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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttttccgatatcattgttttaaagtcaaatctaacattttattgtggattgcagTTTCATTTTGATCAAAGCAAAGTGCGTGCTGAGATTCGCTTGAAGGAAGGCCGGGCAAAACCAATTGATGTTTTGTCCAGAAATCTAAATTCTCCCGACG

Basic information

species Selaginella moellendorffii
transcript EFJ19424
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ19424 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: LOC_Os03g58590.1 (Oryza sativa), 3'ss of exon 5
----------------------------gtttgttttccgatatcattgttttaaagtca---aatctaaca--ttttattgtggattgcagTTTCATTTTGATCAAAGCAAAGTGCGTGCTGAGATTCGCTTGAAGGAAGGCCGGGCAAAACCAATTGATGTTTTGTCCAGAAATCTAAATTCTCCCGACG
                             |||| | ||       |||       | |      || |||||  |||| |  |  ||||||||||||||||||||||||||||||  |  |||||||  | ||    || || ||  ||||||| ||||||||| |    |  ||||| ||||   | || |
gttcatattttacaacatggcaaatatcatttggtctcatgctgaattaagccggacttcttttatgtaacaatttttgtcttctattgcagTTTCATTTTGATCAAAGCAAAGTTAGATCTGAGATCAGGTTACGCGAGGGGCGCACAAAACCTATTGATGTTCTCCTGAAGAATCTCAATTTCTCAGAAG

upper sequence: EFJ19424 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA19G37280.1 (Glycine max), 3'ss of exon 5
-----------------gtttgttttccgatatcattgttttaaagtcaaatctaacatttt----attgtggattgcagTTTCATTTTGATCAAAGCAAAGTGCGTGCTGAGATTCGCTTGAAGGAAGGCCGGGCAAAACCAATTGATGTTTTGTCCAGAAATCTAAATTCTCCCGACG
                 |||  |||||   | |  || ||||| |   || | | |    ||    | | |   |||||||||||||||||||||||||||||  |  | || ||| | |||   ||||| || || | ||||||||||||  |  |||   |||| |||    | || |
gtactactctgtctttagttcattttcatttgttgttattttata--taagtttgatgacttggacaatttaatttgcagTTTCATTTTGATCAAAGCAAAGTTAGGTCAGAAATTAGATTGCGTGAAGGGCGTGCCAGACCAATTGATGTCCTAACCAAGCATCTCAATGGCTCTGATG

upper sequence: EFJ19424 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA03G34590.1 (Glycine max), 3'ss of exon 5
-----------------gtttgttttccgatatcattgttttaaa-------gtcaaatctaacattt---tattgtggattgcagTTTCATTTTGATCAAAGCAAAGTGCGTGCTGAGATTCGCTTGAAGGAAGGCCGGGCAAAACCAATTGATGTTTTGTCCAGAAATCTAAATTCTCCCGACG
                 |||  |||||   | |  || ||||| |       ||||  |  |  | ||    | | |   |||||||||||||||||||||||||||||  |  | || ||| | |||   ||||| || || | ||| || |||||  |  |||   |||| |||    | || |
gtactactctgcctttagttcattttcatttgttgttattttatataatattgtcagtttgatgacttagacaatttaatttgcagTTTCATTTTGATCAAAGCAAAGTTAGGTCAGAAATTAGATTGCGTGAAGGGCGTGCCAGACCCATCGATGTCCTAACCAAGCATCTCAATGGCTCTGATG

upper sequence: EFJ19424 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA13G21200.1 (Glycine max), 3'ss of exon 5
-------------------gtttgttttccgatatcattgttttaaagtc----aaatctaacattt----tattgtggattgcagTTTCATTTTGATCAAAGCAAAGTGCGTGCTGAGATTCGCTTGAAGGAAGGCCGGGCAAAACCAATTGATGTTTTGTCCAGAAATCTAAATTCTCCCGACG
                    ||| |||   | |||  || | ||| |||     |||| | | | ||     | | |    ||||||||||||||||||||||||| ||  |  |||||||| | |||   ||||| || || |  || |||||| |  |  |||   | || |||    | || |
gtatggttccttgaattcattttatttatagttatttttttattatagtatttgaaatatgataattaagacaatttcatgtgcagTTTCATTTTGATCAAAGCAAGGTTAGATCTGAGATTAGATTGCGTGAAGGGCGTGCTAGGCCGATTGATATCCTAACCAAGCACCTCAATGGATCTGATG

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: 35 (upstream exon), 23 (downstream exon)
Score: 7

AAGGGCTATAGAAAAGGCTCAACATGAAGAAGAAATGGCCATGCTAGCGAGAGAGCGAGCAAGAGCGGAGTTTCAGGACTGGGAGAAAAAGGAAGAAGAGgtttgttttc ... tggattgcagTTTCATTTTGATCAAAGCAAAGTGCGTGCTGAGATTCGCTTGAAGGAAGGCCGGGCAAAACCAATTGATGTTTTGTCCAGAAATCTAAATTCTCCCGACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttccgatatcattgttttaaagtcaaatctaacattttattgtggattgcagTTTCATTTTGATCAAAGCAAAGTGCGTGCTGAGATTCGCTTGAAGGAAGGCCGGGCAAAACCAATTGATGTTTTGTCCAGAAATCTAAATTCTCCCGACG
                             atctaac  putative branch site (score: 7)
                 ttttaaagtcaaatct  TA-rich tract