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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggcgcttgccactgaaaagtccttgttggaaatattcttccttctttatgtagGGACAATCCTCAGATGCGACGTAACAGGGAAGATTCTCATGAAGTGCTTTCTATCGGGCATGCCTGATTTAAAGCTCGGGCTCAACGACAAAATAGGACT

Basic information

species Selaginella moellendorffii
transcript EFJ22278
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ22278 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA05G23670.2 (Glycine max), 3'ss of exon 6
--------------gtaaggcgcttgccactgaaaagtccttg-ttggaaatattcttccttcttt----atgtagGGACAATCCTCAGATGCGACGTAACAGGGAAGATTCTCATGAAGTGCTTTCTATCGGGCATGCCTGATTTAAAGCTCGGGCTCAACGACAAAATAGGACT
               ||     ||    | ||| |  | || | |||      | ||  ||  |||    || |||| |   | ||  | || || || || |||||||||||||||||||||||||| || || ||||||||||||||| | ||  | || ||||| || || ||
gtgggctgtgggttttatttttctccatattgatatttgctaggttgcctgcctgctaactggtttgggaatttagGTAGTGTTCTGCGTTGTGATGTCACTGGGAAGATTCTCATGAAGTGCTTTCTTTCTGGAATGCCTGATTTAAAGTTGGGTTTGAATGACAAGATTGGTCT

upper sequence: EFJ22278 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA17G16630.3 (Glycine max), 3'ss of exon 6
--------------gtaaggcgcttgccactgaaaagtccttg-ttggaaatattcttccttctttatg----tagGGACAATCCTCAGATGCGACGTAACAGGGAAGATTCTCATGAAGTGCTTTCTATCGGGCATGCCTGATTTAAAGCTCGGGCTCAACGACAAAATAGGACT
                |     ||    | | | |  | || | |||     || ||  ||  ||| ||    |||| |   | ||  | || || || || ||||||||||| |||||||||||||| || || ||||||||||||||| | || || || ||||| || || ||
gtgggctgtggatttcatttttctccatattaatatttgctaggttgcccgcatgctaactagtttgtgaatttagGTAGTGTTCTGCGTTGTGATGTCACTGGGAAGATTCTTATGAAGTGCTTTCTTTCTGGAATGCCTGATTTAAAGTTGGGTCTGAATGACAAGATTGGTCT

upper sequence: EFJ22278 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: PP1S197_28V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------------------gtaaggcgcttgccactgaaaa---gtccttgttggaaatattc-------ttccttctttatgtagGGACAATCCTCAGATGCGACGTAACAGGGAAGATTCTCATGAAGTGCTTTCTATCGGGCATGCCTGATTTAAAGCTCGGGCTCAACGACAAAATAGGACT
                                  | | ||| ||   | |  | |   || ||||   || || ||         |  ||  |  || ||| || |   |  | || || || || || ||  |||| ||||| |||||||| ||||| ||||| ||| | ||||| ||||||||||| ||||| |||||
ttgcatcgattggtgtaatttggatcttcttatttcatgcgttttggattttatatctgttcttgaacgacatgtttgcactaactatttggtcttgcagGAACTACTTTGCGTTGTGATGTGACTGGAAAAGTTCTAATGAAATGCTTTCTTTCGGGGATGCCGGATCTTAAGCTTGGGCTCAACGATAAAATTGGACT

upper sequence: EFJ22278 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: PP1S54_156V6.1 (Physcomitrella patens), 3'ss of exon 6
------------------------------gtaaggcgcttgccac----tgaaaagtccttgt-tggaaatattcttcc----ttcttta----tgtagGGACAATCCTCAGATGCGACGTAACAGGGAAGATTCTCATGAAGTGCTTTCTATCGGGCATGCCTGATTTAAAGCTCGGGCTCAACGACAAAATAGGACT
                               | ||| | ||    |    || |   ||   |  ||   | | ||||      || |||     || ||| || |   |  | || ||||| || || |||||| | ||||||||||| || ||||| ||||| ||| | || || || ||||||||||||||||||||
acttatttatttctttatttattggaaagcttcaggtggtttatgcatgatgtatcatctcagcctgagtacaatcttgaacggttgtttggtgttgcagGAACTACTTTGCGTTGTGACGTGACTGGCAAGATTTTAATGAAGTGCTTCCTTTCGGGAATGCCGGATCTGAAACTTGGACTCAACGACAAAATAGGACT

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), 20 (downstream exon)
Score: 16

GTGTTTTTGGATATCGTGGAGAGTGTGAACCTTCTTATGTCACAAAAGGgtaaggcgct ... ctttatgtagGGACAATCCTCAGATGCGACGTAACAGGGAAGATTCTCATGAAGTGCTTTCTATCGGGCATGCCTGATTTAAAGCTCGGGCTCAACGACAAAATAGGACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggcgcttgccactgaaaagtccttgttggaaatattcttccttctttatgtagGGACAATCCTCAGATGCGACGTAACAGGGAAGATTCTCATGAAGTGCTTTCTATCGGGCATGCCTGATTTAAAGCTCGGGCTCAACGACAAAATAGGACT
                                  tattcttccttcttta  CT-rich tract
                               aaatattctt  TA-rich tract