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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCTGAAGGACTTACTCTGGAGAAGACATCTTGTCCTTTAGGAGTTGTTTTGGTTGTGTTCGAGTCTCGCCCTGATGCCCTAGTTCAGgtactgtcgagatcctgcgcagtgtgccctgccatacggcttaacgttcctttgcaattgtagatctttgcgcttactcattattatgttttacagtatatgctcaatgtcgtcaaattgtttcactactgaagtgcgacttatgcatcag

Basic information

species Physcomitrella patens
transcript PP1S22_40V6.2
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S22_40V6.2 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA18G03830.1 (Glycine max), 5'ss of exon 10
GTTGCTGAAGGACTTACTCTGGAGAAGACATCTTGTCCTTTAGGAGTTGTTTTGGTTGTGTTCGAGTCTCGCCCTGATGCCCTAGTTCAGgtactgtcgagatcctgcgcagtgtgccctgccatacggcttaacgttcctttgcaattgtagatctttgcgcttactcattattatgttttacagtatatgctcaatgtcgtcaaattgtttcactactgaagtgcgacttatgcatcag
 |||| || || || | | ||||||| ||||| | | ||||||||||| ||||  |||| || ||||||||||||||||| ||||| ||||||   |  | ||  |      | |      || |  |     || |   |    | |   |  |  | ||  ||||   |  |  ||  ||    |||                                                    
CTTGCAGAGGGGCTGATTTTGGAGAAAACATCATCTTCTTTAGGAGTTCTTTTAATTGTTTTTGAGTCTCGCCCTGATGCACTAGTACAGgtaa-attaacattttcatttttctttttcaccttctgttaatacctggttaattattctcaatttctcgcttttacctttcctcttgcctttatttatga--------------------------------------------------

upper sequence: PP1S22_40V6.2 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA03G12240.1 (Glycine max), 5'ss of exon 10
GTTGCTGAAGGACTTACTCTGGAGAAGACATCTTGTCCTTTAGGAGTTGTTTTGGTTGTGTTCGAGTCTCGCCCTGATGCCCTAGTTCAGgtactgtcgagatcctgcgcagtgtgccctgccatacggctt-aacgttcc-tttgcaattgtagatctttgcgcttactcattattatgttttacagtatatgctcaatgtcgtcaaattgtttcactactgaagtgcgacttatgcatcag
 | |  ||   ||| |  |||||||||||||| |||||||| || ||  || ||||| | || |||||||| ||||||||||| ||||||||    |  |||| |    |    |         | |  ||| ||    |   ||  ||    | |  |||| || |  | |  | |      |  ||||                                                     
CTAGTAGATAAACTCATCCTGGAGAAGACATCATGTCCTTTGGGTGTCCTTCTGGTTATATTTGAGTCTCGACCTGATGCCCTTGTTCAGgttaatttaagattcctttcctcttatttgttttttcaacttcaataaactgcttagaaggacaaagatttgagcatgattacaaattatccatttagta-----------------------------------------------------

upper sequence: PP1S22_40V6.2 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA01G24530.1 (Glycine max), 5'ss of exon 11
GTTGCTGAAGGACTTACTCTGGAGAAGACATCTTGTCCTTTAGGAGTTGTTTTGGTTGTGTTCGAGTCTCGCCCTGATGCCCTAGTTCAGgtactgtcgagatcctgcgcagtgtgccctgccatacggctt-aacgttcc-tttgcaattgtagatctttgcgcttactcattattatgttttacagtatatgctcaatgtcgtcaaattgtttcactactgaagtgcgacttatgcatcag
 | |  ||   ||| |  |||||||||| ||| |||||||| || ||  || ||||| | || |||||||| ||||||||||| ||||||||    |  |  |||    |  | |   ||| | | |  ||| ||    |   ||  ||    | |  |||| || |  | |  | |      |  ||||||                                                   
CTAGTAGATAAACTCATCCTGGAGAAGATATCATGTCCTTTGGGTGTCCTTCTGGTTATATTTGAGTCTCGACCTGATGCCCTTGTTCAGgttaatttaaattcccattccttat---ctgtctttcatcttcaataaactgcttagaaggacaaagatttgagcatgattacaaattgtccatttagtataa--------------------------------------------------

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|162184139|gb|FC358885.1|FC358885
EST:     TAGGAGTTGTTTTGGTTGTGTTCGAGTCTCGCCCTGATGCCCTAGTTCAG                         ATAGCATCTCTAGCAATTCGTAGTGGGAACGGGCTTTTGCTGAAGGGCGGG
genomic: TAGGAGTTGTTTTGGTTGTGTTCGAGTCTCGCCCTGATGCCCTAGTTCAGgtactgtcga ... tatgcatcagATAGCATCTCTAGCAATTCGTAGTGGGAACGGGCTTTTGCTGAAGGGCGGG
EST: gi|162257460|gb|FC433321.1|FC433321
EST:     TAGGAGTTGTTTTGGTTGTGTTCGAGTCTCGCCCTGATGCCCTAGTTCAG                         ATAGCATCTCTAGCAATTCGTAGTGGGAACGGGCTTTTGCTGAAGGGCGGG
genomic: TAGGAGTTGTTTTGGTTGTGTTCGAGTCTCGCCCTGATGCCCTAGTTCAGgtactgtcga ... tatgcatcagATAGCATCTCTAGCAATTCGTAGTGGGAACGGGCTTTTGCTGAAGGGCGGG
EST: gi|162276248|gb|FC452602.1|FC452602
EST:     TAGGAGTTGTTTTGGTTGTGTTCGAGTCTCGCCCTGATGCCCTAGTTCAG                         ATAGCATCTCTAGCAATTCGTAGGGGGAACGGGCTTTTGCTGAAGGGCGGG
genomic: TAGGAGTTGTTTTGGTTGTGTTCGAGTCTCGCCCTGATGCCCTAGTTCAGgtactgtcga ... tatgcatcagATAGCATCTCTAGCAATTCGTAGTGGGAACGGGCTTTTGCTGAAGGGCGGG
EST: gi|162191467|gb|FC367171.1|FC367171
EST:     TAGGAGTTGTTTTGGTTGTGTTCGAGTCTCGCCCTGATGCCCTAGTTCAG                         ATAGCATCTCTAGCAATTCGTAGTGGGAACGGGCTTTTGCTGAAGGGCGGG
genomic: TAGGAGTTGTTTTGGTTGTGTTCGAGTCTCGCCCTGATGCCCTAGTTCAGgtactgtcga ... tatgcatcagATAGCATCTCTAGCAATTCGTAGTGGGAACGGGCTTTTGCTGAAGGGCGGG
EST: gi|162210539|gb|FC386835.1|FC386835
EST:     TAGGAGTTGTTTTGGTTGTGTTCGAGTCTCGCCCTGATGCCCTAGTTCAG                         ATAGCATCTCTAGCAATTCGTAGTGGGAACGGGCTTTTGCTGAAGGGCGGG
genomic: TAGGAGTTGTTTTGGTTGTGTTCGAGTCTCGCCCTGATGCCCTAGTTCAGgtactgtcga ... tatgcatcagATAGCATCTCTAGCAATTCGTAGTGGGAACGGGCTTTTGCTGAAGGGCGGG
EST: gi|162167791|gb|FC344521.1|FC344521
EST:     TAGGAGTTGTTTTGGTTGTGTTCGAGTCTCGCCCTGATGCCCTAGTTCAG                         ATAGCATCTCTAGCAATTCGTAGTGGGAACGGGCTTTTGCTGAAGGGCGGG
genomic: TAGGAGTTGTTTTGGTTGTGTTCGAGTCTCGCCCTGATGCCCTAGTTCAGgtactgtcga ... tatgcatcagATAGCATCTCTAGCAATTCGTAGTGGGAACGGGCTTTTGCTGAAGGGCGGG
EST: gi|162153153|gb|FC329559.1|FC329559
EST:     TANGAGTTGTTTTGGTTGTGTTCGAGTCTCGCCCTGATGCCCTAGTTCAG                         ATAGCATCTCTAGCAATT
genomic: TAGGAGTTGTTTTGGTTGTGTTCGAGTCTCGCCCTGATGCCCTAGTTCAGgtactgtcga ... tatgcatcagATAGCATCTCTAGCAATT

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: 32

GTTGCTGAAGGACTTACTCTGGAGAAGACATCTTGTCCTTTAGGAGTTGTTTTGGTTGTGTTCGAGTCTCGCCCTGATGCCCTAGTTCAGgtactgtcga ... tatgcatcagATAGCATCTCTAGCAATTCGTAGTGGGAACGGGCTTTTGCTGAAGGGCGGGAAGGAAGCAGCACGATCGAATGCTATCCTACATAAG




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