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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtcttcacttctttctcatttgcttctcgagcgtgtgtgaggatccgggcttaactttctctcgctttgtcctctccagGTTCGCATAAGAGTTAGAATGAACTACAAGCCTCTGGAGGAGGATGCTTTCCGCCCCGTGCTCCATCACTACGACGGTCCCAAGTTTCGTCTCCAATTGT

Basic information

species Selaginella moellendorffii
transcript EFJ22023
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ22023 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os05g41930.1 (Oryza sativa), 3'ss of exon 4
gtt-tgtcttcacttctttctcatttgcttctcgagcgtgtgtgaggatccgggcttaactttctctcgctttgtcctctccagGTTCGCATAAGAGTTAGAATGAACTACAAGCCTCTGGAGGAGGATGCTTTCCGCCCCGTGCTCCATCACTACGACGGTCCCAAGTTTCGTCTCCAATTGT
||  ||  | ||  |        |||  |||||       | ||       |  || |  ||   ||   ||  | ||  | ||||  | ||  |  |||||| |  || ||||||| |||| |||||||||||| | || ||||| || || ||||| ||||| |||||||||||  |  | |
gtaatggttacagctggcgtgtgtttatttctcatttacttttggtttcatgcactgatattctgctatattcattcta-ctagGTGAGGATCCGCATTAGAAAGCTCTGCAAGCCTTTGGAAGAGGATGCTTTCAGACCAGTGCTGCACCATTACGATGGTCCAAAGTTTCGTCTTGAGCTCT

upper sequence: EFJ22023 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM5G860590_T01 (Zea mays), 3'ss of exon 3
----------gtt--tgtcttcactt---ctttctcatttgcttctcgagcgtgt----gtgaggatccgggcttaactttctctcgctttgtcctctccagGTTCGCATAAGAGTTAGAATGAACTACAAGCCTCTGGAGGAGGATGCTTTCCGCCCCGTGCTCCATCACTACGACGGTCCCAAGTTTCGTCTCCAATTGT
          ||   || ||| | ||   | |   ||| ||  ||   | ||  |    |||  ||||| | || |   |  | ||   |  |||    |||||  |  |   |    | | || ||    ||| ||||||||||| |||||||||||| | ||||| ||||||||||| ||||||||  | ||  |  |  
tttatgtcatgtcagtgccttgagttgcccgtctccatctgtatcatcaacggattactgtgttgatccagtctaataataatatctgatgatccaa--cagGTGAGGGTTGCAACGCGCAAGATCTGTTCGCCGCTGGAGGAGGACGCTTTCCGCCCCATCCTCCACCACTACGACGGCCCCAAGTTCAGGCTGGAGCTCA

upper sequence: EFJ22023 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: AC207342.3_FGT008 (Zea mays), 3'ss of exon 3
--------gtt-tgtcttcacttct----ttctcatttgcttctcgagcgtgt-gtgaggatccgggct-taactttctctcgct--ttgtcctctccagGTTCGCATAAGAGTTAGAATGAACTACAAGCCTCTGGAGGAGGATGCTTTCCGCCCCGTGCTCCATCACTACGACGGTCCCAAGTTTCGTCTCCAATTGT
        ||| | || || | |||     |||     |  ||| |  |  || ||    | ||  |   | ||     |  | |  ||||  | | ||||| ||  |   |    | | || |||| | || ||||||||||| || ||||||||| | || || ||||||||||| ||||||||||| ||| |  | |
tgtagcatgttgtttcatcgcatctaggcctctagggagtatctagtactcgtagttgttacccaagtggtgacgcatgcatgatgtttgtgatgtgcagGTGCGAGTGGCAACGCGGAAGATCTACGATCCACTGGAGGAGGACGCCTTCCGCCCCATCCTTCACCACTACGACGGGCCCAAGTTTCGGCTCGAGCTCT

upper sequence: EFJ22023 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G071154_T01 (Zea mays), 3'ss of exon 3
-----------gtttgtcttcacttctttctcatttgcttctcgagcgtgtgtgaggatccgggcttaac-----tttctctcgctttgtcct-ctccagGTTCGCATAAGAGTTAGAATGAACTACAAGCCTCTGGAGGAGGATGCTTTCCGCCCCGTGCTCCATCACTACGACGGTCCCAAGTTTCGTCTCCAATTGT
               | || ||  |    |    | | | ||  |||   ||        ||   || ||      | ||  || | ||   | || ||||| ||  |   |    | | || |||| | || ||||||||||| || ||||||||| | || || ||||||||||| |||||||| || ||| |  | |
gaggatctggtcgcaggctccaagtgcgaccatctagatgctgtagctgctgcatttcctcgttattgacgcatggtgcttgcgatgtgatgtgctgcagGTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTCCGCCCCATCCTGCACCACTACGACGGGCCCAAGTTCCGGCTCGAGCTCT

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), 35 (downstream exon)
Score: 173

GCTGCGAGTTTTGGGGGCTCAAACATAGATCCTACTGCGTGGGAAGACAAGAAGTGTCGTGGAGAATCTCGGTTCCCTGCACAGgtttgtcttc ... tcctctccagGTTCGCATAAGAGTTAGAATGAACTACAAGCCTCTGGAGGAGGATGCTTTCCGCCCCGTGCTCCATCACTACGACGGTCCCAAGTTTCGTCTCCAATTGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcgagcgtgtgtgaggatccgggcttaactttctctcgctttgtcctctccagGTTCGCATAAGAGTTAGAATGAACTACAAGCCTCTGGAGGAGGATGCTTTCCGCCCCGTGCTCCATCACTACGACGGTCCCAAGTTTCGTCTCCAATTGT
                        gcttaac  putative branch site (score: 173)
                         cttaactttctctcgc  CT-rich tract
                          ttaacttt  TA-rich tract