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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgggaaggtcttgacttgtgctaggttaatattttctgcctttcaccagcatcttttattcatacataaatgatttctgtttgattgtttttatatgcagATGAACGACCAAGTCAAGAACTATTGTCATTTGCTTAACTCTACTCTTACCGCAACTGAGAGAACCCTTTGCTGTATTTTGGAAAATTACCAAACTCCAG

Basic information

species Physcomitrella patens
transcript PP1S13_192V6.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S13_192V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os03g10190.1 (Oryza sativa), 3'ss of exon 8
tgggaaggtcttgacttg--tgctaggttaatattttctgcctttcaccagcatcttttattcatacataaatgatttctgtttgattgtttttatatgcagATGAACGACCAAGTCAAGAACTATTGTCATTTGCTTAACTCTACTCTTACCGCAACTGAGAGAACCCTTTGCTGTATTTTGGAAAATTACCAAACTCCAG
   | |    || |||||  |||| |   |  |  || |    || |    ||||| |||||     |  ||||||||       | ||||   || ||||||   |||| |||  |||| | | |  |||| || | ||||| ||  | || || |||||||| |||||||||||||||||||| || | ||| |      
---gtatcatttcacttggatgctggtggatcaaattat---cttaaaattcatctgttatt-----accaatgattt-------aatgttcaaat-tgcagAATGACGAACAATCCAAGCAATTTGTTCATATGTTGAACTCAACATTGACTGCCACTGAGAGGACCCTTTGCTGTATTTTGGAGAACTTCCAGAGGGAGA

upper sequence: PP1S13_192V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os01g37837.1 (Oryza sativa), 3'ss of exon 8
tgggaaggtcttgacttgtgctaggttaatattttctgcctttcaccagcatcttttattcatacataaatgatttctgtttgattgtttttatatgcagATGAACGACCAAGTCAAGAACTATTGTCATTTGCTTAACTCTACTCTTACCGCAACTGAGAGAACCCTTTGCTGTATTTTGGAAAATTACCAAACTCCAG
   | |  | || |||||      | ||  ||    |    || |    ||||| |||||   ||     ||||||         ||||   || ||||||   | || |||  |||| | |    |||| || | ||||| ||  | || || |||||||| |||||||||||||||||||| || | ||| |      
---gtatcttttcacttggatgctggtag-atcaaattatcttaaaagtcatctgttattgccac-----tgattt-------gatgttcaaat-tgcagAATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACTGCCACTGAGAGGACCCTTTGCTGTATTTTGGAGAACTTCCAGAAGGAGA
















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|37844201|gb|BJ602209.1|BJ602209
EST:     GCACAGATTACCAATCAAGGAATCTTGAAATTCGTTATGGTCAAAAGAAG                         ATGAACGACCAAGTCAAGAACTATTGTCATTTGCTTAACTCTACTCTTACC
genomic: GCACAGATTACCAATCAAGGAATCTTGAAATTCGTTATGGTCAAAAGAAGgttttctcct ... ttatatgcagATGAACGACCAAGTCAAGAACTATTGTCATTTGCTTAACTCTACTCTTACC
EST: gi|37843556|gb|BJ601564.1|BJ601564
EST:     GCACAGATTACCAATCAAGGAATCTTGAAATTCGTTATGGTCAAAAGAAG                         ATGAACGACCAAGTCAAGAACTATTGTCATTTGCTTAACTCTACTCTTACC
genomic: GCACAGATTACCAATCAAGGAATCTTGAAATTCGTTATGGTCAAAAGAAGgttttctcct ... ttatatgcagATGAACGACCAAGTCAAGAACTATTGTCATTTGCTTAACTCTACTCTTACC
EST: gi|18339043|gb|BJ171069.1|BJ171069
EST:     GCACAGATTACCAATCAAGGAATCTTGAAATTCGTTATGGTCAAAAGAAG                         ATGAACGACCAAGTCAAGAACTATTGTCATTTGCTTAACTCTACTCTTACC
genomic: GCACAGATTACCAATCAAGGAATCTTGAAATTCGTTATGGTCAAAAGAAGgttttctcct ... ttatatgcagATGAACGACCAAGTCAAGAACTATTGTCATTTGCTTAACTCTACTCTTACC
EST: gi|162275690|gb|FC451367.1|FC451367
EST:     GCACAGATTACCAATCAAGGAATCTTGAAATTCGTTATGGTCAAAAGAAG                         ATGAACGACCAAGTCAAGAACTATTGTCATTTGCTTAACTCTACTCTTACC
genomic: GCACAGATTACCAATCAAGGAATCTTGAAATTCGTTATGGTCAAAAGAAGgttttctcct ... ttatatgcagATGAACGACCAAGTCAAGAACTATTGTCATTTGCTTAACTCTACTCTTACC
EST: gi|37849719|gb|BJ607727.1|BJ607727
EST:     GCACAGATTACCAATCAAGGAATCTTGAAATTCGTTATGGTCAAAAGAAG                         ATGAACGACCAAGTCAAGAACTATTGTCATTTGCTTAACTCTACTCTTACC
genomic: GCACAGATTACCAATCAAGGAATCTTGAAATTCGTTATGGTCAAAAGAAGgttttctcct ... ttatatgcagATGAACGACCAAGTCAAGAACTATTGTCATTTGCTTAACTCTACTCTTACC

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: 26 (upstream exon), 35 (downstream exon)
Score: 6

GTGGTTTCCGGCCTCCAAGACATACCGTGAGCTTGTATCATGCTCTAATTGCACAGATTACCAATCAAGGAATCTTGAAATTCGTTATGGTCAAAAGAAGgttttctcct ... ttatatgcagATGAACGACCAAGTCAAGAACTATTGTCATTTGCTTAACTCTACTCTTACCGCAACTGAGAGAACCCTTTGCTGTATTTTGGAAAATTACCAAACTCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccagcatcttttattcatacataaatgatttctgtttgattgtttttatatgcagATGAACGACCAAGTCAAGAACTATTGTCATTTGCTTAACTCTACTCTTACCGCAACTGAGAGAACCCTTTGCTGTATTTTGGAAAATTACCAAACTCCAG
                                 gtttgat  putative branch site (score: 6)
                                       ttgttttt  CT-rich tract
        ttttattcatacataa  TA-rich tract