Skip to another splice site:
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAATGTGCTGTTTGCCGGGAGGGCATGGTAGTAGGAGACAAGTTACAAGAAATGCCTTGCAAGCACAACTTCCATCCTGCTTGTCTCAAGCCTTGGCTGgtaggaagtgctcttatataccttatcatctctcgtcattttacctaaattgaatcaggttccttaccactcctattcaagatagtttgtgatcgaaatgactactatgaaaatttctaatgctctacttttcgtccatgcag

Basic information

species Physcomitrella patens
transcript PP1S295_6V6.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S295_6V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: EFJ04849 (Selaginella moellendorffii), 5'ss of exon 4
CGAATGTGCTGTTTGCCGGGAGGGCATGGTAGTAGGAGACAAGTTACAAGAAATGCCTTGCAAGCACAACTTCCATCCTGCTTGTCTCAAGCCTTGGCTGgtaggaagtgctcttatataccttatcatctctcgtcattttacctaaattgaatcaggttccttaccactcctattcaagatagtttgtgatcgaaatgactactatgaaaatttctaatgctctacttttcgtccatgcag
||| ||||| |||||| | || |   |||| || || ||  || | ||||| ||||||||||| ||| |||||||||||   ||||||||||| ||||||||| |  ||||| || | |   || |  | |   |   |  |  ||    |||   | |||   |  |  ||                                                                       
CGAGTGTGCAGTTTGCAGAGAAGTTTTGGTGGTCGGCGATGAGATGCAAGAGATGCCTTGCAAACACTACTTCCATCCTCTCTGTCTCAAGCCATGGCTGgtacgt-gtgctgtttttt--tttttttttttctggattcgtgtcttggctgagaaacgttatatgacgttcgcgcag-----------------------------------------------------------------

upper sequence: PP1S295_6V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: EFJ09851 (Selaginella moellendorffii), 5'ss of exon 4
CGAATGTGCTGTTTGCCGGGAGGGCATGGTAGTAGGAGACAAGTTACAAGAAATGCCTTGCAAGCACAACTTCCATCCTGCTTGTCTCAAGCCTTGGCTGgtaggaagtgctcttatataccttatcatctctcgtcattttacctaaattgaatcaggttccttaccactcctattcaagatagtttgtgatcgaaatgactactatgaaaatttctaatgctctacttttcgtccatgcag
||| ||||| |||||| | || |   |||| || || ||  || | ||||| ||||||||||||||| |||||||||||   ||||||||||| ||||||||| |  ||||| ||       || |  | |   |   |  |  ||    |||   | |||   ||  ||       ||                                                                
CGAGTGTGCAGTTTGCAGAGAAGTTTTGGTGGTCGGCGATGAGATGCAAGAGATGCCTTGCAAGCACTACTTCCATCCTCTCTGTCTCAAGCCATGGCTGgtacgt-gtgctttt-------ttttttttttctggattcgtgtcttggctgagaaacgtt--atatgacgttcgcccag---------------------------------------------------------------
















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|22133444|gb|BQ827740.1|BQ827740
EST:     AAATGCCTTGCAAGCACAACTTCCATCCTGCTTGTCTCAAGCCTTGGCTG                         GATGAACACAATTCATGCCCCATATGCCGGCATGAAATGCCTACC
genomic: AAATGCCTTGCAAGCACAACTTCCATCCTGCTTGTCTCAAGCCTTGGCTGgtaggaagtg ... gtccatgcagGATGAACACAATTCATGCCCCATATGCCGGCATGAAATGCCTACC
EST: gi|37836793|gb|BJ594801.1|BJ594801
EST:     AAATGCCTTGCAAGCACAACTTCCATCCTGCTTGTCTCAAGCCTTGGCTG                         GATGAACACAATTCATGCCCCATATGCCGGCATGAAATGCCTACCGATGAC
genomic: AAATGCCTTGCAAGCACAACTTCCATCCTGCTTGTCTCAAGCCTTGGCTGgtaggaagtg ... gtccatgcagGATGAACACAATTCATGCCCCATATGCCGGCATGAAATGCCTACCGATGAC
EST: gi|162237757|gb|FC413372.1|FC413372
EST:     AAATGCCTTGCAAGCACAACTTCCATCCTGCTTGTCTCAAGCCTGGGCGG                         GATGAACACAATTCATGCCCCATATGCCGGCATGAAATGCCTACCGATGCC
genomic: AAATGCCTTGCAAGCACAACTTCCATCCTGCTTGTCTCAAGCCTTGGCTGgtaggaagtg ... gtccatgcagGATGAACACAATTCATGCCCCATATGCCGGCATGAAATGCCTACCGATGAC
EST: gi|162152798|gb|FC329804.1|FC329804
EST:     AAATGCCTTGCAAGCACAACTTCCATCCTGCTTGTCTCAAGCCTTGGCTG                         GATGAACACAATTCATGCCCCATATGCCGGCATGAAATGCCTACCGATGAC
genomic: AAATGCCTTGCAAGCACAACTTCCATCCTGCTTGTCTCAAGCCTTGGCTGgtaggaagtg ... gtccatgcagGATGAACACAATTCATGCCCCATATGCCGGCATGAAATGCCTACCGATGAC
EST: gi|162261739|gb|FC437028.1|FC437028
EST:     AAATGCCTTGCAAGCACAACTTCCATCATGCTTGTGTCAAGCCTTGGCTG                         GATGAACACAATTCATGCCCCATTTGCCGGCATGAAATGCC
genomic: AAATGCCTTGCAAGCACAACTTCCATCCTGCTTGTCTCAAGCCTTGGCTGgtaggaagtg ... gtccatgcagGATGAACACAATTCATGCCCCATATGCCGGCATGAAATGCC
EST: gi|67701362|gb|BJ961595.1|BJ961595
EST:     AAATGCCTTGCAAGCACAACTTCCATCCTGCTTGTCTCAAGCCTTGGCTG                         GATGAACACAATTCATGCCCCATATGCCGGCATGAAATGCCTACCGATGAC
genomic: AAATGCCTTGCAAGCACAACTTCCATCCTGCTTGTCTCAAGCCTTGGCTGgtaggaagtg ... gtccatgcagGATGAACACAATTCATGCCCCATATGCCGGCATGAAATGCCTACCGATGAC
EST: gi|67692610|gb|BJ952843.1|BJ952843
EST:     AAATGCCTTGCAAGCACAACTTCCATCCTGCTTGTCTCAAGCCTTGGCTG                         GATGAACACAATTCATGCCCCATATGCCGGCATGAAATGCCTACCGATGAC
genomic: AAATGCCTTGCAAGCACAACTTCCATCCTGCTTGTCTCAAGCCTTGGCTGgtaggaagtg ... gtccatgcagGATGAACACAATTCATGCCCCATATGCCGGCATGAAATGCCTACCGATGAC
EST: gi|67693675|gb|BJ953908.1|BJ953908
EST:     AAATGCCTTGCAAGCACAACTTCCATCCTGCTTGTCTCAAGCCTTGGCTG                         GATGAACACAATTCATGCCCCATATGCCGGCATGAAATGCCTACCGATGAC
genomic: AAATGCCTTGCAAGCACAACTTCCATCCTGCTTGTCTCAAGCCTTGGCTGgtaggaagtg ... gtccatgcagGATGAACACAATTCATGCCCCATATGCCGGCATGAAATGCCTACCGATGAC
EST: gi|18341628|gb|BJ173663.1|BJ173663
EST:     AAATGCCTTGCAAGCACAACTTCCATCCTGCTTGTCTCAAGCCTTGGCTG                         GATGAACACAATTCATGCCCCATATGCCGGCATGAAATGCCTACCGATGAC
genomic: AAATGCCTTGCAAGCACAACTTCCATCCTGCTTGTCTCAAGCCTTGGCTGgtaggaagtg ... gtccatgcagGATGAACACAATTCATGCCCCATATGCCGGCATGAAATGCCTACCGATGAC
EST: gi|208364186|gb|DC947290.1|DC947290
EST:     AAATGCCTTGCAAGCACAACTTCCATCCTGCTTGTCTCAAGCCTTGGCTG                         GATGAACACAATTCATGCCCCATATGCCGGCATGAAATGCCTACCGATGAC
genomic: AAATGCCTTGCAAGCACAACTTCCATCCTGCTTGTCTCAAGCCTTGGCTGgtaggaagtg ... gtccatgcagGATGAACACAATTCATGCCCCATATGCCGGCATGAAATGCCTACCGATGAC
EST: gi|162275560|gb|FC451302.1|FC451302
EST:     AAATGCCTTGCAAGCACAACTTCCATCCTGCTTGTCTCAAGCCTTGGCTG                         GATGAACACAATTCATGCCCCATATGCCGGCATGAAATGCCTACCGATGAC
genomic: AAATGCCTTGCAAGCACAACTTCCATCCTGCTTGTCTCAAGCCTTGGCTGgtaggaagtg ... gtccatgcagGATGAACACAATTCATGCCCCATATGCCGGCATGAAATGCCTACCGATGAC

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: 31 (upstream exon), 24 (downstream exon)
Score: 5

CGAATGTGCTGTTTGCCGGGAGGGCATGGTAGTAGGAGACAAGTTACAAGAAATGCCTTGCAAGCACAACTTCCATCCTGCTTGTCTCAAGCCTTGGCTGgtaggaagtg ... gtccatgcagGATGAACACAATTCATGCCCCATATGCCGGCATGAAATGCCTACCGATGACCATGAGTACGAGCGACAGAAGGAGCGAGACAGAGAAGCTGAAGAGGAGC




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