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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGATAGCACAAAGACTGGCAAGGTGACATCCGCTGGCATGTATTTTCTTCATTTCCAAGTGTACAGATTGGATACAACAATGAATGCGgtacgtagcttgctttctttctttttcttgtacttaatgcacgcactctttttattag

Basic information

species Selaginella moellendorffii
transcript EFJ30011
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ30011 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: LOC_Os01g32870.1 (Oryza sativa), 5'ss of exon 8
GAAGATAGCACAAAGACTGGCAAGGTGACATCCGCTGGCATGTATTTTCTTCATTTCCAAGTGTACAGATTGGATACAACAATGAATGCGgtacgtagctt--gctttctttcttt--ttcttgtacttaatgcacgcactctttttattag----------------------
||||||||    |||||||| ||||||||||| || |||||||||||  | ||||| ||||||||  |  ||||| ||||| ||||||||||| |||  ||  ||| | |  ||||  || || | ||   ||  |    | |  |  | ||                      
GAAGATAGTCAGAAGACTGGTAAGGTGACATCTGCAGGCATGTATTTCTTGCATTTTCAAGTGTATCGTATGGATTCAACAGTGAATGCGgtatgtatgttctgctatatagctttagtttttatgctctttgggcctgatgtgat-gtgagactttgctgcttcctactacag

upper sequence: EFJ30011 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: GRMZM2G005753_T02 (Zea mays), 5'ss of exon 9
GAAGATAGCACAAAGACTGGCAAGGTGACATCCGCTGGCATGTATTTTCTTCATTTCCAAGTGTACAGATTGGATACAACAATGAATGCGgtacgtagct-tgctttct-ttctttttcttgtacttaatgcacgcactctttttattag------------
    ||||   ||||||||||||||| ||||| || |||||||||||  | |||||||| |||||  |  ||||  |||||  |||||||||| |||  | ||  | || ||  || |  |||  || ||  ||  | | || || |               
----ATAGTCAAAAGACTGGCAAGGTAACATCAGCAGGCATGTATTTCTTGCATTTCCAGGTGTATCGTATGGACTCAACAGCGAATGCGgtatgtaattctgtgtgctgttagttattctgtgttttata-actgatttttattctctcttacaattacag

upper sequence: EFJ30011 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: GRMZM2G005753_T03 (Zea mays), 5'ss of exon 9
GAAGATAGCACAAAGACTGGCAAGGTGACATCCGCTGGCATGTATTTTCTTCATTTCCAAGTGTACAGATTGGATACAACAATGAATGCGgtacgtagct-tgctttct-ttctttttcttgtacttaatgcacgcactctttttattag------------
||||||||   ||||||||||||||| ||||| || |||||||||||  | |||||||| |||||  |  ||||  |||||  |||||||||| |||  | ||  | || ||  || |  |||  || ||  ||  | | || || |               
GAAGATAGTCAAAAGACTGGCAAGgtaacatcagcaggcatgtatttcttgcatttccaggtgtatcgtatggactcaacagcgaatgcggtatgtaattctgtgtgctgttagttattctgtgttttata-actgatttttattctctcttacaattacag

upper sequence: EFJ30011 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: GLYMA20G25180.1 (Glycine max), 5'ss of exon 7
GAAGATAGCACAAAGACTGGCAAGGTGACATCCGCTGGCATGTATTTTCTTCATTTCCAAGTGTACAGATTGGATACAACAATGAATGCGgtacgtagcttgctttctttctttttcttgtacttaa-tgcacgcactctttttattag-------------------------
||||| ||    |||||||||||||||||||| || || ||||||||  | ||||| |||||||| ||| ||||| ||||  ||||||||||| | |  ||   ||| ||   |||||| | |||   ||   ||  | |    | | |                         
GAAGACAGTGAGAAGACTGGCAAGGTGACATCTGCAGGAATGTATTTCTTACATTTTCAAGTGTATAGAATGGATTCAACGGTGAATGCGgtatgaaaattatgttcattaggtttcttttccttggctgtgggctgtttggaaagtggtggttactgttagtactatgtgcag

upper sequence: EFJ30011 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: GLYMA10G41860.2 (Glycine max), 5'ss of exon 7
GAAGATAGCACAAAGACTGGCAAGGTGACATCCGCTGGCATGTATTTTCTTCATTTCCAAGTGTACAGATTGGATACAACAATGAATGCGgtacgtagcttgctttctttc--tttttcttgtacttaatgcacgcactctttttattag-------------------------
||||| ||    |||||||||||||||||||| || || ||||||||  | ||||| |||||||| ||| ||||| | ||  ||||||||||| | |  ||   ||| ||   ||| | ||    ||  |||  ||  | |    | | |                         
GAAGACAGTGAGAAGACTGGCAAGGTGACATCTGCAGGAATGTATTTCTTACATTTTCAAGTGTATAGAATGGATTCGACGGTGAATGCGgtatgaaaattatgttcattaggtttctttttcctttggtgctggctgtttgggaagtggtggttactgttagtgctatgtgcag

upper sequence: EFJ30011 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: AT1G68370.1 (Arabidopsis thaliana), 5'ss of exon 7
GAAGATAGCACAAAGACTGGCAAGGTGACATCCGCTGGCATGTATTTTCTTCATTTCCAAGTGTACAGATTGGATACAACAATGAATGCGgtacgtagcttgctttctttctttttcttgtacttaatgcacgcactctttttattag-------------------------------------
|||||  |    || || || ||||||||||| ||||||||||||||  | ||||| |||||||| ||| ||||||||||  | ||||||||| | |  ||     || | ||  | |  || |||     |  | |    |    ||                                     
GAAGAGCGTGAGAAAACAGGGAAGGTGACATCAGCTGGCATGTATTTCTTACATTTTCAAGTGTATAGAATGGATACAACTGTCAATGCGgtatgcaagttttgagctcttttcctttcataattagctggcatattagaatatgcagaggtactaaagcaatccacattgtggttattgtgcag

upper sequence: EFJ30011 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: Vv01s0011g03790.t01 (Vitis vinifera), 5'ss of exon 8
GAAGATAGCACAAAGACTGGCAAGGTGACATCCGCTGGCATGTATTTTCTTCATTTCCAAGTGTACAGATTGGATACAACAATGAATGCGgtacgtagcttgctttctttcttt--ttcttgtacttaatgcacgcactctttttattag--------------------------
||||||||    || ||||||||||||||||| || || ||||||||  | ||||| |||||||||||| ||||| ||||  ||||||||||| ||   || | || ||||| |  ||||  |  ||  |   | ||   ||  ||   |                          
GAAGATAGTGAGAAAACTGGCAAGGTGACATCTGCAGGGATGTATTTCTTACATTTTCAAGTGTACAGAATGGATTCAACTTTGAATGCGgtatgtgagttccgttatttctgtagttctcatctttggtcatcacagctttaataagtgatgaattcatttttgtgatggtgcag

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|169103280|gb|FE507309.1|FE507309
EST:     TGTATTTTCTTCATTTCCAAGTGTACAGATTGGATACAACAATGAATGCG                         TTGGCAATGGCAAGGGATCCTGATACTGCATTCTTCAGGAGA
genomic: TGTATTTTCTTCATTTCCAAGTGTACAGATTGGATACAACAATGAATGCGgtacgtagct ... tttttattagTTGGCAATGGCAAGGGATCCTGATACTGCATTCTTCAGGAGA
EST: gi|169043526|gb|FE450774.1|FE450774
EST:     TGTATTTTCTTCATTTCCAAGTGTACAGATTGGATACAACAATGAATGCG                         TTGGCAATGGCAAGGGATCCTGATACTGCATTCTTCAGGAGATTGGAAGGG
genomic: TGTATTTTCTTCATTTCCAAGTGTACAGATTGGATACAACAATGAATGCGgtacgtagct ... tttttattagTTGGCAATGGCAAGGGATCCTGATACTGCATTCTTCAGGAGATTGGAAGGG

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: 33 (upstream exon), 31 (downstream exon)
Score: 21

GAAGATAGCACAAAGACTGGCAAGGTGACATCCGCTGGCATGTATTTTCTTCATTTCCAAGTGTACAGATTGGATACAACAATGAATGCGgtacgtagct ... tttttattagTTGGCAATGGCAAGGGATCCTGATACTGCATTCTTCAGGAGATTGGAAGGGCTTCAACCATGCGAAGTTTTGGGATTGAGAGCCGGCTCACACGTTTTTG




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