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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAGGACGAATGGGATCAATCACTCAAATTCCCATTCTCAGTATGCCAAACGATGgtacgagatgtctgatcatcgagatcatctactgacttactcgcag

Basic information

species Selaginella moellendorffii
transcript EFJ13375
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ13375 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: LOC_Os01g51380.1 (Oryza sativa), 5'ss of exon 10
ATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAGGACGAATGGGATCAATCACTCAAATTCCCATTCTCAGTATGCCAAACGATGgtacgagatgtctgatcatcgagatcatct-actgacttactcgcag---------------------------------------------------------------------------------------------------------------------------------------------------------
|||||||| ||||||||||| || || ||||||||||| || || |||||| |||  |||||||| || || || |||||| | |  ||||| || ||||||  |  || |          | ||  | | |   |  |  | ||                                                                                                                                                           
ATGTATACTGATTTGGCAACTATCTATGAGCGTGCTGGTCGCATAGAAGGAAGAAAAGGATCAATTACGCAGATACCCATTTTAACCATGCCTAATGATGgttagttatttaaatgtgcttacattttatgataaatctttttgcgaaattgcacttttcctttttttaatttgaagtatgtatgttaattgcacagaaaaacatagtgaatcagttttattaatagaataaatgttacatggataactgatattagatgctgccggcaactttctgactcataagtcgtgctgttgtag

upper sequence: EFJ13375 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: GRMZM2G094497_T03 (Zea mays), 5'ss of exon 1
ATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAGGACGAATGGGATCAATCACTCAAATTCCCATTCTCAGTATGCCAAACGATGgtacgagatgtctgatcatcgagatcatctactg-acttactcgcag-----------------------------------------------------
|||||||| |||||||||||||| || ||||||||||| || ||||||||| |||  || || || || || ||||| ||||| |  ||||| |||||||||| |  |       |  |  |     | || |  | |||  |                                                         
ATGTATACTGATTTGGCAACAATATATGAGCGTGCTGGGCGTATTGAAGGAAGAACAGGCTCCATTACCCAGATTCCTATTCTAACAATGCCTAACGATGgtaagtaaccatgtcttttttaatctttatattataattatactttataattatactatgtgccgtattgttattggttttgtacacttatcttctgaac

upper sequence: EFJ13375 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: GRMZM2G181151_T01 (Zea mays), 5'ss of exon 10
ATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAGGACGAATGGGATCAATCACTCAAATTCCCATTCTCAGTATGCCAAACGATGgtacg-------agatgtctgatcatcgagatcatcta-ctgacttactcgcag----------------------------------------------
|||||||| ||| |||||||||| || ||||||||||| || ||||||||| |||  || || || || |||||||| ||||| |  ||||| || ||||||| |        | | | | ||| | |  || || || ||   | |   ||||                                              
ATGTATACTGATCTGGCAACAATATATGAGCGTGCTGGGCGTATTGAAGGAAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATGgtaagtaaccatggcttttttatctttgttattatataactatatgaagggcagacctagtgtagtggttagagctgtctcactgagtcaccaggccatg

upper sequence: EFJ13375 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: GLYMA09G38110.1 (Glycine max), 5'ss of exon 10
ATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAGGACGAATGGGATCAATCACTCAAATTCCCATTCTCAGTATGCCAAACGATGgt-acgagatgtc--tga---tcatcgag-atcatctactgacttactcgcag-----------------------------------
|||||||||||| | |||||||| ||||| ||||||||| ||||||| || ||||  || || || || |||||||| ||||| |  ||||| || |||||| | || || |   |||   | |||    |||||  | | |   |||| ||                                    
ATGTATACAGATCTTGCAACAATATACGAACGTGCTGGAAGAATTGAGGGGCGAAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCTAATGATGgtgatgaaatattattgaatcttatcagctatcatgca-taatgcactctcaattctgactgattgtttttcttgaacttctgtacag

upper sequence: EFJ13375 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: GLYMA18G48280.1 (Glycine max), 5'ss of exon 10
ATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAGGACGAATGGGATCAATCACTCAAATTCCCATTCTCAGTATGCCAAACGATGgt-acgagatgt--ctga---tcatcgag-atcatctactgacttactcgcag------------------------------------
 ||||||||||| | |||||||| ||||| ||||||||| ||||||| || ||||  || || || || |||||||| ||||| |  ||||| || |||||| | || || |   |||   | |||    |||||  | | |   |||| ||                                     
-TGTATACAGATCTTGCAACAATATACGAACGTGCTGGAAGAATTGAGGGGCGAAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCTAATGATGGtgatgaaatattattgaatcttatcagctatcatgcatt-atgcactctcaattctgactgattatttttcttgaacttctgtacaga

upper sequence: EFJ13375 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 5'ss of exon 10
ATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAGGACGAATGGGATCAATCACTCAAATTCCCATTCTCAGTATGCCAAACGATGgtacgagatgtctgatcatcgagatcatctactgacttactcgcag-----------------------------------------------------------
|||||||| ||| | ||||||||||| |||||||||||||| || ||||| ||||  || || ||||| |||||||| ||| | |  ||||| || |||||||      |  |  |||    |     ||| |  ||| |  |||                                                            
ATGTATACTGATCTTGCAACAATTTATGAGCGTGCTGGACGTATAGAAGGGCGAAAAGGCTCCATCACACAAATTCCTATTTTAACCATGCCTAATGATGgtaatgttagcattttcaggatgtctggctatt--cttccctgcacatcagttcttgtaatagtgaacagacattacctgaaaccaattattttttgtccaccag

upper sequence: EFJ13375 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 5'ss of exon 10
ATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAGGACGAATGGGATCAATCACTCAAATTCCCATTCTCAGTATGCCAAACGATGgta-cgagatgtctgatc-atcgagatcatctactgacttactcgcag--------------------------------------
|||||||| ||| |||| || ||||| || ||||||||||| ||||||||||| | ||| || || || ||||| || ||| | | |||||| || |||||||  |  | |  | ||| ||   ||||   |  |||     || ||                                       
ATGTATACTGATCTGGCGACGATTTATGAACGTGCTGGACGTATTGAAGGACGGAAGGGTTCCATTACACAAATCCCAATTTTAACTATGCCCAATGATGgtaatgtcaagcatcatccatattgatctagtggtgagaatttctcattatagtggcactacactcactgaacctgattttcacag

upper sequence: EFJ13375 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 5'ss of exon 9
ATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAGGACGAATGGGATCAATCACTCAAATTCCCATTCTCAGTATGCCAAACGATGgtacgagatgtc------tgatcatcgagatcatctact----gacttactcgcag---------------------------------------------------------------------------------------------------------------------------------
||||| || ||| | || || |||||||| |||||||| |||||||| || || |  || || |||||||| ||||||||||| | |||||| |||||||||  |     ||      | ||||   |  || | || |    |||||| |    |                                                                                                                                 
ATGTACACGGATCTTGCCACTATTTACGAACGTGCTGGGCGAATTGAGGGCCGCAAAGGGTCTATCACTCAGATTCCCATTCTAACTATGCCTAACGATGgttagttgcatcctccatttatcactaatttcttatattagtggacttagtgatggagaactacccttatttgatactttgtttctgtccttacttgaccttctacaggccttaatttatttctttgaattgtgatttttttttctttaggttactgagtttcgtgtatgtcgtactttttgcag

upper sequence: EFJ13375 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 5'ss of exon 9
ATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAGGACGAATGGGATCAATCACTCAAATTCCCATTCTCAGTATGCCAAACGATGgtacgagatgtc------tgatcatcgagatcatctactgacttactcgcag-----------------------------------------------------------------------------------------------------------------
|||||||| ||| |||| || ||||| || |||||||||||||| ||||| || |  ||||| || ||||| ||||| ||||| | |||||| || ||||||  |     ||      |  ||||| || |    || |  ||| ||   |                                                                                                                  
ATGTATACTGATCTGGCCACCATTTATGAACGTGCTGGACGAATCGAAGGCCGTAAAGGATCTATTACTCAGATTCCTATTCTAACTATGCCGAATGATGgtcagttgcatccttcctttgtcatcaagtttcagtatttgctttctttgaaatgggcattttactttgttatattatttttgctctttcttgactgcgtgcagtcttcgactgtggacttctccttgtctgtactaagcttcacctttgtggcatttcgtgcag

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 31 (upstream exon), 30 (downstream exon)
Score: 21

ATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAGGACGAATGGGATCAATCACTCAAATTCCCATTCTCAGTATGCCAAACGATGgtacgagatg ... ttactcgcagATATCACTCATCCGATTCCTGATCTCACTGGTTACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAG




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