||| | ||        | | |||  ||  |                        
TTGAAGAAAGGTCCTTGGACACCTGAAGAAGATCAAAAGCTTATTGACCACATTCAAAAATATGGTCATGCAAGCTGGAGGGCTCTTCCAAAACTTGCAGgtactactatatttattgtattttagtgtcaagaatctcataatta-aatattttctcatcttatgccacatatataactaatggggatggtcatttgtatttggtaatag

upper sequence: Vv18s0001g05670.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: PP1S106_216V6.1 (Physcomitrella patens), 5'ss of exon 1
CTGAAGAAAGGGCCTTGGACTCCTGAAGAAGATCAGAAGCTGGTCAGCTACGTTCAGAAACATGGCCATGGAAGCTGGAGAGCTCTCCCTAAGCTTGCAGgt---ctatgt--taattaattggatccctctccctgtctctcattttttcagtacttcaccattt----catcatttcccttttactcctgcag-----
 ||||||| ||||| ||||| || || || ||||||||||||||    ||| ||||| ||||||| |||||||||||| | |  |||||| ||   || |||   ||  ||  |  ||       |  |      | |||  |||     || ||| |  |  | |    |  ||  |      |     |||||     
GTGAAGAAGGGGCCGTGGACGCCAGAGGAGGATCAGAAGCTGGTGGCATACATTCAGGAACATGGTCATGGAAGCTGGCGGGAGCTCCCTGAGAAAGCCGgtaagctgcgtcctgcttcgaaaagtgacgaattttttcttgcatgagaccattacattgcgttcttcgaccccaggttttggatggatttgcagttaga

upper sequence: Vv18s0001g05670.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: PP1S326_37V6.1 (Physcomitrella patens), 5'ss of exon 1
CTGAAGAAAGGGCCTTGGACTCCTGAAGAAGATCAGAAGCTGGTCAGCTACGTTCAGAAACATGGCCATGGAAGCTGGAGAGCTCTCCCT----AAGCTTGCAGgtc----tatgttaattaattggatccctctccctgtctctcattttttcagtacttcaccatttcatcatttcccttttactcctgcag------
|||||||| ||||| ||||| ||||| || ||||||||||||||    ||| ||||| |||| || |||||||||||| | || ||||||    ||||| | | |||    | || | |||    |  | ||    | || ||   |  || |      |  |   |    ||| ||| |  ||    |  | |      
CTGAAGAAGGGGCCGTGGACACCTGATGAGGATCAGAAGCTGGTGGCTTACATTCAGGAACACGGTCATGGAAGCTGGCGCGCACTCCCTGAGAAAGCTGgtacgtcgcactctgctgattctcagtgtgcccgcgcttggctgcgacgttcttgtggttgtatgttcaggtcaattcacgcttgaatcaactggattct

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGAAGAAAGGGCCTTGGACTCCTGAAGAAGATCAGAAGCTGGTCAGCTACGTTCAGAAACATGGCCATGGAAGCTGGAGAGCTCTCCCTAAGCTTGCAGgtctatgttaattaattggatccctctccctgtctctcattttttcagtacttcaccatttcatcatttcccttttactcctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT