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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctgtatcgtatcgatcgagtctgactttaagttggctgacgagaagatgaaaaaaaaaatgtttttttctgttagATCTTGATTCCACAGCTGGAGCCCCTCACCGAGCAGCAGCTGATGGGAATTTGCAACCTCCAGCAATCCTCGCAGCAGGCCGAGGACGCTTTGTCGCAGG

Basic information

species Selaginella moellendorffii
transcript EFJ30797
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ30797 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os06g15480.2 (Oryza sativa), 3'ss of exon 7
------gtaagctgtatcg--tatcgatcgagtctgactttaagttgg----ctgacgagaagatgaaaaaaaa-----aatgtttttttctgt-tagATCTTGATTCCACAGCTGGAGCCCCTCACCGAGCAGCAGCTGATGGGAATTTGCAACCTCCAGCAATCCTCGCAGCAGGCCGAGGACGCTTTGTCGCAGG
        | | |  |  |   | | | | | |    |   |||        |||| |  |  ||  |     |      ||| | || | |||  || |  |       || || ||||| || || || |||||||||||||| || |||||||| ||||| || ||||||||||||||||||||  |||||||||
gttttgacacgatcgagtgatcacccacccaattcagcaacaagcaaagaatctgaagctaccattgaccgccattgttgatgatgttgtttgtgcagGTTCTTGCCAGCCATCTTGAGCCGCTGACGGATCAGCAGCTGATGGGCATCTGCAACCTGCAGCAGTCGTCGCAGCAGGCCGAGGACGCGCTGTCGCAGG

upper sequence: EFJ30797 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os10g41640.1 (Oryza sativa), 3'ss of exon 1
-------------------gtaagctgtatcgtatcgatc---gagtctgactttaa-gttggctg--acgagaagatgaaaaaaaaaatgtttttttctgttagATCTTGATTCCACAGCTGGAGCCCCTCACCGAGCAGCAGCTGATGGGAATTTGCAACCTCCAGCAATCCTCGCAGCAGGCCGAGGACGCTTTGTCGCAGG
                     |  |  |   ||| | | |   || |||||   ||   ||| |||  |       ||||  |  |  ||||| |||  ||   |  |||||   | || || ||||| || ||  | |||||| ||||||| || |||||||| ||||| || ||||||||||||||||||||  |||| ||||
gtttgacacgagtgatcacccacccaattcagtaacaagcaaagaatctgaagctaccattgactgctattgttgaatgatgatgatgatgttgtttg-tgcagGTACTTGAGAGC-CATCTTGAGCCGCTGACGAATCAGCAGTTGATGGGCATCTGCAACCTGCAGCAGTCGTCGCAGCAGGCCGAGGACGCGCTGTCACAGG

upper sequence: EFJ30797 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os01g65970.1 (Oryza sativa), 3'ss of exon 1
----------------gtaagctgtatcgtatcgatcgagtctgactttaa-gttggctgacg-----agaagatgaaaaaaaaaatgtttttttctgttagATCTTGATTCCACAGCTGGAGCCCCTCACCGAGCAGCAGCTGATGGGAATTTGCAACCTCCAGCAATCCTCGCAGCAGGCCGAGGACGCTTTGTCGCAGG
                 | |  |   |   |   |  || |||||   ||   ||| |||          | |||||  |  |  ||||| |||  ||   | ||||||   | || || ||||| || || || |||  | | ||||| || |||||||| ||||| ||||||||||||| |||||||||  |||||||||
cacgagtgatcacccactcaattcagtaacaagcaaagaatctgaagctaccattgactgctattgttgaatgatgatgatgatgatgttgtttg-tgcagGTTCTTGAGAGC-CATCTTGAGCCACTGACGGATCAGTTGTTTATGGGCATCTGCAACCTACAGCAGTCCTCGCAGCAGGTCGAGGACGCGCTGTCGCAGG

upper sequence: EFJ30797 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA15G37220.1 (Glycine max), 3'ss of exon 6
-------------------gtaagctgtatcgtatcgatcgagtctgactttaagttggctgacgagaagatgaaaaa-aaaaatgtttttttctgttagATCTTGATTCCACAGCTGGAGCCCCTCACCGAGCAGCAGCTGATGGGAATTTGCAACCTCCAGCAATCCTCGCAGCAGGCCGAGGACGCTTTGTCGCAGG
                         | | ||| ||   | |||||    | ||| ||   ||||    |  | |        ||| |  ||   |   || |  || ||   ||  ||||||| ||||| ||||||||||||||||| |||  |||| | ||||||||||| || || || || || || || || ||||
ttcataattgtggctactgaggttttatttcggatatgtggagtcattttataatttccttgactttgactttagtcctgtgaatttggttgcattgcagCTGCTGGTTAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATTACCAACTTGCAGCAATCCTCCCAACAAGCAGAAGATGCATTATCTCAGG

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: 33 (upstream exon), 35 (downstream exon)
Score: 10

CAAGGCCGACGTCTTCCACCTCGTCTCCGGGATGTGGAAGTCTCCCGCCGAGCGCTGCTTCATGTGGATGGGAGGATTCAGACCCTCGGAGCTTCTCAAGgtaagctgta ... tttctgttagATCTTGATTCCACAGCTGGAGCCCCTCACCGAGCAGCAGCTGATGGGAATTTGCAACCTCCAGCAATCCTCGCAGCAGGCCGAGGACGCTTTGTCGCAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgactttaagttggctgacgagaagatgaaaaaaaaaatgtttttttctgttagATCTTGATTCCACAGCTGGAGCCCCTCACCGAGCAGCAGCTGATGGGAATTTGCAACCTCCAGCAATCCTCGCAGCAGGCCGAGGACGCTTTGTCGCAGG
             ggctgac  putative branch site (score: 10)
                                       tgtttttttctgtt  putative PPT
                          atgaaaaaaaaaatgt  TA-rich tract