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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatttgcagctgtgctctcttgtagaagtctcggagtatcttgtatgatttattctgcacaggacaaatttgctcagttgataacaattgtttttggcagAGACTGGCATCAGACTTTTTGTCGAACTACATCTTCCTTGCCGTGGGTAGGGTGGGGTCCAGTACAGAACTGATAGTGCAACGCGTAGAATATGTGCAAG

Basic information

species Physcomitrella patens
transcript PP1S48_51V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S48_51V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os06g40020.1 (Oryza sativa), 3'ss of exon 3
-------tatttgcagctgtgctctcttgtagaagtctcggagtatcttgtatgatttattctgcacaggacaaatttgctcagttgataacaattgtttttggcagAGACTGGCATCAGACTTTTTGTCGAACTACATCTTCCTTGCCGTGGGTAGGGTGGGGTCCAGTACAGAACTGATAGTGCAACGCGTAGAATATGTGCAAG
       ||| || || |  | |    |   | | |       |||||  | ||||  |||   |        || || || | ||  | |   |||||||   ||||||||||| || |||||||||||||||||||| ||  |  | || || |||||||| || ||||| || || ||  ||||    || |||    |    |
atcagtatatctg-agtttagtttaactaatgcatttgacttttatctgctgtgatacatttgacttgtattcaactttctgaatt--tgatc-ttgtttt---cagAGACTGGCTTCGGACTTTTTGTCGAACTACATATTTATCACTGTTGGGAGGGTGGGTTCAAGTACTGACCTAATTATGCAGAAGGTTGAACTCCTCTCTG
















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|100401714|gb|BY954670.1|BY954670
EST:     GTGAACGTCAAACCATGCTGTTTAGCGCCACCTTTCCTAGAG------A-                         A-A-T----TCAGACTTTTTGTCGAACTACATCTTCCTTGCCGTGGGTAGG
genomic: GTGAACGTCAAACCATGCTGTTTAGCGCCACCTTTCCTAGAGAAATTCAGgtacttgggt ... tttttggcagAGACTGGCATCAGACTTTTTGTCGAACTACATCTTCCTTGCCGTGGGTAGG
EST: gi|162189005|gb|FC365123.1|FC365123
EST:     GTGAACGTCAAACCATGCTGTTTAGCGCCACCTTTCCTAGAGAAATTCAG                         AGACTGGCATCAGACTTTTTGTCGAACTACATCTTCCTTGCCGTGGGTAGG
genomic: GTGAACGTCAAACCATGCTGTTTAGCGCCACCTTTCCTAGAGAAATTCAGgtacttgggt ... tttttggcagAGACTGGCATCAGACTTTTTGTCGAACTACATCTTCCTTGCCGTGGGTAGG

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: 34 (upstream exon), 33 (downstream exon)
Score: 20

CGAACCCCAAATTCGTAGAATAGTGGAACAAATGGATATGCCACCGGCTGGTGAACGTCAAACCATGCTGTTTAGCGCCACCTTTCCTAGAGAAATTCAGgtacttgggt ... tttttggcagAGACTGGCATCAGACTTTTTGTCGAACTACATCTTCCTTGCCGTGGGTAGGGTGGGGTCCAGTACAGAACTGATAGTGCAACGCGTAGAATATGTGCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatttattctgcacaggacaaatttgctcagttgataacaattgtttttggcagAGACTGGCATCAGACTTTTTGTCGAACTACATCTTCCTTGCCGTGGGTAGGGTGGGGTCCAGTACAGAACTGATAGTGCAACGCGTAGAATATGTGCAAG
                                 tgataac  putative branch site (score: 20)
                                          ttgttttt  putative PPT
                                   ataacaattgttttt  TA-rich tract