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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttttcttcactgaaccttccaacgatggttttcgttaagtttattcgttttgttggaggaagttccatcatcagcttttttggacggtccattatcatgcaggccctaatgcatttccatcaatttcgcgattcgtttggattatagtgggagaatgttgcattgatgtggcagGTGGGTGTATCATCATTATTGTGCAATGGTGATGGCACTGGTGAGTCTTACATGGGGTCATCCTAGTTGCATTCGCAAACAG

Basic information

species Physcomitrella patens
transcript PP1S359_2V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S359_2V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA20G38960.2 (Glycine max), 3'ss of exon 5
gtacttttcttcactgaaccttccaacgatggttttcgttaagtttattcgttttgttggaggaagttccatcatcagcttt-tttggacggtccattatcatgcaggccctaatgcatttccatcaatttcgcgattcgtttggattatagtgggagaatgttgcattgatgtggcagGTGGGTGTATCATCATTATTGTGCAATGGTGATGGCACTGGTGAGTCTTACATGGG---------GTCATCCTAGTTGCATTCGCAAACAG
                                                                 |  |   ||  |  ||| |||||   |    ||   ||      |||  | |||| |     || | | ||  | ||| |   |       | ||  || |  |   ||  ||||||| | ||||||||||||||||| ||||||||||| || |||||||| || ||||         | || ||    ||       || |||
-----------------------------------------------------------------gggcggacaggaattttatttggtttgcgtgttgatattgtcatcct--tacattgc-----atattgggaaaccttttggcaa-------ataaacttactatatggttacagGTGGATATATCATCATTATTGTGCTATGGTGATGGCCCTCGTGAGTCTCACTTGGGAGATTAAAGGACAACCAGACTGTGCAAAAAAGCAG

upper sequence: PP1S359_2V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA10G44190.3 (Glycine max), 3'ss of exon 4
gtacttttcttcactgaaccttccaacgatggttttcgttaagtttattcgttttgttggaggaagttccatcatcagcttttttggacggtccattatcatgcaggccctaatgcatttccatcaatttcgcgattcgtttggattatagtgggagaatgttgcattgatgtggcagGTGGGTGTATCATCATTATTGTGCAATGGTGATGGCACTGGTGAGTCTTACATGGG---------GTCATCCTAGTTGCATTCGCAAACAG
                                                             || ||  |    ||    || || ||   |    |||  ||      |||  | |||| |    |  || |  | || |||||   |||     |   | ||  || | |    ||||||| | |||||||| |||||||| ||||||||||| || |||||||| || ||||         | || ||    ||       || |||
-------------------------------------------------------------gggaggacagaaatt---ttattcggtttgcgtgttaatattgtcatcct--tacattgc----atattgggaaatcttttggcaaata-----aacttattatatggtta---cagGTGGATATATCATCACTATTGTGCTATGGTGATGGCCCTCGTGAGTCTCACTTGGGAGATTAAAGGACAACCAGACTGTGCAAAAAAGCAG
















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|67724944|gb|BJ975203.1|BJ975203
EST:     GCTCTGCGAGAAAACATTTTGAGGGTCAACGGTAGTGACATACGGCCATG                         GTGGGTGTATCATCATTATTGTGCAATGGTGATGGCACTGGTGAGTCTTAC
genomic: GCTCTGCGAGAAAACATTTTGAGGGTCAACGGTAGTGACATACGGCCATGgtacttttct ... gatgtggcagGTGGGTGTATCATCATTATTGTGCAATGGTGATGGCACTGGTGAGTCTTAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaatttcgcgattcgtttggattatagtgggagaatgttgcattgatgtggcagGTGGGTGTATCATCATTATTGTGCAATGGTGATGGCACTGGTGAGTCTTACATGGGGTCATCCTAGTTGCATTCGCAAACAG
                                         cattgat  putative branch site (score: 4)
                     attatagt  TA-rich tract