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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGGATCTATCGAGGAGGAGATCTTGGAGCGAGCAAAGTCAAAGATGGGAATCGACGCAAAAGTTATCCAGGCTGGGCTTTTCAACACCACATCCACCCgtaacgtttttataacctttgtttttcctatttctaacttacgctttctgtgttcttccag

Basic information

species Selaginella moellendorffii
transcript EFJ23933
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ23933 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: LOC_Os05g05230.1 (Oryza sativa), 5'ss of exon 11
GTGGGATCTATCGAGGAGGAGATCTTGGAGCGAGCAAAGTCAAAGATGGGAATCGACGCAAAAGTTATCCAGGCTGGGCTTTTCAACACCACATCCACCCgt-------aacgtttttataacctttgtttttcctatttctaac----ttacgctttctgtgttcttccag----------------------------
|| || || || || || ||||||||||| || |||||    |||||||| || || ||||||||||||||||||||||| |||||||| || |||||  ||       ||   |   | ||  ||  |  ||||| | | | |     | |  ||||||    |   |||                             
GTTGGCTCAATTGAAGAAGAGATCTTGGACCGTGCAAAACAGAAGATGGGTATTGATGCAAAAGTTATCCAGGCTGGGCTGTTCAACACAACCTCCACAGgttagattaaatcctcgaacaaaattcatacttcctctgtttcatattataagactttctagcattgcccacattcacatatatgttaatgaatctagat

upper sequence: EFJ23933 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GRMZM2G097289_T02 (Zea mays), 5'ss of exon 6
GTGGGATCTATCGAGGAGGAGATCTTGGAGCGAGCAAAGTCAAAGATGGGAATCGACGCAAAAGTTATCCAGGCTGGGCTTTTCAACACCACATCCACCCgtaacgtttttataacctttgtttttcctatttctaacttacgctttctgtgttcttccag------------------------------------
|| || || || || || |||||| |||| || |||||   ||||||||| ||||| ||||||||||||||||||||| | || ||||| || |||||  || | ||||   | | ||   |  |   |||||  || ||  |  | ||       |  |                                     
GTCGGCTCCATTGAAGAAGAGATCCTGGACCGTGCAAAACAAAAGATGGGTATCGATGCAAAAGTTATCCAGGCTGGGTTGTTTAACACAACTTCCACAGgtga-gtttgagtgatctaattcctatttattt--aatttttgtctactacacgactggaactcgcatgacattttcacgttcatttcccactacag

upper sequence: EFJ23933 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: AT3G06010.1 (Arabidopsis thaliana), 5'ss of exon 11
GTGGGATCTATCGAGGAGGAGATCTTGGAGCGAGCAAAGTCAAAGATGGGAATCGACGCAAAAGTTATCCAGGCTGGGCTTTTCAACACCACATCCACCCgta---------------acgtttttataacctttgtttttcctatttctaacttacgctttctgtgttcttccag---------------
|| || ||| | || || |  || |||||||| ||||||  ||||||||| || ||||| ||||| || || ||||| ||||||||||| || |||||  |||               ||  | | |   | | || |||   |||   ||   ||  || |   |||  ||   |               
GTTGGCTCTGTTGAAGAAGTAATATTGGAGCGTGCAAAGCAAAAGATGGGCATTGACGCCAAAGTCATACAAGCTGGACTTTTCAACACAACTTCCACTGgtatgtctgtccgaaagaacaatatgagggcttctgctttctatatcgatatggtaatctcttgatgtggtttttgtgattatatcaacag

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: 32 (upstream exon), 21 (downstream exon)
Score: 4

GTGGGATCTATCGAGGAGGAGATCTTGGAGCGAGCAAAGTCAAAGATGGGAATCGACGCAAAAGTTATCCAGGCTGGGCTTTTCAACACCACATCCACCCgtaacgtttt ... gttcttccagCTCAGGAGAGGCGGGAACTTCTCGAGGAGATCATGAGAAAAGGAACGTCCAACTTGTCGGCGGACGTCCCAAGCGAGCGGGAGATCAACCGCTTGACGGC




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