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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGACTACTGGAGGCTGCCAAAGGACGCCAAGATCCGCGACGTTGTCCAAGTTGTCCGCGCCGACGAGGCTCACCACCGGGACGTGAACCACTTCGCAGCGgtaagcctcggatgcaagaagaagggatgggaattctaacgagtttgctcacgcccag

Basic information

species Selaginella moellendorffii
transcript EFJ27318
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ27318 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os02g47200.1 (Oryza sativa), 5'ss of exon 3
CGACTACTGGAGGCTGCCAAAGGACGCCAAGATCCGCGACGTTGTCCAAGTTGTCCGCGCCGACGAGGCTCACCACCGGGACGTGAACCACTTCGCAGCGgtaagc---ctcggatgcaagaagaagggatgggaattctaacgagtttgctcacgcccag------------------------------
|||||||||| | || ||    | ||||| | ||   ||||| |||   || ||||||||||||||||| |||||||| ||||| |||||||||||  ||||| |       | || |   |    |   ||||  || |     | ||| | | | |  |                              
CGACTACTGGCGCCTCCCCGCCGGCGCCACGCTCAAGGACGTCGTCGTCGTCGTCCGCGCCGACGAGGCACACCACCGCGACGTCAACCACTTCGCGTCGgtacgtgcgtgtgaattcctaagtttgctgtgggctttgtgtacggcttg-tgatgactggattgttcttttgcttgtgatgtgcatgcag

upper sequence: EFJ27318 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os04g51150.1 (Oryza sativa), 5'ss of exon 3
CGACTACTGGAGGCTGCCAAAGGACGCCAAGATCCGCGACGTTGTCCAAGTTGTCCGCGCCGACGAGGCTCACCACCGGGACGTGAACCACTTCGCAGCGgtaagcctcggatgcaagaagaagggatgggaattctaacgagtttg---ctcacgcccag-----------------------------------------
|||||||||| | || ||     |||||| | ||   ||||| |||   || || ||||||||||||||||||||||| ||||| || ||||||||| ||||| || |        ||       | |      |||  |   || |      | |   |                                          
CGACTACTGGCGCCTCCCCGCCAACGCCACGCTCAAGGACGTCGTCACCGTCGTGCGCGCCGACGAGGCTCACCACCGCGACGTCAATCACTTCGCATCGgtacgcatgcatgatcagcgatcttgctctttgatctcgccttttggggatgtatgttgaattggttctgacgtgtgatctggtctggcttgtgatgtgcag

upper sequence: EFJ27318 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os06g07570.1 (Oryza sativa), 5'ss of exon 1
---CGACTACTGGAGGCTGCCAAAGGACGCCAAGATCCGCGACGTTGTCCAAGTTGTCCGCGCCGACGAGGCTCACCACCGGGACGTGAACCACTTCGCAGCGgtaagc-ctcggatgcaaga----agaagggatgggaattctaacgagtttgctcacgcccag----------------------------
    ||||||||| |||| ||    | ||||| | ||   |||||||||    | ||||||||||||||||| |||||||| ||||| ||||| |||||| ||||| |  |  |  ||  |      |     |||| |   | |    || ||  | | | |                               
CATTGACTACTGGCGGCTCCCCGCCGGCGCCACGCTCAAGGACGTTGTC---ATCGTCCGCGCCGACGAGGCGCACCACCGCGACGTCAACCATTTCGCATCGgtacgtgcgtgcgtgtgaattcccaagcttgatgtgtgctttgtgtaggtttgtgatgactgaattatttttacttgtgatgtgcatgcag

upper sequence: EFJ27318 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os02g21300.1 (Oryza sativa), 5'ss of exon 3
CGACTACTGGAGGCTGCCAAAGGACGCCAAGATCCGCGACGTTGTCCAAGTTGTCCGCGCCGACGAGGCTCACCACCGGGACGTGAACCACTTCGCAGCGgtaagcctcg---gatgcaagaagaagggatgggaattctaacgagtttgctcacgcccag-------------------------------------------------------------------
|||||||||| | || ||    |||||||   || | ||||| |||   || ||||||||||||||||| |||||||| ||||| ||||||| |||  | ||| || ||      | |   |    | | |||    |  | |  || |    |   | |                                                                    
CGACTACTGGCGCCTCCCCGCCGACGCCACCCTCAGGGACGTCGTCATGGTCGTCCGCGCCGACGAGGCCCACCACCGCGACGTCAACCACTACGCCTCCgtacgcttccctcactccctcaccttgtgttggacgatgcatcatgtctcgcaatttcgaagcaaaacaaaaaggagaagaaatttgaacgaattttgctaactttgtccatggctgtggatgtgcag

upper sequence: EFJ27318 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os04g46770.1 (Oryza sativa), 5'ss of exon 1
CGACTACTGGAGGCTGCCAAAGGACGCCAAGATCCGCGACGTTGTCCAAGTTGTCCGCGCCGACGAGGCTCACCACCGGGACGTGAACCACTTCGCAGCGgtaagc-ctcggatgcaaga----agaagggatgggaattctaacgagtttgctcacgcccag----------------------------
|||||||||| |||| ||    | ||||| | ||   ||||| |||   ||||| || ||||||||||| |||||||| ||||| ||||| |||||| ||||| |  |  |  ||  |      |     |||| |   | |    || ||  | | | |                               
CGACTACTGGCGGCTCCCCGCCGGCGCCACGCTCAAGGACGTCGTCGTTGTTGTTCGTGCCGACGAGGCGCACCACCGCGACGTCAACCATTTCGCATCGgtacgttcgtgcgtgtgaattcccaatcttgatgtgtgctttgtgtaggtttgtgatgactgaattatttttgcttgtgatgtgcatgcag

upper sequence: EFJ27318 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os04g51160.1 (Oryza sativa), 5'ss of exon 2
CGACTACTGGAGGCTGCCAAAGGACGCCAAGATCCGCGACGTTGTCCAAGTTGTCCGCGCCGACGAGGCTCACCACCGGGACGTGAACCACTTCGCAGCGgtaagcctcggatgcaagaagaagggatgggaattctaacgagtttgctcacgcccag-----------------------------------------------------
|||||||||| | || ||    ||||||| | ||   ||||| |||   ||  |||||||||||||||| |||||||| ||| | ||||| |||||| ||||| || |   |||| ||    |        |||     |   ||   |   |                                                          
CGACTACTGGCGCCTCCCCGCCGACGCCACGCTCAAGGACGTCGTCACCGTCATCCGCGCCGACGAGGCGCACCACCGCGACCTCAACCATTTCGCATCGgtacgcat---atgccagcctgaaaacaaccaatctcgcctgcttaatttttgtgtgaacgggtttgagctaaccgatcgcgtttctcgtgttggtacatcacttgtgcag

upper sequence: EFJ27318 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G125669_T01 (Zea mays), 5'ss of exon 3
CGACTACTGGAGGCTGCCAAAGGACGCCAAGATCCGCGACGTTGTCCAAGTTGTCCGCGCCGACGAGGCTCACCACCGGGACGTGAACCACTTCGCAGCGgtaagcctcggatgcaagaagaagggatgggaattctaacgagtttgctcacgcccag---------------------------------------------
|||||||||| | || ||     |||||| | ||   ||||| |||   || |||||||||||||||||||||||||| ||||| |||||||| ||| ||||| |  |    | | |     |      | || |||      | |  || ||    |                                             
CGACTACTGGCGCCTCCCCGCTAACGCCACGCTCAAGGACGTAGTCACCGTCGTCCGCGCCGACGAGGCTCACCACCGCGACGTCAACCACTTTGCATCGgtacggat-acttccgaattccaataccagcaactctgcttgatctcatctcgttatgggattggttctgaaatctgaattggtatgagcttgtgccgtgcag

upper sequence: EFJ27318 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G074743_T01 (Zea mays), 5'ss of exon 3
CGACTACTGGAGGCTGCCAAAGGACGCCAAGATCCGCGACGTTGTCCAAGTTGTCCGCGCCGACGAGGCTCACCACCGGGACGTGAACCACTTCGCAGCGgtaagc-ctcggatgcaagaagaagggatgggaattctaacgagtttgct-cacgcccag-----------------------------------------------
|||||||||| | || ||    ||||||||| ||   ||||| |||   || || |||||||||||||| |||||||| ||||| |||||||||||  ||||| || ||| |   |  | |  |||  |      | | |  | | | |  ||   | ||                                               
CGACTACTGGCGCCTCCCCGCCGACGCCAAGCTCAAGGACGTCGTCACCGTCGTGCGCGCCGACGAGGCGCACCACCGCGACGTCAACCACTTCGCGTCGgtacgcactctgcaccttgcaacaggattcattgctgtgagcaatctccagcagttctagctaattcattggtttatgtttgcttaatggagtacattattttgcag

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: 16 (upstream exon), 20 (downstream exon)
Score: 1

CGACTACTGGAGGCTGCCAAAGGACGCCAAGATCCGCGACGTTGTCCAAGTTGTCCGCGCCGACGAGGCTCACCACCGGGACGTGAACCACTTCGCAGCGgtaagcctcg ... tcacgcccagGATATTCATCTCAAAGGCAAGCAGCTGCGAGAGGCCCCCGCTCCTCTAGGATACCACTGA




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