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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATTGCAAGTGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTGgtaagtcctcttcatccaaacgagcaaagttttgatgcaaaatacctcctttgcgtctccag

Basic information

species Selaginella moellendorffii
transcript EFJ17782
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ17782 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os08g32620.2 (Oryza sativa), 5'ss of exon 2
-------------------------------GTATTGCAAGTGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTGgtaagtcctcttcatccaaacgagcaaagttttgatgcaaaata-cctcctttgcgtctccag----------------------------------------
                                || ||||||||||||||||||||||| ||||| ||| | ||||| ||||||||   ||||||||| |||||| |||  || ||  ||||   |   ||| |||||||    |  ||   | | |  |  |                                         
TGCTTGTGTTTTCTTTTTCGTTTTTCTGAAGATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTGgtaattcca-ttaat--aaaccgcctctgttatgatgcatttcagtctatatagtgaatgtacactggaaaatcatggtaacaataatgaaattggcacccat

upper sequence: EFJ17782 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os08g32620.1 (Oryza sativa), 5'ss of exon 3
GTATTGCAAGTGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTGgtaagtcctcttcatccaaacgagcaaagttttgatgcaaaata-cctcctttgcgtctccag----------------------------------------
 || ||||||||||||||||||||||| ||||| ||| | ||||| ||||||||   ||||||||| |||||| |||  || ||  ||||   |   ||| |||||||    |  ||   | | |  |  |                                         
ATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTGgtaattcca-ttaat--aaaccgcctctgttatgatgcatttcagtctatatagtgaatgtacactggaaaatcatggtaacaataatgaaattggcacccat

upper sequence: EFJ17782 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os07g08880.3 (Oryza sativa), 5'ss of exon 3
GTATTGCAAGTGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTGgtaagtcctc--ttcatccaaacgagcaaagttttgatgcaaaatac-ctcctttgcgtctccag----------------
||  |||||||||||||||||||||||||| || ||  | ||| | || || |||   |||   ||||||| |||  |    | || ||    |    |  |||      || | | ||  | | | | |   |                
GTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATgtgaggaatgctctgattggtgagtaatgaaataattcatttaaattcatctttttcctgaactgcgctggtgtacattttatggttttatccctcttgc

upper sequence: EFJ17782 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os07g08880.2 (Oryza sativa), 5'ss of exon 3
GTATTGCAAGTGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTGgtaagtcctc--ttcatccaaacgagcaaagttttgatgcaaaatac-ctcctttgcgtctccag-----------------------------------
||  |||||||||||||||||||||||||| || ||  | ||| | || || |||   |||   ||||||| |||  |    | || ||    |    |  |||      || | | ||  | | | | |   |                                   
GTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTGgtgagtaatgaaataattcatttaaattcatctttttcctgaactgcgctggtgtacattttatggttttatccctcttgccactgggtgaataggacaa

upper sequence: EFJ17782 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G119357_T01 (Zea mays), 5'ss of exon 3
GTATTGCAAGTGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTGgtaagtcctcttcatccaaa--cgagcaaagttttgatgcaaaatacctcctttgcgtctccag------------------------------------
||||||||| ||||||||||||||||| ||||| ||  | ||||| ||||||||  | |||||||| |||||  |     |||   |    | |   |  |||   ||  |  | |||   ||  ||||                                        
GTATTGCAAATGTGAGATGCCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTGgtacatttgtctcaatgattttcaatttacatttcactgatatttgcctttgttcagtctattttatgcttctacaaagcaaatgctttaaatctctgga

upper sequence: EFJ17782 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S307_14V6.1 (Physcomitrella patens), 5'ss of exon 3
GTATTGCAAGTGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTGgtaagtcctcttcatc-caaacgagcaaagt---tttgatgcaaaatacctcctttgcgtctccag----------------------------------
|||||| || ||||||||||| || ||||| || |||||||||||||| || ||| | ||||| ||||||||||| ||||||||| ||  |      |||   | |  ||  |    | |   |||    || ||                                  
GTATTGTAAATGTGAGATGCCTTATAATCCAGATGATTTGATGGTTCAATGTGAGACTTGCAAAGATTGgtaagttctcttcatctcatccttatttagtcagtatattgtgagcagcttgtcttgtacttcaagaggcaaattgtagagtctgaatcactgaagcctt

upper sequence: EFJ17782 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S56_182V6.1 (Physcomitrella patens), 5'ss of exon 3
GTATTGCAAGTGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTGgtaag----------tcctcttcatccaaacgagcaaagttttgatgcaaaatacctcctttgcg----tctccag------------------------
 |||||||||||||| |||||||||||||| ||||| ||||||||||| || ||   |||||| || ||||  |          |||| |  || |||  |       || |  |  ||  |   |   |  |     | ||| |                        
TTATTGCAAGTGTGAAATGCCATACAATCCTGACGACTTGATGGTTCAATGTGAAATCTGCAAAGACTGgttggtctatattcctcctttctatgcaagtgcagtggattattgtagaagttgtttttatctcagtattttcctgaatattcgcaaggtgaacttaccc

upper sequence: EFJ17782 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S298_65V6.1 (Physcomitrella patens), 5'ss of exon 3
GTATTGCAAGTGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTGgtaagtcc-----tcttcatccaaacgagcaaagttttgatgcaaaatacct-cctttgcgtctccag--------------------------------
 ||||||||||| |||||||| |||||||| || || ||||||||||| || ||   |||||| || ||||| | |      |||   | |||  | |  ||  |    | |    ||  | ||      | | ||                                 
TTATTGCAAGTGCGAGATGCCTTACAATCCTGATGACTTGATGGTTCAATGTGAAATCTGCAAAGACTGgtaggcctatgcttctctgttcaactgcgacaaagtgcatttctttgtatttgcccggatatttgcaagaggacggtttcttgagtgaggagcttgcacc

upper sequence: EFJ17782 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S384_37V6.1 (Physcomitrella patens), 5'ss of exon 3
GTATTGCAAGTGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTGgtaagtcctcttcatccaaacgagcaaagttttgatgcaaaatacctcctttgc--gtctccag----------------------------------------
||||||||||||||||||||||||||| || ||| |  ||||| |  | ||| |    ||||| || |||| ||    ||     | ||     |  | |     |  || | | | ||  |   |||   |                                         
GTATTGCAAGTGTGAGATGCCATACAACCCTGACCACGTGATGCTGGAATGCAACAGTTGCAAAGACTGgtgaggttgctgtgctctaat----attgctcatcagtgaagtgcttgctcagtcagtcagtaaagactcgtgcctcgacctaagtctcgtgcgcttgaagctt

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: 28 (upstream exon), 34 (downstream exon)
Score: 2

GTATTGCAAGTGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTGgtaagtcctc ... gcgtctccagGTTCCATCCGACCTGCATGAGTCTATCTCCTGACCAAGTCAAGAAGTTGGAATCGTTCCATTGCCCGGAGTGCTCTTCTTCTCCGCCCGACGAGAAGAAA




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