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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGTCACTTTTATCTTGCTGACGTTCAGTTCTTGGTTCCTAGCTTTATCCTGGCTTTTCGCACCCTACATATTTAATCCATCTGGTTTTGAGTGGCAAAAgtaagcacgattcttccctttgattatgtttcattgggaaccttattggttagcaattaaacagggtacgatattcttttcacgttgaaaccttgagtacaatgacaattgaggatgtgaatttatgtgctgcag

Basic information

species Physcomitrella patens
transcript PP1S88_136V6.1
intron # 44
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S88_136V6.1 (Physcomitrella patens), 5'ss of exon 44
lower sequence: LOC_Os03g02756.2 (Oryza sativa), 5'ss of exon 12
CAGTCACTTTTATCTTGCTGACGTTCAGTTCTTGGTTCCTAGCTTTATCCTGGCTTTTCGCACCCTACATATTTAATCCATCTGGTTTTGAGTGGCAAAAgtaagcacgattcttccctttgattatgtttcattg-ggaaccttattggttagc--aattaaacagggtacgatattcttttcacgttgaaaccttgagtacaatgacaattgaggatgtgaatttatgtgctgcag
||||    |  || |||||  |  | |||   |||||  | ||  | || |||||||| || || |||||||| ||||||||||| ||||| ||||| ||||||||           || ||  | |||| |  || | ||   |||| |  |    |||||    |  ||  |||    | |||                                                     
CAGTTGGCTACATTTTGCTTTCCATAAGTAGCTGGTTTATGGCAGTTTCTTGGCTTTTTGCTCCATACATATTCAATCCATCTGGATTTGAATGGCAGAAgtaagctgctaagcattctatgcatgtgttactctgcgtaattatatttgaaattcgaattatcaggattaaaatacctctctcag----------------------------------------------------

upper sequence: PP1S88_136V6.1 (Physcomitrella patens), 5'ss of exon 44
lower sequence: LOC_Os06g02260.1 (Oryza sativa), 5'ss of exon 8
CAGTCACTTTTATCTTGCTGACGTTCAGTTCTTGGTTCCTAGCTTTATCCTGGCTTTTCGCACCCTACATATTTAATCCATCTGGTTTTGAGTGGCAAAAgtaagcacgattcttccctttgattatgtttcattgggaaccttattggttagcaattaaacagggtacgatattcttttcacgttgaaaccttgagtacaatgacaattgaggatgtgaatttatgtgctgcag
||    | |||||  |  | ||  |||||  ||||||||| |   | |||||||| |||||||| ||||| || || || |||||||| |||||||||||||| |  |      | |||      || ||| | |      ||  || |||  | |  |  ||||  |    |    |     | | ||| |  | |     | |                              
CATCTTCCTTTATTCTATTAACTATCAGTAGTTGGTTCCTCGTCGTGTCCTGGCTCTTCGCACCATACATTTTCAACCCTTCTGGTTTCGAGTGGCAAAAgtatgttcagaatattcct------atcttttagttaatttctctttagttgcctaacattcaggtaatatcaccagtgattgggtaaaatcaagggattgttcaa-----------------------------

upper sequence: PP1S88_136V6.1 (Physcomitrella patens), 5'ss of exon 44
lower sequence: GRMZM2G326643_T02 (Zea mays), 5'ss of exon 45
CAGTCACTTTTATCTTGCTGACGTTCAGTTCTTGGTTCCTAGCTTTATCCTGGCTTTTCGCACCCTACATATTTAATCCATCTGGTTTTGAGTGGCAAAAgtaagcacg-attcttccctttgattatgtttcattgggaaccttattggttagcaattaaacagggtacgatattcttttcacgttgaaaccttgagtacaatgacaattgaggatgtgaatttatgtgctgcag
||    | |||||  || | ||  |||||  ||||||||| | | | |||||||||||||| || ||||| || || || |||||||| |||||||||||||| |     || | |  |  | |||   |||| ||       |     |||  || || ||   |                     |||||| | |    ||| |   ||| | |||  |||| ||         
CATCTTCATTTATTCTGATTACTATCAGTAGTTGGTTCCTCGTTATGTCCTGGCTTTTCGCGCCTTACATTTTCAACCCTTCTGGTTTCGAGTGGCAAAAgtatgtttatatccatatccataatttattttcctttaaggttt-----gttgtcatttgaattaga--------------------gaaaccctaaccctaatcagggttgggaatg--aattgat---------

upper sequence: PP1S88_136V6.1 (Physcomitrella patens), 5'ss of exon 44
lower sequence: GLYMA04G36710.1 (Glycine max), 5'ss of exon 23
CAGTCACTTTTATCTTGCTGACGTTCAGTTCTTGGTTCCTAGCTTTATCCTGGCTTTTCGCACCCTACATATTTAATCCATCTGGTTTTGAGTGGCAAAAgtaagcacgattcttccctttgattatgtttcattgggaaccttattggt-tagcaattaaacagggtacgatattcttttcacgttgaaaccttgagtacaatgacaattgaggatgtgaatttatgtgctgcag
| || || | | | ||||| ||  | ||   ||||||||| |   | || ||||||||||| || ||||| || || || |||||||| ||||||||||||||||    |  ||    ||| |||| ||  |||   ||   ||| || | ||  |  |  | ||   ||     | ||    |    ||| | | | |   |                                 
CTGTTACGTATGTTTTGCTAACTCTTAGCAGTTGGTTCCTTGTCATTTCTTGGCTTTTCGCTCCTTACATTTTCAACCCCTCTGGTTTCGAGTGGCAAAAgtaagttgaaagctgt--tttaattacgtc-cat---gagttttaatgttatattatcttgatagtaaacacctattttggtcctccaaaagcataaatgttactg------------------------------

upper sequence: PP1S88_136V6.1 (Physcomitrella patens), 5'ss of exon 44
lower sequence: Vv06s0004g01200.t01 (Vitis vinifera), 5'ss of exon 43
CAGTCACTTTTATCTTGCTGACGTTCAGTTCTTGGTTCCTAGCTTTATCCTGGCTTTTCGCACCCTACATATTTAATCCATCTGGTTTTGAGTGGCAAAAgtaagcacgattcttccctttgattatgtttcattgggaaccttattggttagcaattaaacagggtacgatattcttttcacgttgaaaccttgagtacaatgacaattgaggatgtgaatttatgtgctgcag
|| |  | |  ||  | || |   | ||   ||||||| | ||| | || |||||||| || |||||  | || ||||||||||||||||||||||| ||||||| |  ||| |||   ||  || | | |||| |     || ||   |||  ||  |       |    ||  | ||| |                                                     
CACTATCGTACATTCTTCTTAGCATTAGCAGTTGGTTCATGGCTCTTTCTTGGCTTTTTGCTCCCTATTTGTTCAATCCATCTGGTTTTGAGTGGCAGAAgtaagtatcatttttctaatt--ttctctctcatggatttgctcatgttttattaaccatt-----tgttttaccccttttag----------------------------------------------------

upper sequence: PP1S88_136V6.1 (Physcomitrella patens), 5'ss of exon 44
lower sequence: Vv17s0000g10010.t01 (Vitis vinifera), 5'ss of exon 40
CAGTCACTTTTATCTTGCTGACGTTCAGTTCTTGGTTCCTAGCTTTATCCTGGCTTTTCGCACCCTACATATTTAATCCATCTGGTTTTGAGTGGCAAAAgtaagcacgattcttccctttgattatgtttcattgggaaccttat--tggttagcaattaaacagggtacgatattcttttcacgttgaaaccttgagtacaatgacaattgaggatgtgaat-ttatgtgctgcag-------------------------------------------------------------
| ||  |||||||  || | ||  | ||   ||||||||| |   |||| ||||| || || || || || |||||||| || ||||||||||||||||||||||  |   | |    |   ||||  ||||  | |    ||| |  |  ||  | |||        ||     || ||||     || | |      |    |  |  ||   | | ||||| |||       | |                                                             
CTGTGTCTTTTATTCTGTTAACTCTTAGCAGTTGGTTCCTTGTCATATCATGGCTCTTTGCTCCTTATATTTTTAATCCCTCAGGTTTTGAGTGGCAAAAgtaagtgctgctgtatatt---attaactttctgtagctttcttcttttaattgtccattctgagtattattcatttgttttattagtgtagctcgctttggcttttctttttgtgttctgaatattactaaactctgcttctcttaaaagcactgatcagccctcatgaatcttacaatcttaccatgcaataaacag

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: 25 (upstream exon), 32 (downstream exon)
Score: 4

CAGTCACTTTTATCTTGCTGACGTTCAGTTCTTGGTTCCTAGCTTTATCCTGGCTTTTCGCACCCTACATATTTAATCCATCTGGTTTTGAGTGGCAAAAgtaagcacga ... tgtgctgcagGACAGTTGAGGACTTTGAGGACTGGACTAATTGGTTGTTTTACAAAGGAGGAGTTGCTGTCAAAACTGATAACAGCTGGGAAGCTTGGTGGGTTGATGAG




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