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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGTCGGAGGCTGAAATCCGTCAGCTCTGTGTTGCATCGAAGGACATATTTTTGTCCCAGCCTAATCTTCTCGAGCTCGAGGCTCCAATTAAGATTTGTGgtttgccctgaacttgcactgcgtccgtcattcaacgtctacacaccagtcgtcgtgacgacatgtttgagtagtacgagatagttgaataggtctttta...

Basic information

species Physcomitrella patens
transcript PP1S97_286V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S97_286V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA08G02180.1 (Glycine max), 5'ss of exon 1
CTGTCGGAGGCTGAAATCCGTCAGCTCTGTGTTGCATCGAAGGACATATTTTTGTCCCAGCCTAATCTTCTCGAGCTCGAGGCTCCAATTAAGATTTGTGgtttgccctga-acttgcactgcgtccgtcattcaacgtctacacaccagtcgtcgtgacgacatgtttgagtagtacgagatagttgaataggtctttta-
||  | ||||| ||||| ||||| ||||||||| | || || || || ||| |   ||| |||||||||||||| ||||||||||| ||||||||||||||| |    |     |    | |  |   | |||||  ||   |   |  || ||  |    |  | |||   | ||   |  | ||  | |  |   | |  
CTTACCGAGGCGGAAATTCGTCAACTCTGTGTTTCCTCCAAAGAGATCTTTCTCAGCCAACCTAATCTTCTCGAACTCGAGGCTCCTATTAAGATTTGTGgtatattttattgataattccgattaattgattcattgtaaccttgcttgttgttttattaattttttttttttgtgtaa--ttgtgaattgtgatgtgtgg

upper sequence: PP1S97_286V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA05G37370.1 (Glycine max), 5'ss of exon 1
CTGTCGGAGGCTGAAATCCGTCAGCTCTGTGTTGCATCGAAGGACATATTTTTGTCCCAGCCTAATCTTCTCGAGCTCGAGGCTCCAATTAAGATTTGTGgt----ttgccctgaacttgcactgcgtccgtcattcaacgtctacacaccagtcgtcgtgacgacatgtttgagtagtacgagatagttgaataggtctttta-
||  ||||||| ||||| || || ||||||||| | || || || || ||| |    || |||||||||||||| ||||||||||| |||||||||||||||    || | |   | || |  |   |   | | |      ||     |  || ||  |       | ||||  | || | | || ||  | |  |     |  
CTTACGGAGGCAGAAATTCGACAACTCTGTGTTTCCTCCAAAGAGATCTTTCTCAGTCAACCTAATCTTCTCGAACTCGAGGCTCCTATTAAGATTTGTGgtatatttactcgatatttccgattaattgattaattgtaacct---tgcttgttgttttattagttt-tttgttttgtgcta-attgtgaattgtgatgcgtgg

upper sequence: PP1S97_286V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AT1G64040.1 (Arabidopsis thaliana), 5'ss of exon 1
CTGTCGGAGGCTGAAATCCGTCAGCTCTGTGTTGCATCGAAGGACATATTTTTGTCCCAGCCTAATCTTCTCGAGCTCGAGGCTCCAATTAAGATTTGTGgtttgccctgaac--ttgcactgcgtccgtcattcaacgtctacac-accagtcgtcgtgacgac-atgtttgagtagtacgagatagttgaataggtctttta
 || |||||||||| ||    || || |||  | |  | ||| | || ||| |  | || ||||||||||| || ||||||||||| ||||||||||||||| | |  | | |  ||    |   |||       |   |||   | || ||   | | |  ||  |||||||| ||       ||||    | || |   |||
TTGACGGAGGCTGAGATTAAACATCTTTGTTCTACCGCTAAGCAGATCTTTCTCACTCAACCTAATCTTCTTGAACTCGAGGCTCCTATTAAGATTTGTGgtattcattcatcaattttgttctctcctcttcaaattttcttttctacgaggatttgcgtagattatgtttgattatcc----atagaactagagattgatta

upper sequence: PP1S97_286V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AT4G11240.1 (Arabidopsis thaliana), 5'ss of exon 1
CTGTCGGAGGCTGAAATCCGTCAGCTCTGTGTTGCATCGAAGGACATATTTTTGTCCCAGCCTAATCTTCTCGAGCTCGAGGCTCCAATTAAGATTTGTGgt--ttgccctgaactt-gcactgcgtccgtcattcaacgt--ctacacaccagtcgtcgtgacg-acatgtttgagtagtacgagatagttgaataggtctttta
 |  | ||| | || || |||||||| ||| | || || || ||  | ||| |    ||||||||||| ||||||||||||||||| || |||||||| |||  |    |||||    | | ||  ||  ||  |  || |        |   ||  | |||  |    | |||||  | |   | ||  ||  ||          
ATTACTGAGACGGAGATACGTCAGCTATGTTTAGCTTCAAAAGAGGTTTTTCTCAGTCAGCCTAATCTCCTCGAGCTCGAGGCTCCTATCAAGATTTGCGgtaatgttactgaatagagaaatgtttctctctgtttactttatcttgaattcgtttttgtgttgtgggtttttgatcaattttacattttttgatgtaa------

upper sequence: PP1S97_286V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv06s0004g05530.t01 (Vitis vinifera), 5'ss of exon 1
CTGTCGGAGGCTGAAATCCGTCAGCTCTGTGTTGCATCGAAGGACATATTTTTGTCCCAGCCTAATCTTCTCGAGCTCGAGGCTCCAATTAAGATTTGTGgtttgccctgaacttgcactgcgtccgtcattcaacgtctacacaccagtcgtcgtgacgacatg-tttgagtagtacgagatagttgaataggtctttta
|||  |||| | || ||||| |||||||||  ||  || |  || || ||| |    |||||||||||||| ||||| ||||| ||||||||||| || |||  |        |  |  |   |      || || ||           | ||  ||      || |||  | |||    |   |||    || ||||   
CTGATGGAGTCGGAGATCCGCCAGCTCTGTACTGTTTCCAGAGAGATCTTTCTTCAGCAGCCTAATCTTCTTGAGCTGGAGGCACCAATTAAGATCTGCGgtgcgtttccttttaactttttcttttgggttgaatgtggggttgatt-tggttttgtttttgtgatttttggagtttttgggggtttttaagatcttggt

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|18328385|gb|BJ160390.1|BJ160390
EST:     TTTGTCCCAGCCTAATCTTCTCGAGCTCGAGGCTCCAATTAAGATTTGTG                         GTGATATCCATGGTCAATATTCTGACCTCTTGAGGTTGTTCGAATATGGTG
genomic: TTTGTCCCAGCCTAATCTTCTCGAGCTCGAGGCTCCAATTAAGATTTGTGgtttgccctg ... gatggtgcagGTGATATCCATGGTCAATATTCTGACCTCTTGAGGTTGTTCGAATATGGTG
EST: gi|67508068|gb|BJ940939.1|BJ940939
EST:     TTTGTCCCAGCCTAATCTTCTCGAGCTCGAGGCTCCAATTAAGATTTGTG                         GTGATATCCATGGTCAATATTCTGACCTCTTGAGGTTGTTCGAATATGGTG
genomic: TTTGTCCCAGCCTAATCTTCTCGAGCTCGAGGCTCCAATTAAGATTTGTGgtttgccctg ... gatggtgcagGTGATATCCATGGTCAATATTCTGACCTCTTGAGGTTGTTCGAATATGGTG
EST: gi|18364036|gb|BJ196109.1|BJ196109
EST:     TTTGTCCCAGCCTAATCTTCTCGAGCTCGAGGCTCCAATTAAGATTTGTG                         GTGATATCCATGGTCAATATTCTGACCTCTTGAGGTTGTTCGAATATGGTG
genomic: TTTGTCCCAGCCTAATCTTCTCGAGCTCGAGGCTCCAATTAAGATTTGTGgtttgccctg ... gatggtgcagGTGATATCCATGGTCAATATTCTGACCTCTTGAGGTTGTTCGAATATGGTG
EST: gi|18343007|gb|BJ175044.1|BJ175044
EST:     TTTGTCCCAGCCTAATCTTCTCGAGCTCGAGGCTCCAATTAAGATTTGTG                         GTGATATCCATGGTCAATATTCTGACCTCTTGAGGTTGTTCGAATATGGTG
genomic: TTTGTCCCAGCCTAATCTTCTCGAGCTCGAGGCTCCAATTAAGATTTGTGgtttgccctg ... gatggtgcagGTGATATCCATGGTCAATATTCTGACCTCTTGAGGTTGTTCGAATATGGTG
EST: gi|100390429|gb|BY952837.1|BY952837
EST:     TTTGTCCCAGCCTAATCTTCTCGAGCTCGAGGCTCCAATTAGGATTTGTG                         GTGATATCCATGGTCAATATTCTGACCTCTTGAGGTTGTTCGAATATGGTG
genomic: TTTGTCCCAGCCTAATCTTCTCGAGCTCGAGGCTCCAATTAAGATTTGTGgtttgccctg ... gatggtgcagGTGATATCCATGGTCAATATTCTGACCTCTTGAGGTTGTTCGAATATGGTG
EST: gi|208390001|gb|DC938056.1|DC938056
EST:     TTTGTCCCAGCCTAATCTCCTCGAGCTCGAGGCTCCAATTAAGATTTGTG                         GTGATATCCATGGTCAATATTCTGACCTCTTGAGGTTGTTCGAATATGGTG
genomic: TTTGTCCCAGCCTAATCTTCTCGAGCTCGAGGCTCCAATTAAGATTTGTGgtttgccctg ... gatggtgcagGTGATATCCATGGTCAATATTCTGACCTCTTGAGGTTGTTCGAATATGGTG
EST: gi|100372677|gb|BY948650.1|BY948650
EST:     TTTGTCCCAGCCTAATCTTCTCGAGCTCGAGGCTCCAATTAAGATTTGTG                         GTGATATCCATGGTCAATATTCTGACCTCTTGAGGTTGTTCGAATATGGTG
genomic: TTTGTCCCAGCCTAATCTTCTCGAGCTCGAGGCTCCAATTAAGATTTGTGgtttgccctg ... gatggtgcagGTGATATCCATGGTCAATATTCTGACCTCTTGAGGTTGTTCGAATATGGTG

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), 34 (downstream exon)
Score: 6

CTGTCGGAGGCTGAAATCCGTCAGCTCTGTGTTGCATCGAAGGACATATTTTTGTCCCAGCCTAATCTTCTCGAGCTCGAGGCTCCAATTAAGATTTGTGgtttgccctg ... gatggtgcagGTGATATCCATGGTCAATATTCTGACCTCTTGAGGTTGTTCGAATATGGTGGCTTCCCACCTGAGGCTAATTACCTATTTTTAGGGGATTATGTTGACAG




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