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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGGCGTCGGCGCCAAGATGGATTCCATGGACCTGGAGCGCGAGAAAGGGATCACCATCCAGTCCGCAGCGACGCACTGCGTTTGGGGTGACCACCAGgtgagatggacgtttttcattcccttacaaagtttcgactttgtttctttctag

Basic information

species Selaginella moellendorffii
transcript EFJ36205
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ36205 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os03g36780.1 (Oryza sativa), 5'ss of exon 1
GGATGGCGTCGGCGCCAAGATGGATTCCATGGACCTGGAGCGCGAGAAAGGGATCACCATCCAGTCCGCAGCGACGCACTGCGTTTGGGGTGACCACCAGgtgagatggacgtttttcattcccttacaaagtttcgactttgtttctttctag-----------------------------------------------
 || ||||| ||||| |||||||| ||||||||||| ||||||||||| || ||||||||||||||||| || ||  |||||   |||  ||   |||||||       |  | |  |  || |    |   |||| | |   ||  | |  |                                                
CGACGGCGTGGGCGCAAAGATGGACTCCATGGACCTCGAGCGCGAGAAGGGCATCACCATCCAGTCCGCTGCAACCTACTGCACCTGGAATGGATACCAGgtccatcaaatttctgcccgtctcacttatc-tttctattcgattcgtatacatccgattgcctgctagatcaccatgttttggctatcgaaaggaaactt

upper sequence: EFJ36205 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G056393_T01 (Zea mays), 5'ss of exon 1
GGATGGCGTCGGCGCCAAGATGGATTCCATGGACCTGGAGCGCGAGAAAGGGATCACCATCCAGTCCGCAGCGACGCACTGCGTTTGGGGTGACCACCAGgtgagatggacgtttttcattcccttacaaagtttcgactttgtttctttctag----------------------------------------------
 || |||||||| || |||||||| ||||||||||| |||||||| || ||||||||||| ||||| || || ||  |||||   |||   ||  |||||||  | | |   ||  |||  | ||    |  | |    | || ||  |                                                   
TGACGGCGTCGGTGCTAAGATGGACTCCATGGACCTAGAGCGCGAAAAGGGGATCACCATTCAGTCTGCTGCCACCTACTGCACCTGGAAGGATTACCAGgtccgtttgtttttgctcagcctctctttatttgtttgttctgattgatcgatccgtttccctttgttatagaccccggatggttgtgatttcgttgttg

upper sequence: EFJ36205 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA11G16460.1 (Glycine max), 5'ss of exon 1
GGATGGCGTCGGCGCCAAGATGGATTCCATGGACCTGGAGCGCGAGAAAGGGATCACCATCCAGTCCGCAGCGACGCACTGCGTTTGGGGTGACCACCAGgtgaga---tggacgttt--ttcattcccttacaaagtttcgactttgtttctttctag-----------------------------------------
||| || ||||||||||||||||| ||||||||| ||||| | ||||| || |||||||| ||||| || || ||  |||||   |||   ||  |  ||||  |    ||   |||   ||||     | | | | | | |     |||  | |   |                                         
GGACGGAGTCGGCGCCAAGATGGACTCCATGGACTTGGAGAGGGAGAAGGGAATCACCATTCAGTCTGCTGCCACCTACTGCACGTGGAAAGATTATAAGgtttggttttgtttgttgaattcaactagtgaaataatgttgggagagttattgtggtgttggttcagttctaattgaatttgaatttaggtcctgtttg

upper sequence: EFJ36205 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: AT1G45332.1 (Arabidopsis thaliana), 5'ss of exon 1
GGATGGCGTCGGCGCCAAGATGGATTCCATGGACCTGGAGCGCGAGAAAGGGATCACCATCCAGTCCGCAGCGACGCACTGCGTTTGGGGTGACCACCAGgtgag---atggacgtttttcattcccttacaaa-gtttcgactttgtttctttctag---------
 |||||||||||||| || ||||||||||||||| | || || |||||||| ||||||||||| || || || ||  ||||   ||||   ||  || |||||||   || ||    |     ||  |   ||    | | | |   ||    | |           
AGATGGCGTCGGCGCTAAAATGGATTCCATGGACTTAGAACGAGAGAAAGGTATCACCATCCAATCAGCCGCTACCTACTGTACTTGGAAGGATTACAAGgtgagcagatagatagatagagatctttcttaattaatcctattgaattgagctttgaaatgaacag

upper sequence: EFJ36205 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: AT2G45030.1 (Arabidopsis thaliana), 5'ss of exon 1
GGATGGCGTCGGCGCCAAGATGGATTCCATGGACCTGGAGCGCGAGAAAGGGATCACCATCCAGTCCGCAGCGACGCACTGCGTTTGGGGTGACCACCAGgtg---agatggacgtttttcattcccttacaaagttt-cgactttg-tttctttctag--------------------------------------------------------------------------------------
 |||||||||||||| || ||||| || |||||| ||||||| |||||||| ||||| |||||||| || || ||  ||||   ||||   ||  || |||||   |||| ||          | ||||    | | |  || | |  ||||||   ||                                                                                      
AGATGGCGTCGGCGCTAAAATGGACTCTATGGACTTGGAGCGAGAGAAAGGTATCACTATCCAGTCAGCCGCTACTTACTGTACTTGGAAGGATTACAAGgtgaggagatagaaaaaaagatcttccttgtggattctgtgattctaatttcttctcagattcgtcaaaattggccttggttgtttaattgtgtagtaatcctattgcattgagctttgaaatttgttgttatgattgttgtcag

upper sequence: EFJ36205 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S100_33V6.1 (Physcomitrella patens), 5'ss of exon 1
GGATGGCGTCGGCGCCAAGATGGATTCCATGGACCTGGAGCGCGAGAAAGGGATCACCATCCAGTCCGCAGCGACGCACTGCGTTTGGGGTGACCACCAGgtgagatggacgtttttcattcccttaca-aagtttcgactttgtttctttctag------------------------------------------------
|||||| |||||||| ||||||||||| ||||||||||| || ||||| || || ||||| |||||||| || ||| ||||   |||||||||  | |||||    ||| | |||||  | | || |||  ||   ||           |   ||                                                
GGATGGAGTCGGCGCGAAGATGGATTCTATGGACCTGGAACGAGAGAAGGGAATTACCATTCAGTCCGCTGCTACGTACTGTACTTGGGGTGATAATCAGgtt---tgggcattttttctgcgctgacatgagcgacgggccaccggaatctaaggtgtaattaagagagggattgtaaagttgatgagaacaatagatatca

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), 31 (downstream exon)
Score: 5

GGATGGCGTCGGCGCCAAGATGGATTCCATGGACCTGGAGCGCGAGAAAGGGATCACCATCCAGTCCGCAGCGACGCACTGCGTTTGGGGTGACCACCAGgtgagatgga ... ttctttctagATCAACATCATCGATACTCCTGGGCACGTCGACTTTACGATCGAAGTGGAGCGAGCTTTGCGCGTGCTGGATGGCGCAATTCTTGTGCTGTGCAGCGTGA




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