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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaatcatcttgctcttgtctgaatgcatatggaagattaattggtggaccgctccagGGCGAGAAGGACGATAAGATCATCGCCGTGTGCGCTGACGATCCCGAGTTCACACACTACCAAGACATCAAGGATCTCCCACCCCACAGGCTGGCAGAGA

Basic information

species Selaginella moellendorffii
transcript EFJ27219
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ27219 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os10g26600.1 (Oryza sativa), 3'ss of exon 6
----------------------------------------gtaacaatcatcttgctcttgtctgaatgcatatggaagattaattggtggaccgctccagGGCGAGAAGGACGATAAGATCATCGCCGTGTGCGCTGACGATCCCGAGTTCACACACTACCAAGACATCAAGGATCTCCCACCCCACAGGCTGGCAGAGA
                                          ||      |||  || |  | |  ||  | ||||   | |  ||  |||| |     |||| ||||| || |||||||||||||| || |||| ||| ||||||||||||   |||| | | ||  ||||||| ||| | || ||| | || || || |
gcatgacaacttcattcttttttggcagagttttattgtgaaaattgctgtctcactttgttgttgatcta-atggtgcacttgtttttggaacataaaagGGTGAGAAAGATGATAAGATCATCGCGGTTTGCGTTGATGATCCCGAGTTCCGCCACTTCAATGATCTCAAGGAGCTCTCTCCTCACCGACTTGCTGAAA

upper sequence: EFJ27219 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G026470_T02 (Zea mays), 3'ss of exon 3
-------------------gtaacaatcatc-ttgctcttgtctgaa----tgcatatggaagattaattggtggaccgctccagGGCGAGAAGGACGATAAGATCATCGCCGTGTGCGCTGACGATCCCGAGTTCACACACTACCAAGACATCAAGGATCTCCCACCCCACAGGCTGGCAGAGA
                     || ||||  |  | | | | |||  |    |  |  |   |    ||  | ||||    | ||||| ||||||||||| |||||||||||||| ||||| ||||| ||||||| |   |||||| | |||||||  || ||| | || ||| | ||    ||||
gtaggccgcccgagacggaccaataatccccactccccatatctagagtcttttacttaccaagcaaagcgctgga--attgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTACCGCCACTACAACGACATCAGCGAGCTCTCCCCTCACCGCCTCCAGGAGA

upper sequence: EFJ27219 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------gtaacaatca--tcttgctcttgtctgaatgcatatggaagattaattggtggaccgctccagGGCGAGAAGGACGATAAGATCATCGCCGTGTGCGCTGACGATCCCGAGTTCACACACTACCAAGACATCAAGGATCTCCCACCCCACAGGCTGGCAGAGA
                            | ||| || |  ||||     ||  |  | ||||||| ||  | | ||  |    |   |||||| ||||| |||||||||||||| || || |||||||||||||| || |    |||||||   |||||||| || || ||||| || || || || ||||
gtgatgtcatttctctcaagcaaatcatgcaaccattagttcttcacagtgagttgaggcatatgaaat-tcagttctttattcataccagGGAGAGAATGACGATAAGATCATTGCTGTATGCGCTGACGATCCAGAATATCGACACTACACTGACATCAAAGAGCTTCCACCTCATAGACTAGCTGAGA

upper sequence: EFJ27219 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S552_1V6.1 (Physcomitrella patens), 3'ss of exon 6
--------------------------------------------gtaacaatcat---cttgctcttgtctgaatgcatatggaagattaattggtggaccgctccagGGCGAGAAGGACGATAAGATCATCGCCGTGTGCGCTGACGATCCCGAGTTCACACACTACCAAGACATCAAGGATCTCCCACCCCACAGGCTGGCAGAGA
                                            | ||   |  |     || | |   | |  |    | |  ||||   ||   |||  ||   |||| ||||||||||| ||||||||||||||||| || ||||| ||||||| || ||| | | | |||||||| ||                          
gttagaagctgttgcgctcgcactgtgtggctgtttgtgtcgtggaaaaggttgtggatgtgttttctgcgggttagCAACGTGAGATCTGTT--CGGAATGC---AGGGTGAGAAGGACGACAAGATCATCGCCGTGTGTGCCGACGACCCCGAGTACAGACATTTCAAGGACATCAACGA--------------------------

upper sequence: EFJ27219 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S315_67V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------------------------------------gtaacaatcat---cttgctcttgtctgaatgcatatggaagattaattggtggaccgctccagGGCGAGAAGGACGATAAGATCATCGCCGTGTGCGCTGACGATCCCGAGTTCACACACTACCAAGACATCAAGGATCTCCCACCCCACAGGCTGGCAGAGA
                                            | ||   |  |     || | |   | |  |    | |  ||||   ||   |||  ||   |||| ||||||||||| ||||||||||||||||| || ||||| ||||||| || ||| | | | |||||||| || || ||||| ||| |  |||| ||||
gttagaagctgttgcgctcgcactgtgtggctgtttgtgtcgtggaaaaggttgtggatgtgttttctgcgggttagcaacgtgagatctgtt--cggaatgc---agGGTGAGAAGGACGACAAGATCATCGCCGTGTGTGCCGACGACCCCGAGTACAGACATTTCAAGGACATCAACGAGCTTCCACCGCACCGATTGGCGGAGA

upper sequence: EFJ27219 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S46_53V6.1 (Physcomitrella patens), 3'ss of exon 7
----------------------------------------------------------------gtaacaatcat--cttgctcttgtctgaatgcatatggaagattaa-ttggtggaccgctccagGGCGAGAAGGACGATAAGATCATCGCCGTGTGCGCTGACGATCCCGAGTTCACACACTACCAAGACATCAAGGATCTCCCACCCCACAGGCTGGCAGAGA
                                                                 ||    || |  ||     |   ||  ||| | ||  ||  |||| || ||      ||  |||| |||||||| || ||||||||||| || || ||||||||||| ||||  | ||||| | |||||||||| ||  | || || ||  | || || || |
gtgagggactattatgccgtactctttgacggaaaccaaactagcttgtattgatcatgttctcatattgttcgtacctaatcatccactatatgtaaatctaatgttaaatttgtaaggacctgtagGGAGAGAAGGATGACAAGATCATCGCTGTCTGTGCTGACGATCCGGAGTATAGACACTTCAAAGACATCAATGAGTTTCCTCCACATCGACTTGCCGAAA

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: 78

GAGCCTGTGTTGCCTGGATGCTTTCTGCGAGCGAGAGCGATTGGACTGATGCCGATGATTGATCAGgtaacaatca ... accgctccagGGCGAGAAGGACGATAAGATCATCGCCGTGTGCGCTGACGATCCCGAGTTCACACACTACCAAGACATCAAGGATCTCCCACCCCACAGGCTGGCAGAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcatcttgctcttgtctgaatgcatatggaagattaattggtggaccgctccagGGCGAGAAGGACGATAAGATCATCGCCGTGTGCGCTGACGATCCCGAGTTCACACACTACCAAGACATCAAGGATCTCCCACCCCACAGGCTGGCAGAGA
                                gattaat  putative branch site (score: 78)
                                              ccgctcc  putative PPT
                              aagattaatt  TA-rich tract