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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgcatcaaacaaaggatggacatatctgactctcctttttttcaagGATTATGTTGCGACTAGGTGGTACCGAGCCCCCGAACTATGTGGCTCCTTCTTTTCCAAG

Basic information

species Selaginella moellendorffii
transcript EFJ38694
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ38694 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G089484_T01 (Zea mays), 3'ss of exon 3
-------------------------------------gtaagtgcatcaaacaaaggatggaca-tatctgactctcctttttttcaagGATTATGTTGCGACTAGGTGGTACCGAGCCCCCGAACTATGTGGCTCCTTCTTTTCCAAG
                                     |  ||   |||   | |  | ||   | | ||| |||||  ||||     ||||||||||||| ||||||||||||||||| || ||  | ||||| || ||||| ||||||
gtatgacattttttgaccactatgctattcagttgttgctaggctatctttctagtggtgtctagtttcttactcttgtttt-----agGATTATGTTGCAACTAGGTGGTACCGAGCACCAGAGTTGTGTGGATCTTTCTTCTCCAAG

upper sequence: EFJ38694 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G017351_T01 (Zea mays), 3'ss of exon 2
--------------------------------gtaagtgcatcaaacaaagg---atggacatatctgactctcc--tttttttcaagGATTATGTTGCGACTAGGTGGTACCGAGCCCCCGAACTATGTGGCTCCTTCTTTTCCAAG
                                 |   || | | |     |     | ||     || | |      | | |||  ||||||||||||| ||||||||||||||||| || || || ||||| || || || || |||
gtatgccatcttttcaaccagtatacttttcaattcttgtacctagtctggctttgtagaatcggctaatttcttaatctgtttttagGATTATGTTGCAACTAGGTGGTACCGAGCACCGGAGCTGTGTGGATCATTTTTCTCAAAG
















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: 24 (upstream exon), 34 (downstream exon)
Score: 23

AAAAAACATTCTTGCGAATGCCGACTGCAAGCTAAAAATCTGTGATTTTGGACTTGCTCGAGTTGCTTTTAACGATGCTCCGACGGCCATCTTTTGGACAgtaagtgcat ... ttttttcaagGATTATGTTGCGACTAGGTGGTACCGAGCCCCCGAACTATGTGGCTCCTTCTTTTCCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagtgcatcaaacaaaggatggacatatctgactctcctttttttcaagGATTATGTTGCGACTAGGTGGTACCGAGCCCCCGAACTATGTGGCTCCTTCTTTTCCAAG
                                atctgac  putative branch site (score: 23)
                               tatctgactctccttt  CT-rich tract
                                            tttttttcaa  TA-rich tract