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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtcctgagcatctttcagggcgttgcttgtagcctctactgatagtcttggctgatgtgtaccctcaaatttgtgtctcagggttgtcgcatggtgaagATGACATGTGCAGAGCACGATCGGTATGCAGCGGGGAGCCAATTCATCACTCACACCGTTGGGAG

Basic information

species Physcomitrella patens
transcript PP1S55_261V6.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S55_261V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G324297_T04 (Zea mays), 3'ss of exon 2
----------------------------tgtcctgagcatctttca-----gggcgtt--gcttgtagcctctactgatagtcttgg-ctgatgtgtaccctcaaatttgtg-----------tctcagggttgtcgcatggtgaagATGACATGTGCAGAGCACGATCGGTATGCAGCGGGGAGCCAATTCATCACTCACACCGTTGGGAG-------------------------
                            ||   |||   || | ||     |||| ||    ||||||   |||||||   | | |   |  |||||    |  | ||  |            |   |||||||| | |||||| ||||| | ||||| ||||| ||||| || || ||||||||||| |||||||| |||||  |||||||                         
gtaactctaccagaactcatgatctctttgatttgatgttcatccacactggggcatttaatttgtaggagctactgaacatgtggaatttttgtgtgtgtttcatttcattctagacaattcttgtagggttgtagGATGGTGGAGATGTCGTGTGCCGAGCATGATCGCTACGCCGCGGGGAGCCAGTTCATCACGCACACAATTGGGAGGTCAGCAACATTGCATATATCTGGA

upper sequence: PP1S55_261V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G324297_T02 (Zea mays), 3'ss of exon 2
----------------------------tgtcctgagcatctttca-----gggcgtt--gcttgtagcctctactgat-------agtcttggctgatgtgtaccctcaaatttg-----tgtctcagggttgtcgcatggtgaagATGACATGTGCAGAGCACGATCGGTATGCAGCGGGGAGCCAATTCATCACTCACACCGTTGGGAG
                            ||   |||   || | ||     |||| ||    ||||||   |||||||        | | || |    ||| |    |||   | |     | |   |||||||| | |||||| ||||| | ||||| ||||| ||||| || || ||||||||||| |||||||| |||||  |||||||
gtaactctaccagaactcatgatctctttgatttgatgttcatccacactggggcatttaatttgtaggagctactgaacatgtggaatttttgtgtgtgtttcatttcattctagacaattcttgtagGGTTGTAGGATGGTGGAGATGTCGTGTGCCGAGCATGATCGCTACGCCGCGGGGAGCCAGTTCATCACGCACACAATTGGGAG
















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|37821009|gb|BJ579075.1|BJ579075
EST:     GCCGACGGTCCAGGATCGCTGACCGGTTCCTGGACATTTTTGCGAGTGAG                         ATGACATGTGCAGAGCACGATCGGTATGCAGCGGGGAGCCAATTCATCACT
genomic: GCCGACGGTCCAGGATCGCTGACCGGTTCCTGGACATTTTTGCGAGTGAGgtaaaccaca ... catggtgaagATGACATGTGCAGAGCACGATCGGTATGCAGCGGGGAGCCAATTCATCACT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcttggctgatgtgtaccctcaaatttgtgtctcagggttgtcgcatggtgaagATGACATGTGCAGAGCACGATCGGTATGCAGCGGGGAGCCAATTCATCACTCACACCGTTGGGAG
     ggctgat  putative branch site (score: 4)
                    tcaaattt  TA-rich tract