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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_51V6.2
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


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatttattctgcacaggacaaatttgctcagttgataacaattgtttttggcagAGACTGGCATCAGACTTTTTGTCGAACTACATCTTCCTTGCCGTGGGTAGGGTGGGGTCCAGTACAGAACTGATAGTGCAACGCGTAGAATATGTGCAAG
                                 tgataac  putative branch site (score: 2)
                                          ttgttttt  putative PPT
                                   ataacaattgttttt  TA-rich tract