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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAATTCCAAACCTTGTCCAAAGTGTAAAAGACCGATCGAAAAATCTCAAGGATGCATGCATATAACGTGTACGCCTCCGTGCAAGTTTGAGTTTTGCTGgtaggtgttttctttttctcgctgatgactgattgatgtgtggtag

Basic information

species Selaginella moellendorffii
transcript EFJ17699
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ17699 (Selaginella moellendorffii), 5'ss of exon 8
lower sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 8
CCAATTCCAAACCTTGTCCAAAGTGTAAAAGACCGATCGAAAAATCTCAAGGATGCATGCATATAACGTGTACGCCTCCGTGCAAGTTTGAGTTTTGCTGgtaggtgttttctttttctc-gctgatgactgattgatgtgtggtag---------------------------------------
| ||||| || |||||||| ||||| ||  | || || ||||||   || ||||||||||| || || || || ||||| ||||| ||||||||||||||||| ||  |     | |||| | | |||        |    | | ||                                       
CTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGAAAAAAACCAGGGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAGTTTTGCTGgtatgtaatcataatctctctgtttatgctcttcatagcacttgcagtctcatatggcttgtatgtacttgttctatataacgcag

upper sequence: EFJ17699 (Selaginella moellendorffii), 5'ss of exon 8
lower sequence: LOC_Os09g33876.1 (Oryza sativa), 5'ss of exon 8
CCAATTCCAAACCTTGTCCAAAGTGTAAAAGACCGATCGAAAAATCTCAAGGATGCATGCATATAACGTGTACGCCTCCGTGCAAGTTTGAGTTTTGCTGgtaggtgttttc---------tttttctcgctgatgactgattgatgtgtggtag----------------------------------------
|  |||| || || ||||| || || ||| |||| || || ||   ||| |||||||||||||| || || || ||||| || || ||||||||||||||||| |  |             ||| | | | || ||| ||  | |  | | | |                                         
CTTATTCTAAGCCCTGTCCGAAATGCAAACGACCTATAGAGAAGAATCAGGGATGCATGCATATGACATGCACTCCTCCTTGTAAATTTGAGTTTTGCTGgtaagcttccctctcggcatatttgttttgatggtgattgtgt-acattttgcattgaaattgtttatctttggtctgattttccatggttgcag

upper sequence: EFJ17699 (Selaginella moellendorffii), 5'ss of exon 8
lower sequence: Vv00s0207g00090.t01 (Vitis vinifera), 5'ss of exon 8
CCAATTCCAAACCTTGTCCAAAGTGTAAAAGACCGATCGAAAAATCTCAAGGATGCATGCATATAACGTGTACGCCTCCGTGCAAGTTTGAGTTTTGCTGgtaggtgt-tttctttttctcgctgat-gactgattgatgtgtggtag----------------------------------------------------
| |||||||| |||||||||||||||||  | || |||||||||   ||||| || |||||||| || || || || || || || ||||||||||||||||| || | | |  | || |    ||| |||| |    | | | | ||                                                    
CTAATTCCAAGCCTTGTCCAAAGTGTAAGCGGCCAATCGAAAAAAACCAAGGTTGTATGCATATCACATGCACACCGCCATGTAAATTTGAGTTTTGCTGgtaagtttatatactcttgttctagatagactcacatgtatttaggaggtctggtctttattccattttgtatccacttggcaacactagcattatcaag

upper sequence: EFJ17699 (Selaginella moellendorffii), 5'ss of exon 8
lower sequence: PP1S178_72V6.3 (Physcomitrella patens), 5'ss of exon 8
CCAATTCCAAACCTTGTCCAAAGTGTAAAAGACCGATCGAAAAATCTCAAGGATGCATGCATATAACGTGTACGCCTCCGTGCAAGTTTGAGTTTTGCTGgtaggtgttt--tctttttctcgctgatgactgattgatgtgtggtag------------------------------------------------------------------------------------------------------------------------
| ||   |||||| || || || ||||| |||||||| ||||||   ||||| ||||||||||| || || || || || ||||| ||||||||||||||||| ||  |   | || ||||  ||   |    ||| | ||    ||                                                                                                                         
CAAACAGCAAACCCTGCCCTAAATGTAAGAGACCGATTGAAAAAAACCAAGGCTGCATGCATATTACTTGCACACCACCTTGCAAATTTGAGTTTTGCTGgtaagttgtaaatattattcttactttagttaaattaaagttacttaattggatttagtactattaatatgtgaaagtcaccatgcttataaggtcatcaactcagctgctgcaattcatgttgcctcattctcaagtgtagcttttgaaccttgacttctttggcag

upper sequence: EFJ17699 (Selaginella moellendorffii), 5'ss of exon 8
lower sequence: PP1S9_199V6.1 (Physcomitrella patens), 5'ss of exon 9
CCAATTCCAAACCTTGTCCAAAGTGTAAAAGACCGATCGAAAAATCTCAAGGATGCATGCATATAACGTGTACGCCTCCGTGCAAGTTTGAGTTTTGCTGgtaggtgttttctttttctcgctgat----gactgattgatgtgtggtag------------------------------------------------------------------------------------------------------------------------------------------------
| ||   |||||| ||||| || |||||||| || ||||||||   |||||| |||||||| || || || || || || ||||| ||||||||||||||||| ||  |   |  ||     |||      | | || ||||  |  |                                                                                                                                                  
CGAACAGCAAACCCTGTCCCAAATGTAAAAGGCCAATCGAAAAGAATCAAGGCTGCATGCACATTACTTGCACACCACCTTGCAAATTTGAGTTTTGCTGgtaagtaatggataatttcaattgaatctaaagtcatggatggatcatgattcattcttaccttaattttatagacacagctacttaagtttacgttgcttcactctgagtatgttgacaccagtggttggtaagtctatcacttataagcaaccaaatttattcactcagttttatttatgcgtttttgacag

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), 33 (downstream exon)
Score: 15

CCAATTCCAAACCTTGTCCAAAGTGTAAAAGACCGATCGAAAAATCTCAAGGATGCATGCATATAACGTGTACGCCTCCGTGCAAGTTTGAGTTTTGCTGgtaggtgttt ... tgtgtggtagGCTTTGTCTTGGACCGTGGTCCGAACACGGTGAGCGCACAGGGGGATTTTATGCTTGTAATCGGTATGAAGCTGCTAAGCAGGAAGGAGTG




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