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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatagtttgtcttgttttgacgtgattgacaaagcttttgggaactatcgaattgtgtcactgcttcatataagtagtcaatctaaatgttcatgctttcttgtgcagATTGTTGAGTGCCGACGTGTATTGAAATGGACATATGCTTATGGGTATTACTTGCCCGAGAACGAGCAAACAAAAAGGCAATTCTTTGAGTATTCACAAG

Basic information

species Physcomitrella patens
transcript PP1S178_72V6.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S178_72V6.3 (Physcomitrella patens), 3'ss of exon 11
lower sequence: LOC_Os09g33876.1 (Oryza sativa), 3'ss of exon 12
gtatgatagtttgtcttgttttgacgtgattgacaaagcttttgggaactatcgaattgtgtcactgcttcatataagtagtcaatctaaatgttcatgctttcttgtg-cagATTGTTGAGTGCCGACGTGTATTGAAATGGACATATGCTTATGGGTATTACTTGCCCGAGAACGAGCAAACAAAAAGGCAATTCTTTGAGTATTCACAAG
                                    || | ||   ||  ||    || | |  |   || |  |   ||   ||| || ||||||||  ||  ||||| |||||  | || ||| | || ||  ||||||||||||||||||||||||| ||  | | | | ||      | | || ||  | || |||| |||    ||||
---------------------------------gttagatattataaatcatt---ttctattgcccattgac-tgtttatgtaatttacatgttcattattcgttgtgacagATCATAGAATGCAGGCGAGTGCTGAAATGGACATATGCTTATGGGTACTATCTACACAACAA------AGCGAAGAGTGATTTTTTTGTGTACCTCCAAG
















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|22132083|gb|BQ826972.1|BQ826972
EST:     AATGTCAACCTGTCTCGCAACTGAAATTTGTGACAGATGCATGGCTGCAG                         ATTGTTGAGTGCCGACGTGTATTGAAATGGACATATGCTTAT
genomic: AATGTCAACCTGTCTCGCAACTGAAATTTGTGACAGATGCATGGCTGCAGgtatgatagt ... tcttgtgcagATTGTTGAGTGCCGACGTGTATTGAAATGGACATATGCTTAT
EST: gi|162233180|gb|FC409003.1|FC409003
EST:     AATGTCAACCTGTCTCGCAACTGAAATTTGTGACAGATGCATGGCTGCAG                         ATTGTTGAGTGCCGACGTGTATTGAAATGGACATATGCTTATGGGTATTAC
genomic: AATGTCAACCTGTCTCGCAACTGAAATTTGTGACAGATGCATGGCTGCAGgtatgatagt ... tcttgtgcagATTGTTGAGTGCCGACGTGTATTGAAATGGACATATGCTTATGGGTATTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtcactgcttcatataagtagtcaatctaaatgttcatgctttcttgtgcagATTGTTGAGTGCCGACGTGTATTGAAATGGACATATGCTTATGGGTATTACTTGCCCGAGAACGAGCAAACAAAAAGGCAATTCTTTGAGTATTCACAAG
                           atctaaa  putative branch site (score: 3)
                                        tgctttctt  putative PPT
           ttcatataa  TA-rich tract