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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtagttcgggcttttgaatcgatttttataaacgctgctgcgttacagGTTCTAGAAGCAAGGGCTGGATTTTACGAAAAGCCAATTGCCACGCTTGATTTTGCATCACTGTACCCATCAATTATGATGGCTTACAATCTTTGCTATT

Basic information

species Selaginella moellendorffii
transcript EFJ15224
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ15982 (Selaginella moellendorffii), 3'ss of exon 13
lower sequence: GLYMA06G16110.1 (Glycine max), 3'ss of exon 14
-------------------------------------------------gtaagtagttcgggcttttgaatcgatttttataaacgctgctgcgttacagGTTCTAGAAGCAAGGGCTGGATTTTACGAAAAGCCAATTGCCACGCTTGATTTTGCATCACTGTACCCATCAATTATGATGGCTTACAATCTTTGCTATT
                                                   |||  ||   | |||||||  |     || | |||  | |  | || |||||  | || ||||||||||||||||| ||||| |||||||| ||  | |||||||||||  |||| ||||| ||||||||||| || ||| | || ||||
ttaatgttctacaccttttcctgtatttgccttttggacgtttcacttgtcaagctgtgttgccttttgatgcatgcattttgaactttacaac-ttgcagGTATTGGAGGCAAGGGCTGGATTTTATGAAAAACCAATTGCTACTTTAGATTTTGCATCCTTGTATCCATCTATTATGATGGCCTATAATTTATGTTATT

upper sequence: EFJ15982 (Selaginella moellendorffii), 3'ss of exon 13
lower sequence: GLYMA04G38800.1 (Glycine max), 3'ss of exon 14
-------------------------------------------gtaagtagttcgg------gcttttgaatcgatttttataaacgctgctgcgttacagGTTCTAGAAGCAAGGGCTGGATTTTACGAAAAGCCAATTGCCACGCTTGATTTTGCATCACTGTACCCATCAATTATGATGGCTTACAATCTTTGCTATT
                                            | ||| ||   |       |||||||  |    ||| | |||  | |  | || |||||  | || ||||||||||||||||| ||||| |||||||| ||  | |||||||||||  |||| ||||| ||||||||||| || ||  | || ||||
atgtgctacaccttttcctatatttgtcttttggagttaatgtttcagttgtcgagctgtctccttttgatgcatgatttttgaactttacaac-ttgcagGTATTGGAGGCAAGGGCTGGATTTTATGAAAAACCAATTGCTACTTTAGATTTTGCATCCTTGTATCCATCTATTATGATGGCCTATAACTTATGTTATT

upper sequence: EFJ15982 (Selaginella moellendorffii), 3'ss of exon 13
lower sequence: AT5G63960.1 (Arabidopsis thaliana), 3'ss of exon 14
-------------------------------------------------------gtaagtagttcgggcttttgaatcgatttttataaacgctgctgcgttacagGTTCTAGAAGCAAGGGCTGGATTTTACGAAAAGCCAATTGCCACGCTTGATTTTGCATCACTGTACCCATCAATTATGATGGCTTACAATCTTTGCTATT
                                                        |     |||| | | | |   | | |||  |||       |    || |||||| ||||||||||  | || || || |||||||||||||| ||  | |||||||| ||||||||||| |||||||||||||| || ||||| ||||| |
gtaagtgggtgatttatggatctaacatttccttttggcctatcggttgcattaattccactgttccgacatgtttgttgttttggatatgtcaaacgatatt-cagGTTTTAGAAGCAAGAACAGGTTTCTATGAAAAGCCAATTGCAACTTTGGATTTTGCTTCACTGTACCCGTCAATTATGATGGCATATAATCTGTGCTACT

upper sequence: EFJ15982 (Selaginella moellendorffii), 3'ss of exon 13
lower sequence: PP1S54_271V6.1 (Physcomitrella patens), 3'ss of exon 14
------------------------------------------------------------------------------------------gtaag-tagttcgggcttttgaatcgatttttataaacgc------tgctgcgttacagGTTCTAGAAGCAAGGGCTGGATTTTACGAAAAGCCAATTGCCACGCTTGATTTTGCATCACTGTACCCATCAATTATGATGGCTTACAATCTTTGCTATT
                                                                                           || | ||  ||        ||| |   |||   || | |      |   |  | ||||||  |||| || |  || || |  || || ||||||||||||||  | |||||||||||| ||||||| || || |||||||| ||||||||||| || |
gtaagttttttaattttatttttaaaacaatattattgttgttacatttcttttgcatgagaaatgttgtgcactagttgttacattaccatatgctatctcctttccaagaacctggtttatcaagctcatcgggtctcgtttgacagGTATTAGATGCTAAAGCAGGGTACTATGACAAGCCAATTGCCACTTTGGATTTTGCATCATTGTACCCCTCCATCATGATGGCGTACAATCTTTGTTACT

upper sequence: EFJ15982 (Selaginella moellendorffii), 3'ss of exon 13
lower sequence: PP1S14_182V6.1 (Physcomitrella patens), 3'ss of exon 14
-----------------------------------------------------------------gtaagtagttcgggcttttgaatcgatttttataaacgctgctgcgtt---acagGTTCTAGAAGCAAGGGCTGGATTTTACGAAAAGCCAATTGCCACGCTTGATTTTGCATCACTGTACCCATCAATTATGATGGCTTACAATCTTTGCTATT
                                                                  || ||  |||   | |   |     |  |  | |||  || |  |||   ||||||  | || || |  ||||| | ||| || ||||||||||| ||||| ||||| ||||| ||||| || || ||||||||||| ||||| ||||| || |
gtaagtctttgttcaacttttgagaaatgactttgtacttataatagtttgtatgcagctatctgctaggtcattccctcgtaccagattctcctagttaaccatgttttgttttgacagGTGTTGGATGCCAAAGCTGGGTATTATGACAAGCCAATTGCTACGCTGGATTTCGCATCGCTGTATCCCTCCATTATGATGGCCTACAACCTTTGTTACT

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: 27 (upstream exon), 34 (downstream exon)
Score: 5

GTGCTTTCACAAATTCTAAGAAAATGCAGACAACGAAACTTTGTCGTGCCAAACATTAAGGGACAAGGGGCTGGGCAGGAAACCTTTGAAGGTGCAACCgtaagtagtt ... tgcgttacagGTTCTAGAAGCAAGGGCTGGATTTTACGAAAAGCCAATTGCCACGCTTGATTTTGCATCACTGTACCCATCAATTATGATGGCTTACAATCTTTGCTATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagtagttcgggcttttgaatcgatttttataaacgctgctgcgttacagGTTCTAGAAGCAAGGGCTGGATTTTACGAAAAGCCAATTGCCACGCTTGATTTTGCATCACTGTACCCATCAATTATGATGGCTTACAATCTTTGCTATT
                       ttttgaatcgattttt  TA-rich tract